diff --git a/scicrunch-registry.ttl b/scicrunch-registry.ttl index 3450433d..097f56a3 100644 --- a/scicrunch-registry.ttl +++ b/scicrunch-registry.ttl @@ -14,9 +14,9 @@ rdfs:label "scicrunch registry exported ontology" ; skos:altLabel "screxp" ; rdfs:comment "Turtle export of the SciCrunch Registry" ; - owl:versionInfo "2023-07-26" ; + owl:versionInfo "2024-01-26" ; prov:wasDerivedFrom SCR:005400 ; - prov:wasGeneratedBy . + prov:wasGeneratedBy . ### Classes @@ -137,7 +137,7 @@ SCR:000013 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_01846" ; rdfs:label "BSmooth-align" ; - definition: "A statistics and alignment pipeline software that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements." . + definition: "Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements." . SCR:000014 a NLX:63400, owl:NamedIndividual ; @@ -146,7 +146,7 @@ SCR:000014 a NLX:63400, NIFRID:synonym "Conte Center for the Neuroscience of Mental Disorders" ; NIFRID:abbrev "Conte Center", "Pitt CCNMD" ; - definition: "The Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. The Center, directed by David A. Lewis, MD, integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University. Collectively, the CCNMD represents a broad array of expertise spanning molecular, systems, cognitive, computational and clinical neuroscience that provides complementary approaches to testing one central hypothesis about the disease process of schizophrenia: A distinctive pattern of molecular alterations in subpopulations of GABA neurons (pathology) creates disturbances in cortical network oscillations (pathophysiology) that underlie the information processing deficits (clinical syndrome) of schizophrenia. The Center's hypothesis is based on widely-replicated data showing reduced expression of the gene that synthesizes the neurotransmitter GABA in the cerebral cortex of individuals with schizophrenia. CCNMD investigators are working to understand how the resulting reduced levels of GABA could lead to impaired synchronization of other networks of neurons in the cerebral cortex specifically, the neuronal networks which subserve cognitive functions that are disturbed in schizophrenia. The CCNMD is composed of 5 research projects that are designed to provide convergent tests of this hypothesis. The synergism of these projects facilitates a translational approach to schizophrenia research, making laboratory findings readily relevant to clinical treatment. The CCNMD's work is directed at identifying pathophysiology-based molecular targets for new therapeutic interventions and at developing biomarkers of this pathophysiology that can be used to monitor the efficacy of such interventions. Thus, the CCNMD is a multi-disciplinary effort directed at testing a mechanistic hypothesis in order to improve our understanding of a core component of the disease process of schizophrenia. In addition, the Conte Center represents a rich environment for training and career development in which individuals can become involved in studies that bring the methods and knowledge of basic neuroscience to address critical questions in clinical schizophrenia research, The CCNMD hopes to help propel the development of new and more effective treatments for individuals with schizophrenia and to provide a vehicle for disseminating the knowledge gained from translational studies of schizophrenia to the broader scientific and lay communities. The Post-Doctoral Training Program in Schizophrenia Research provides extensive training in cutting-edge basic and clinical research strategies for schizophrenia. The National Institute of Mental Health Conte Center for the Neuroscience of Mental Disorders (CCNMD) Undergraduate Research Fellowship provides highly talented undergraduate students with early-career, hands-on engagement in cutting edge neuroscience research. Research opportunities focus on schizophrenia and related disorders and are primarily translational in approach; that is, the CCNMD research approach begins with clinical observations about the disease process that are converted into hypotheses that can be tested in the more tractable conditions of the laboratory in order to guide the development of novel therapeutic interventions." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. Integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University." . SCR:000015 a NLX:63400, owl:NamedIndividual ; @@ -159,7 +159,7 @@ SCR:000016 a NLX:63400, oboInOwl:hasDbXref "biotools:csdeconv", "OMICS_00436" ; rdfs:label "CSDeconv" ; - definition: "A software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach." . + definition: "Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach." . SCR:000017 a NLX:63400, owl:NamedIndividual ; @@ -188,12 +188,11 @@ SCR:000020 a NLX:63400, NIFRID:abbrev "Ludwig Boltzmann Cluster Translational Oncology" ; definition: "The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project." . -SCR:000021 a NLX:63400, - owl:NamedIndividual ; +SCR:000021 a owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_91897" ; rdfs:label "MNI Podcasts" ; NIFRID:synonym "Montreal Neurological Institute Podcasts" ; - definition: "A collection of podcasts which features experts of the Montreal Neurological Institute and Hospital talking about their research, along with important issues and current events regarding it." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Collection of podcasts which features experts of the Montreal Neurological Institute and Hospital talking about their research, along with important issues and current events regarding it." . SCR:000022 a NLX:63400, owl:NamedIndividual ; @@ -210,14 +209,10 @@ SCR:000023 a NLX:63400, rdfs:label "EM-DECODER" ; definition: "A haplotype inference program." . -SCR:000024 a NLX:152328, - owl:NamedIndividual ; +SCR:000024 a owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_4372" ; rdfs:label "Cleveland Clinic Lerner Research Institute Labs and Facilities" ; - NIFRID:synonym "Cleveland Clinic Lerner Research Institute Labs & Facilities", - "Cleveland Clinic LRI Labs & Facilities", - "Cleveland Clinic LRI Labs and Facilities" ; - definition: "An organization which offers services in peptide synthesis, peptide modification, purification and quality analysis, N-terminal protein sequencing by Edman degradation, biomolecular interaction analysis and equilibrium and kinetic measurements." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023.Offers services in peptide synthesis, peptide modification, purification and quality analysis, N-terminal protein sequencing by Edman degradation, biomolecular interaction analysis and equilibrium and kinetic measurements." . SCR:000025 a NLX:63400, owl:NamedIndividual ; @@ -240,7 +235,7 @@ SCR:000027 a NLX:63400, rdfs:label "Multiple Sclerosis Discovery Forum" ; NIFRID:synonym "MS Discovery Forum" ; NIFRID:abbrev "MSDF" ; - definition: "An online community and information portal that aims to inspire connections, clinical advances and accelerate progress toward multiple sclerosis cures. MSDF updates its site with news and information about topics relevant to multiple sclerosis and hosts discussions about controversial subjects with the goal of spreading information and enabling collaboration between researchers. MSDF provides access to drug development pipelines, tissue repositories, the MS gene, animal models, and clinical trials." . + definition: "Portal that aims to inspire connections, clinical advances and accelerate progress toward multiple sclerosis cures. MSDF updates its site with news and information about topics relevant to multiple sclerosis and hosts discussions about controversial subjects with the goal of spreading information and enabling collaboration between researchers. MSDF provides access to drug development pipelines, tissue repositories, the MS gene, animal models, and clinical trials." . SCR:000028 a NLX:63400, owl:NamedIndividual ; @@ -255,7 +250,7 @@ SCR:000029 a NLX:63400, NIFRID:synonym "Diffusion Imaging In Python", "NIPY Diffusion Imaging Analysis" ; NIFRID:abbrev "DIPY" ; - definition: "Software Python package for analyzing diffusion data." . + definition: "Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data." . SCR:000030 a NLX:63400, owl:NamedIndividual ; @@ -276,7 +271,7 @@ SCR:000032 a NLX:63400, oboInOwl:hasDbXref "OMICS_01229" ; rdfs:label "BlackOPs" ; NIFRID:synonym "BlackOPs: RNA-Seq Variant Blacklist Tool" ; - definition: "Software used to characterize the mappability of RNA-Seq reads and create a blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls." . + definition: "Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls." . SCR:000033 a NLX:63400, owl:NamedIndividual ; @@ -286,18 +281,16 @@ SCR:000033 a NLX:63400, NIFRID:abbrev "Mouse SNP" ; definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This website contains a database of the mouse SNP. DNA sequencing was performed along with genotyping. There is information on genotyping, mouse strain, and haplotype map." . -SCR:000034 a NLX:152342, +SCR:000034 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciRes_000168" ; - rdfs:label "Patchmaster" ; - definition: "Multi-channel data acquisition software." . + NIFRID:synonym "PATCHMASTER" ; + definition: "Multi-channel data acquisition software. Multi-channel stimulation/acquisition software with programmable experiment control and automation, software Lock-in amplifier and Photometry/Imaging extension. PATCHMASTER supports all HEKA amplifiers and data acquisition hardware." . SCR:000035 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-31399" ; - rdfs:label "RCSB PDB Software Tools" ; - NIFRID:synonym "RCSB Software Tools" ; - definition: "A variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools." . + NIFRID:synonym "RCSB Software Tools" . SCR:000036 a NLX:63400, owl:NamedIndividual ; @@ -313,7 +306,7 @@ SCR:000037 a NLX:63400, NIFRID:synonym "Treatment for Adolescents with Depression Study", "Treatment for Adolescents with Depression Study (TADS)" ; NIFRID:abbrev "TADS" ; - definition: "A multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression. It is our hope that the overall study results will improve the future care of adolescents with depression. This study has been completed. TADS is designed to compare the effectiveness of established treatments for teenagers suffering from major depressive disorder (MDD). The treatments are: psychotherapy (talking therapy); medication; and the combination of psychotherapy and medication. Altogether, 432 teenagers (both males and females) ages 12 to 17, will take part in this study at 12 sites in the United States. The TADS design will provide answers to the following questions: What is the long-term effectiveness of medication treatment of teenagers who have major depression? What is the long-term effectiveness of a specific psychotherapy (talking therapy) in the treatment of teenagers who have major depression? How does medication treatment compare with psychotherapy in terms of effectiveness, tolerability and teenager and family acceptance? And, What is the cost-effectiveness of medication, psychotherapy and combined treatments? The medication being used in this study is called fluoxetine. Fluoxetine is also known as Prozac. Research has shown that medications like Prozac help depression in young persons. Fluoxetine has been approved by the FDA for use in the treatment of child and adolescent (ages 7 to 17 years) depression. The psychotherapy or talking therapy being used in this study is called Cognitive Behavioral Therapy (CBT). CBT is a talking therapy that will teach both the teenager and his or her family member (e.g., parent) new skills to cope better with depression. Specific topics include education about depression and the causes of depression, setting goals, monitoring mood, increasing pleasant activities, social problem-solving, correcting negative thinking, negotiation, compromise and assertiveness. CBT sessions may also help with resolving disagreements as they affect families. For more information see, http://www.clinicaltrials.gov/ct/show/NCT00006286?order=1 and http://www.nimh.nih.gov/trials/practical/tads/index.shtml" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression." . SCR:000038 a NLX:63400, owl:NamedIndividual ; @@ -327,7 +320,7 @@ SCR:000038 a NLX:63400, "UTK Genome Science & Technology" ; NIFRID:abbrev "UT Knoxville GST", "UTK GST" ; - definition: "The Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST. Consequently, GST student projects are quite diverse, as indicated by the five themes spelled out below. Themes * Molecular Genetics and Systems Biology * Computational Molecular Biophysics * Structural and Nanoscale Biology * Bioinformatics * Analytical Technologies for Bioenergy and the Environment While some students work on projects that are primarily computational, many other students focus their experimental work at the bench. Increasingly, both types of students are realizing the growing need for work at both the theoretical/computational level and at the practical experimental level. This is the nature of most modern interdisciplinary research. Because individual research groups are generally small, there is much opportunity for interaction between groups employing different experimental or computational strategies. A hallmark of the GST Program is its involvement of faculty from two distinct research environmentsthe University of Tennessee, Knoxville, (UTK) and Oak Ridge National Laboratory (ORNL). The program is enriched by the different research philosophies encountered at a university, emphasizing autonomy, and at a National Lab, emphasizing team effort. Researchers at the two campuses have access to a wide range of research tools and facilities including: * High-field NMR spectroscopy * X-ray crystallography * Mass spectroscopy * Next generation sequencing * Molecular modeling and supercomputing The program is designed to educate PhD-level scientists who are equipped to tackle the complex world of biology using modern technologies. A Master's track is also available for some students. The GST curriculum lays a firm foundation in molecular genetics, biochemistry, and bioinformatics, followed by specialization in the area of the student's dissertation research. GST welcomes students with a solid undergraduate academic background in biological sciences, physical sciences, or computational sciences. New NSF Fellowships Available for Students in Computational Biology." . + definition: "Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST." . SCR:000039 a NLX:152328, owl:NamedIndividual ; @@ -350,7 +343,7 @@ SCR:000041 a NLX:63400, rdfs:label " MTOPS Prostate Samples Analysis Consortium " ; NIFRID:synonym "MTOPS Prostate Samples Analysis (MPSA) Consortium" ; NIFRID:abbrev "MPSA Consortium" ; - definition: "Cross-disciplinary, multi-institutional network with a wide range of experts to analyze serum and tissue samples collected in the Medical Therapy of Prostatic Symptoms (MTOPS) trial. The consortium aims to discover and validate biomarkers for the detection, risk assessment, and disease progression assessment of benign prostatic hyperplasia (BPH). Analysis of the samples will also allow a biological evaluation of patients' responses to pharmacological treatments employed in MTOPS and correlation with BPH clinical parameters. Investigators will perform cooperative studies using the MTOPS material to evaluate genetic, immunologic, or biochemical biomarkers relevant to the progression of BPH, response-to-therapy, and the concurrent development of prostate cancer. The consortium will generate and validate biomarkers that will be made available to research community for use in a variety of investigations, including testing strategies for early detection, prevention, therapeutics, or imaging. The consortium will also produce research tools such as serum protein arrays, layered expression arrays, or tissue arrays that can be used by the research community. To identify novel targets for use as validated BPH markers, the consortium is currently exploring novel aspects of BPH biology and response to therapy. Several groups are using proteomic approaches, including SELDI, other types of mass spectrometry analysis, and 2D electrophoresis. Other groups are pursuing gene expression microarray analysis. The consortium is also organizing available data to identify current gaps. Groups with additional microarray data that has focused on BPH have compiled a common database of genes with expression patterns that are altered with the disease. This combined dataset will be used to identify some novel biomarkers revealed by single-site analyses. These novel biomarkers will then be validated using the tissues and serum microarrays that are being assembled. Another collaborative effort of the consortium involves construction of common tissue and serum resources and tissue microarrays (TMAs). Lists of available resources at each of the consortium member sites have been assembled along with information addressing secondary outcomes such as prediction of prostate growth and prediction of disease progression. Initial tissue microarrays composed of tissues from a number of sites have been constructed. Additional TMAs and serum microarrays are being constructed; these microarrays will be used by consortium members to aid in the validation of potential biomarkers. Participating in the MPSA network are one pathology-coordination center, six biomarker units, and a data coordinating center. The consortium comprises UT Southwestern, Vanderbilt University, Brigham and Women's Hospital, Harvard/University of Michigan, Baylor College of Medicine, University of Pittsburgh, and University of Colorado." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Cross-disciplinary, multi-institutional network with wide range of experts to analyze serum and tissue samples collected in the Medical Therapy of Prostatic Symptoms (MTOPS) trial. Consortium aims to discover and validate biomarkers for the detection, risk assessment, and disease progression assessment of benign prostatic hyperplasia (BPH)." . SCR:000042 a NLX:63400, owl:NamedIndividual ; @@ -362,7 +355,7 @@ SCR:000043 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_155578" ; rdfs:label "3DMeshMetric" ; - definition: "A visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling ( based on the source code of MeshValmet ). 3dMeshMetric also offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation." . + definition: "Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation." . SCR:000044 a NLX:63400, owl:NamedIndividual ; @@ -374,7 +367,7 @@ SCR:000045 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_04052" ; rdfs:label "UTR" ; - definition: "A software application that uses a change-point model for detecting 3-prime UTR changes by RNA-Seq." . + definition: "Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq." . SCR:000046 a NLX:63400, owl:NamedIndividual ; @@ -429,7 +422,7 @@ SCR:000053 a NLX:63400, "OMICS_03636" ; rdfs:label "CorMut" ; NIFRID:synonym "CorMut - Detect the correlated mutations based on selection pressure" ; - definition: "A software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network." . SCR:000054 a NLX:63400, owl:NamedIndividual ; @@ -468,15 +461,14 @@ SCR:000058 a NLX:63400, rdfs:label "Dissect" ; NIFRID:synonym "DIScovery of Structural Events Containing Transcripts", "Dissect: DIScovery of Structural Events Containing Transcripts" ; - definition: "A transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions." . + definition: "Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions." . SCR:000059 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "biotools:fusionanalyser", "OMICS_01347" ; rdfs:label "Fusion Analyser" ; - NIFRID:synonym "FusionAnalyser" ; - definition: "Software used to detect gene fusions from paired-end RNA-Seq data." . + NIFRID:synonym "FusionAnalyser" . SCR:000060 a NLX:63400, owl:NamedIndividual ; @@ -485,8 +477,7 @@ SCR:000060 a NLX:63400, rdfs:label "FusionCatcher" ; definition: "Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples." . -SCR:000061 a NLX:63400, - owl:NamedIndividual ; +SCR:000061 a owl:NamedIndividual ; oboInOwl:hasDbXref "biotools:gasv", "OMICS_01352" ; rdfs:label "GASV" ; @@ -496,10 +487,9 @@ SCR:000061 a NLX:63400, SCR:000062 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_02563" ; - rdfs:label "GHOSTM" ; NIFRID:synonym "ghostm: GPU-based HOmology Search Tool for Metagenomics", "GPU-based HOmology Search Tool for Metagenomics" ; - definition: "A homology search software tool for huge short reads generated by next-generation sequencers. It can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique." . + definition: "Software homology search tool for huge short reads generated by next-generation sequencers.Can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique." . SCR:000063 a NLX:152328, owl:NamedIndividual ; @@ -521,7 +511,7 @@ SCR:000065 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_155796" ; rdfs:label "MPScope" ; - definition: "A comprehensive software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, the analysis program MPView and several software utilities." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, analysis program MPView and several software utilities." . SCR:000066 a NLX:63400, owl:NamedIndividual ; @@ -530,14 +520,11 @@ SCR:000066 a NLX:63400, NIFRID:synonym "nFuse: Discovery of Complex Genomic Rearrangements in Cancer" ; definition: "Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS)." . -SCR:000067 a NLX:63400, - owl:NamedIndividual ; +SCR:000067 a owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_155983" ; - rdfs:label "Image Registration Toolkit" ; NIFRID:synonym "Medical Image Registration ToolKit" ; NIFRID:abbrev "IRTK", - "MIRTK" ; - definition: "Image registration toolkit for research purposes.Medical Image Registration ToolKit , the successor of the IRTK, contains common CMake build configuration files, core libraries, and basic command-line tools." . + "MIRTK" . SCR:000068 a NLX:63400, owl:NamedIndividual ; @@ -632,8 +619,7 @@ SCR:000081 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_152542" ; rdfs:label "StratML" ; - NIFRID:synonym "Strategy Markup Language" ; - definition: "An XML vocabulary and schema for strategic plans, designed to create a world wide web of intentions, stakeholders and results." . + NIFRID:synonym "Strategy Markup Language" . SCR:000082 a NLX:63400, owl:NamedIndividual ; @@ -725,14 +711,13 @@ SCR:000093 a NLX:63400, oboInOwl:hasDbXref "nlx_143740" ; rdfs:label "EPIGEN" ; NIFRID:synonym "EPIGEN Consortium", - "EPIGEN: An international consortium dedicated to tackling epilepsy through genetics" ; - definition: "A group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres. Core Founding Institutes * The Centre for Genomics and Population Genetics. Duke University Institute for Genome Sciences and Policy, North Carolina, USA. (Prof. David Goldstein) * The UCL Institute of Neurology, Queen Square, London, UK. (Prof. Sanjay Sisodiya) * Beaumont Hospital and the Royal College of Surgeons in Ireland. (Dr. Norman Delanty and Dr. Gianpiero Cavalleri) * Hôpital Erasme, Université Libre de Bruxelles, Belgium. (Dr. Chantal Depondt and Prof. Massimo Pandolfo) Collaborating Institutes * The Departments of Medicine and Neurology, The Royal Melbourne Hospital, The University of Melbourne, Victoria, Australia. (Dr. Terence O'Brien and Dr. Cassandra Szoeke) * Murdoch Childrens Research Institute, Department of Paediatrics, The University of Melbourne, Melbourne, Australia. (Dr. Leslie Sheffield) They are currently working on several pharmacogenomic and epilepsy predisposition projects: * The development and implementation of electronic patient records to enhance the quality and efficiency of both patient care and genomics research. * The clinical relevance of genetic variation in vigabatrin induced visual field contriction. * The clinical relevance of genetic variation in weight fluctuation due to anti-convulsant medication. * The role of genetic variation in mesial temporal sclerosis and other \"focal\" epilepsies. * The potential of magnetic resonance imaging to deliver novel endophenotypes to help resolve the genetic component to epilepsy. The following resources are available to the EPIGEN consortium.. * Over 5000 epilepsy patients recruited from the following hospitals: ** The Institute of Neurology, Queen Square, London, UK. ** Beaumont Hospital, Dublin, Ireland. ** Hopital Erasme, Universite Libre de Bruxelles, Belgium. ** Duke University Hospital, Durham, North Carolina, USA. * Core genotyping facility: The EPIGEN consortium has access to Duke University Institute Genome Sciences and Policy high throughput genotyping facility. Availing of ABI taqman and Illumina Bead Array technology, this facility provides the EPIGEN consortium with genotyping for projects of all sizes. *Statistical support: Research conducted by the EPIGEN consortium can call on statistical support from Duke University IGSP, and the genetics programmes at RCSI and the ION." . + "EPIGEN: An international consortium dedicated to tackling epilepsy through genetics" . SCR:000094 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-00540" ; - rdfs:label "Neuron Registry" ; - NIFRID:synonym "Neuron Registry Curator Interface" ; + rdfs:label "Neuron Registry Curator Interface" ; + NIFRID:synonym "INCF Neuron Registry" ; NIFRID:abbrev "NRCI" ; definition: "Repository of neuron types characterized by machine-readable part-relation-value triple-based neuron properties. A Curator Interface facilitates the direct knowledge transfer of information from the participating neuroscientist for entry into the Neuron Registry." . @@ -753,7 +738,7 @@ SCR:000097 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_02333" ; rdfs:label "AutoPrime" ; - definition: "Server to rapidly design primers for real-time PCR measurement of eukaryotic expression." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Server to rapidly design primers for real-time PCR measurement of eukaryotic expression." . SCR:000098 a NLX:63400, owl:NamedIndividual ; @@ -801,7 +786,7 @@ SCR:000104 a NLX:63400, oboInOwl:hasDbXref "nlx_143693" ; rdfs:label "National MS Society" ; NIFRID:synonym "National Multiple Sclerosis Society" ; - definition: "The National MS Society is a collective of passionate individuals who want to do something about MS nowto move together toward a world free of multiple sclerosis. MS stops people from moving. We exist to make sure it doesn't. We help each person address the challenges of living with MS through our 50-state network of chapters. The Society helps people affected by MS by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward. * We are moving research forward by relentlessly pursuing prevention, treatment and cure. * We are moving to reach out and respond to individuals, families and communities living with multiple sclerosis. * We are moving politicians and legislation to champion the needs of people with MS through activism, advocacy and influence. * We are moving to mobilize the millions of people who want to do something about MS now. Through the Society's fifty-state network of chapters, assistance is provided to over a million people annually. Chapters encourage personal empowerment with employment counseling, family programs, volunteer opportunities, and advocacy issues. Each National MS Society chapter also organizes a variety of events to raise funds and awareness. Harry Weaver Neuroscience Scholar Awards: Harry Weaver, Ph.D., known worldwide for his contribution to neurosciences and multiple sclerosis research, was the Society's Director of Research from 1966-1977. Throughout his tenure with the Society and throughout his career, Dr. Weaver continued to encourage young investigators to enter and pursue MS research, and to broaden our understanding of basic and clinical aspects of MS. In recognition of Dr. Weaver's contribution to the neurosciences and MS research, and to his dedication to young researchers, the Society named this prestigious Award in his honor. A limited number of awards are offered to highly qualified candidates who have concluded their research training and begun academic careers as independent investigators in an area related to multiple sclerosis. The awards are designed to provide salary and grant support for a five year period, thus permitting the awardee to establish competence in his/her chosen research area. Application must be made jointly by a candidate and the institution in which an appointment is held. FUNDING OPPORTUNITIES * Research Grants * Pilot Research * Training Grants and Fellowships * Health Care Delivery And Policy Research Contracts * Collaborative MS Research Centers * Patient Management, Care And Rehabilitation Research Grants Other Awards and Prizes * The John Dystel Prize for MS Research * The Ralph I. Straus Award for MS * Outside Meeting Support Program" . + definition: "Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward." . SCR:000105 a NLX:63400, owl:NamedIndividual ; @@ -817,7 +802,7 @@ SCR:000106 a NLX:63400, NIFRID:synonym "Laser Biomedical Research Center (LBRC)", "MIT Laser Biomedical Research Center" ; NIFRID:abbrev "LBRC" ; - definition: "Biomedical technology research center that develops the basic scientific understanding and new techniques required for advancing the clinical applications of lasers and spectroscopy. To fulfill the need for a more comprehensive and potentially non-invasive understanding of the human body, the LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques. Specifically, researchers at the LBRC study the biophysics and biochemistry of healthy and diseased biological structures from the subcellular to the entire-organ scale. For example, spectral diagnosis instruments based on near-infrared Raman scattering, intrinsic fluorescence, diffuse reflectance, and single light scattering provide complementary data on human disease. Combining these techniques into a single, multimodal instrument is applied for diagnostics in various organs, including cervix, oral cavity, Barrett's esophagus, artery, breast, skin, as well as for transcutaneous measurements of blood constituents. The LBRC has been and continues to be a pioneer in the field of developing novel optical probes for use under direct visualization or with endoscopes and biopsy devices. Similarly, new microscopy tools based on interferometry are designed and exploited for measuring cellular structures and their dynamics. In particular, these techniques provide the crucial and unique ability to non-invasively study cells in their native states at remarkably high spatial and temporal resolutions. Using these novel microscopy tools, the LBRC has conducted critical studies to elucidate the fundamental biology of diseases as diverse as malaria and multiple myeloma, and physiological processes such as cell growth and cell division. The interferometry concepts have also been vital in Center's research efforts to develop optical tools for deep-tissue imaging while minimizing the adverse effects of light scattering or diffusion. Furthermore, the unique and powerful combination of the interferometric microscopy and vibrational spectroscopy tools adds a hitherto unexplored dimension to optical sensing by simultaneous probing of morphological and chemical information. A unique feature of the LBRC is its ability to form strong clinical collaborations with outside investigators in areas of common interest that further the Center's mandated research objectives. As a National Research Resource Center, the LBRC makes available its facilities, along with technical and scientific support, to outside researchers for the purpose of pursuing independent research projects in the area of laser biomedical applications. The facilities are available on a time-shared basis, free-of-cost policy to qualified scientists, engineers and physicians throughout the United States." . + definition: "Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale." . SCR:000107 a NLX:63400, owl:NamedIndividual ; @@ -868,7 +853,7 @@ SCR:000113 a NLX:63400, oboInOwl:hasDbXref "nlx_51508" ; rdfs:label "BrainTechSci." ; NIFRID:synonym "BrainTechSci" ; - definition: "A blog about brain technology and science news that covers topics such as high-resolution brain imaging, brain maps API and whole-brain atlases." . + definition: "Blog about brain technology and science news that covers topics such as high-resolution brain imaging, brain maps API and whole-brain atlases." . SCR:000114 a NLX:63400, owl:NamedIndividual ; @@ -921,7 +906,7 @@ SCR:000121 a NLX:63400, rdfs:label "Parallel-META" ; NIFRID:synonym "Parallel META", "Parallel Meta" ; - definition: "Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis." . SCR:000122 a NLX:63400, owl:NamedIndividual ; @@ -962,7 +947,7 @@ SCR:000126 a NLX:63400, oboInOwl:hasDbXref "covalentdock_cloud", "OMICS_01597" ; rdfs:label "CovalentDock Cloud" ; - definition: "A web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor." . SCR:000127 a NLX:63400, owl:NamedIndividual ; @@ -1134,7 +1119,7 @@ SCR:000147 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_149123" ; rdfs:label "GenNav" ; - definition: "GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. Platform: Online tool" . + definition: "GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG." . SCR:000148 a NLX:63400, owl:NamedIndividual ; @@ -1198,7 +1183,7 @@ SCR:000154 a NLX:63400, oboInOwl:hasDbXref "biotools:deseq", "OMICS_01306" ; rdfs:label "DESeq" ; - definition: "A software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression." . SCR:000155 a NLX:63400, owl:NamedIndividual ; @@ -1209,8 +1194,7 @@ SCR:000155 a NLX:63400, "mBIRN_calib", "Morphometry BIRN Multi-site Multi-session Structural MRI Data", "Morphometry Testbed" ; - NIFRID:abbrev "MBIRN" ; - definition: "Calibration data set of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems) pooled by the Morphometry Testbed's (MBIRN). Some subjects were also scanned a single time at another site. One subject was only scanned twice at three sites (subject 73213384) and once at another site. For each subject, four Fast Low-Angle Shot (FLASH) scans with flip angles of 3, 5, 20, and 30 degrees were obtained in a single scan session, from which tissue proton density and T1 maps can be derived. These data were acquired to investigate various metrics of within-site and across-site reproducibility. The images have been defaced so that no facial features can be reconstructed from these data. The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focused on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer's disease. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th,2023. Calibration data set of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems) pooled by the Morphometry Testbed's (MBIRN). Some subjects were also scanned a single time at another site. One subject was only scanned twice at three sites (subject 73213384) and once at another site. For each subject, four Fast Low-Angle Shot (FLASH) scans with flip angles of 3, 5, 20, and 30 degrees were obtained in a single scan session, from which tissue proton density and T1 maps can be derived. These data were acquired to investigate various metrics of within-site and across-site reproducibility. The images have been defaced so that no facial features can be reconstructed from these data. The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focused on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer's disease. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains." . SCR:000156 a NLX:63400, owl:NamedIndividual ; @@ -1269,7 +1253,7 @@ SCR:000163 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_00361" ; rdfs:label "miRanalyzer" ; - definition: "A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed." . SCR:000164 a NLX:63400, owl:NamedIndividual ; @@ -1362,7 +1346,7 @@ SCR:000176 a NLX:63400, NIFRID:synonym "University of Vermont Labs & Facilities" ; NIFRID:abbrev "UVM Labs & Facilities", "UVM Labs and Facilities" ; - definition: "A university-based lab facility for research in biomedicine and neuroscience. The center was created to expand neuroscience research and training, develop shared core facilities and provide funding for research by neuroscience faculty. There is an emphasis on interdisciplinary neuroscience research and dialogue between basic and clinical neuroscientists." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A university-based lab facility for research in biomedicine and neuroscience. The center was created to expand neuroscience research and training, develop shared core facilities and provide funding for research by neuroscience faculty. There is an emphasis on interdisciplinary neuroscience research and dialogue between basic and clinical neuroscientists." . SCR:000177 a NLX:63400, owl:NamedIndividual ; @@ -1590,7 +1574,7 @@ SCR:000207 a NLX:152328, NIFRID:abbrev "MMRF" ; definition: "Research foundation that funds research to develop new treatments for multiple myeloma, an incurable blood cancer." . -SCR:000208 a NLX:63400, +SCR:000208 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_4541" ; rdfs:label "Queensland Cyber Infrastructure Foundation Ltd" ; @@ -1598,14 +1582,14 @@ SCR:000208 a NLX:63400, "Queensland Parallel Supercomputing Foundation", "the Queensland Cyber Infrastructure Foundation" ; NIFRID:abbrev "QCIF" ; - definition: "Organization provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Operates with its members and partners delivering services to research throughout Queensland and increasingly via Commonwealth programs to the nation. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services." . + definition: "Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services." . -SCR:000209 a NLX:63400, +SCR:000209 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_157910" ; rdfs:label "PKD Foundation" ; NIFRID:synonym "Polycystic Kidney Disease Foundation" ; - definition: "An organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support." . + definition: "Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support." . SCR:000210 a NLX:63400, owl:NamedIndividual ; @@ -1640,11 +1624,12 @@ SCR:000212 a NLX:63400, SCR:000213 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_157284" ; - rdfs:label "ANU Centre for Advanced Microscopy" ; + rdfs:label "ANU Centre for Advanced Microscopy Core Facility" ; NIFRID:synonym "ANU Center for Advanced Microscopy", + "ANU Centre for Advanced Microscopy", "Australian National University Centre for Advanced Microscopy" ; NIFRID:abbrev "ANU CAM" ; - definition: "Core facility that provides the microscopy infrastructure necessary to support frontline research in biological and physical sciences at the Australian National University. Teaching and training is also available." . + definition: "Centre for Advanced Microscopy provides open access, state-of-the art microscopy and microanalysis equipment and expertise to national and international researchers, students and industry partners in the materials and life sciences. Offers services to support experimental design, data acquisition and analysis, train users in the use of instruments and help with sample preparation, provide research collaboration." . SCR:000214 a NLX:152328, owl:NamedIndividual ; @@ -1685,7 +1670,7 @@ SCR:000218 a NLX:63400, rdfs:label "Inferelator" ; definition: "Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models." . -SCR:000219 a NLX:63400, +SCR:000219 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_157914" ; rdfs:label "Clinical Data Interchange Standards Consortium" ; @@ -1704,7 +1689,7 @@ SCR:000221 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-30274" ; rdfs:label "CRASH" ; - definition: "A website which describes the experimental procedure for a placebo controlled trial of the effects of a 48-hour infusion of corticosteroids on adults with head injury and some impairment of consciousness. The outcomes will be measured by rates of death and neurological disability. Patients are recruited (or entered by their doctors when informed consent is not obtainable due to impaired cognitive functioning) on a case-by-case basis as head injured patients come through emergency departments. Randomization is done via a 24-hour telephone line that will denote which pack of medication (either the corticosteroids or saline solution as control) to give." . + definition: "Portal for placebo controlled trial of the effects of 48-hour infusion of corticosteroids on death and on neurological disability, among adults with head injury and some impairment of consciousness. The outcomes will be measured by rates of death and neurological disability. Patients are recruited (or entered by their doctors when informed consent is not obtainable due to impaired cognitive functioning) on a case-by-case basis as head injured patients come through emergency departments. Randomization is done via a 24-hour telephone line that will denote which pack of medication (either the corticosteroids or saline solution as control) to give." . SCR:000222 a NLX:63400, owl:NamedIndividual ; @@ -1756,11 +1741,11 @@ SCR:000228 a NLX:63400, rdfs:label "OHSU MRI Support Core Laboratory" ; definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: MRI examination of sedated non-human primate subjects. The magnetic resonance imaging (MRI) core provides ONPRC investigators with equipment and assistance to perform MRI exams of sedated NHP subjects." . -SCR:000229 a NLX:152342, +SCR:000229 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_01808" ; rdfs:label "ChromasPro" ; - definition: "A software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available." . SCR:000230 a NLX:152328, owl:NamedIndividual ; @@ -1787,7 +1772,7 @@ SCR:000233 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_153905" ; rdfs:label "SimToolDB" ; - definition: "Location for storing and efficiently retrieving tools which aid simulations of neuronal and network compartmental models. Simulation tools can be coded in any language for any environment. Simulation tools code can be viewed before downloading or auto-launching" . + definition: "Provides accessible location for storing and efficiently retrieving tools which aid simulations of neuronal and network compartmental models. Simulation tools can be coded in any language for any environment. Simulation tools code can be viewed before downloading or auto-launching." . SCR:000234 a NLX:63400, owl:NamedIndividual ; @@ -1818,7 +1803,7 @@ SCR:000237 a NLX:63400, "OMICS_04004" ; rdfs:label "TAPIR: target prediction for plant microRNAs" ; NIFRID:abbrev "TAPIR" ; - definition: "A web server designed for the prediction of plant microRNA targets." . + definition: "Web server designed for prediction of plant microRNA targets." . SCR:000238 a NLX:63400, owl:NamedIndividual ; @@ -1854,8 +1839,7 @@ SCR:000242 a NLX:63400, "SCR_017663" ; rdfs:label "Cistrome" ; NIFRID:synonym "Galaxy Cistrome" ; - definition: """Galaxy-based web service for analysis of Chromatin Immuno Precipitation (ChIP) data. -Integrative platform for transcriptional regulation studies. Data analysis platform based on Galaxy open source framework. Besides standard Galaxy functions, Cistrome has ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Used to conduct data integration to mine hidden biological insights from publicly available high throughput data.""" . + definition: "Web based integrative platform for transcriptional regulation studies." . SCR:000243 a NLX:63400, owl:NamedIndividual ; @@ -2094,7 +2078,7 @@ SCR:000265 a NLX:63400, oboInOwl:hasDbXref "OMICS_02292" ; rdfs:label "M(at)CBETH" ; NIFRID:synonym "MicroArray Classification BEnchmarking Tool on Host server" ; - definition: "A web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset." . SCR:000266 a NLX:63400, owl:NamedIndividual ; @@ -2229,7 +2213,7 @@ SCR:000282 a NLX:63400, NIFRID:synonym "GEArray" ; definition: "THIS RESOURCE HAS BEEN DISCONTINUED, documented April 15, 2016. New GEArray Expression Analysis Suite 2.0 was released at Dec 21, 2006, please read Release Notices for details. SABiosciences' GEArray Analysis Suite uses advanced Java functionality. In order to experience full functionality of this Portal, the following free programs and upgrades for PC and Macs should be properly installed. PC Environment Downloads Browser compatibility is not an issue on Windows systems, so all operating systems running Windows 98 and above and either Internet explorer or Netscape should be fine. Java 1.4.1 or above is required--this should download automatically upon the first entry into the Portal. If this does not happen, Java 1.5 is available for download from the following URL: Java 1.5 Mac Environment Downloads Browser compatibility is an issue, and Mac Operating Systems prior to Panther are not able to fully take advantage of this Portal's functionality. These programs need to be downloaded and installed in a specific order as follows: Panther 10.3.5 (Operating System), Safari 1.2 (Compatible Internet Browser) and Java 1.4.2 (Java environment). Abstract. INTRODUCTION: Toll-like receptors (TLR) comprehend an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes. Surgical trauma and ischemia-reperfusion injury are likely to provide exposure to endogenous ligands for TLR in virtually all kidney transplant recipients. METHODS: Macroarray (GEArray OHS-018.2 Series-Superarray) analyses of 128 genes involved in TLR signaling pathway were performed in nephrectomy samples of patients with chronic allograft nephropathy (CAN) and acute rejection (AR, vascular and non vascular). The analysis of each membrane was performed by GEArray Expression Analysis Suite 2.0. RESULTS: Macroarray profile identified a gene expression signature that could discriminate CAN and AR. Three genes were significantly expressed between CAN and vascular AR: Pellino 2; IL 8 and UBE2V1. In relation to vascular and non-vascular AR, there were only two genes with statistical significance: IL-6 and IRAK-3. CONCLUSION: Vascular and non-vascular AR and CAN showed different expression of a few genes in TLR pathway. The analysis of nephrectomy showed that activation of TLR pathway is present in AR and CAN. Sponsor. This work was supported by the inconditional grant from Fundao de Amparo a Pesquisa do Estado de So Paulo (FAPESP, 04/08311-6), from Conselho Nacional de Pesquisa e Desenvolvimento (CNPq) and from Fundao Osvaldo Ramos." . -SCR:000283 a "Commercial", +SCR:000283 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_01810" ; rdfs:label "Lasergene's SeqMan Pro" ; @@ -2279,7 +2263,7 @@ SCR:000289 a NLX:63400, "OMICS_02060" ; rdfs:label "cn.FARMS" ; NIFRID:synonym "cn.farms - factor analysis for copy number estimation" ; - definition: "Software package for copy number variation (CNV) analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff." . + definition: "Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff." . SCR:000290 a NLX:63400, owl:NamedIndividual ; @@ -2313,11 +2297,11 @@ SCR:000293 a NLX:63400, NIFRID:synonym "Clonality - Clonality testing" ; definition: "Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles." . -SCR:000294 a NLX:152342, +SCR:000294 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_02050" ; rdfs:label "oneClickCGH" ; - definition: "A platform-independent array Copy Number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes." . + definition: "Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes." . SCR:000295 a NLX:152342, owl:NamedIndividual ; @@ -2382,7 +2366,7 @@ SCR:000304 a NLX:63400, rdfs:label "Penn Community Outreach Using Health System Informatics Core" ; NIFRID:synonym "Penn COHSI" ; NIFRID:abbrev "COHSI" ; - definition: "An informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System." . SCR:000305 a NLX:63400, owl:NamedIndividual ; @@ -2534,13 +2518,13 @@ SCR:000326 a NLX:152328, rdfs:label "AxoGen" ; definition: "A medical technology company whose research and products revolve around peripheral nerve repair." . -SCR:000327 a NLX:152328, +SCR:000327 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_940" ; rdfs:label "Georgia Institute of Technology Labs and Facilities" ; NIFRID:abbrev "Georgia Tech Labs & Facilities", "Georgia Tech Labs and Facilities" ; - definition: "A university affiliated laboratory which is composed of two main departments, the Center for Organic Photonics and Electronics (COPE) and the Magnetic Resonance Laboratory. COPE creates flexible organic photonic and electronic materials and devices. The Magnetic Resonance Laboratory performs MRI and magnetic bore." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. University affiliated laboratory which is composed of two main departments, the Center for Organic Photonics and Electronics (COPE) and the Magnetic Resonance Laboratory. COPE creates flexible organic photonic and electronic materials and devices. The Magnetic Resonance Laboratory performs MRI and magnetic bore." . SCR:000328 a NLX:63400, owl:NamedIndividual ; @@ -2606,7 +2590,7 @@ SCR:000334 a NLX:63400, "USC CCB" ; definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. This area has a long tradition of sophisticated mathematical and computational techniques. Nevertheless, new developments in related areas of mathematics and computational science have emerged in recent years, some from related application areas such as Computer Graphics, Computer Vision, and Image Processing, as well as from Computational Mathematics and the Computational Sciences. We are confident that many of these ideas can be applied beneficially to neuroimaging." . -SCR:000335 a NIFSTD:birnlex_2431, +SCR:000335 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_152538" ; rdfs:label "National Health Research Institutes; Taipei; Taiwan" ; @@ -2680,8 +2664,10 @@ SCR:000343 a NLX:152328, "nlx_47548", "Wikidata:Q777403" ; rdfs:label "Washington University in St. Louis; Missouri; USA" ; - NIFRID:abbrev "WUSTL" ; - definition: "Private research university in Greater St. Louis with its main campus mostly in unincorporated St. Louis County, Missouri, and Clayton, Missouri. Offers both undergraduate and graduate degrees." . + NIFRID:synonym "Washington University" ; + NIFRID:abbrev "WashU", + "WUSTL" ; + definition: "Private research university in Greater St. Louis with its main campus mostly in unincorporated St. Louis County, Missouri and Clayton, Missouri." . SCR:000344 a NLX:152328, owl:NamedIndividual ; @@ -2987,7 +2973,7 @@ SCR:000385 a NLX:63400, oboInOwl:hasDbXref "nlx_152884" ; rdfs:label "LiGraph" ; NIFRID:synonym "LiGraph - Convert a sugar graph to ASCII IUPAC sugar nomenclature or as a graph" ; - definition: "Service that generates schematic drawings of oligosaccharides which are often used to display glycan structure." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Web service that generates schematic drawings of oligosaccharides which are often used to display glycan structure." . SCR:000386 a NLX:63400, owl:NamedIndividual ; @@ -3037,8 +3023,9 @@ SCR:000392 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-10668" ; rdfs:label "WILEY Interdisciplinary Reviews" ; - NIFRID:synonym "WIREs" ; - definition: "WIREs are unique hybrid publications that emphasize the importance of interdisciplinary collaboration in research and education. Publications include Nanomedicine and Nanobiotechnology and Systems Biology and Medicine with future publications coming soon: Computational Statistics (2009), Climate Change (2010), Cognitive Science (2010), Computational Molecular Science (2011), Data Mining and Knowledge Discovery (2011), Developmental Biology (2011), and RNA (2011). Key points include: *High quality reviews commissioned from expert contributors *uthoritative, encyclopedic coverage of diverse scientific fields *Fully citable, qualifying for abstracting, indexing, and ISI ranking Article types are designed to cater to a variety of end users *Overviews provide a broad and non-technical treatment of important topics suitable for advanced students and for researchers without a strong background in the field. *Advanced Reviews examine key areas of research in a citation-rich format suitable for researchers and advanced students. *Focus Articles present specific real-world issues, examples and implementations. *Opinions provide a forum for thought-leaders to offer a more individual perspective. *Editorial Commentaries provide an opportunity for WIREs Editors to offer their own syntheses of broad areas of research in a less formal and more flexible style. The WIREs publishing model: The WIREs combine the most powerful features of online review journals (high online visibility, immediacy, full abstracting and indexing) with the traditional strengths of the encyclopedic reference model (structure, authority, and comprehensiveness of coverage). A built-in mechanism for updating previously published content further differentiates the WIREs from traditional review journals. With their deliberate focus on high-impact topics at the interfaces of the traditional research fields, together with a strong emphasis on interdisciplinary outreach at the level of the individual article, the WIREs will, we hope, offer a valuable new forum for cross-disciplinary communication in scientific and scholarly research. Register for free online access to the WIREs Interdisciplinary Reviews: Each WIREs title will initially be made available via free online access to institutional subscribers. This will allow institutions to gauge end-user interest prior to making a purchasing decision. Institutions may also request one free print subscription when registering for free online access for a given WIREs Interdisciplinary Reviews. Institutions can opt to receive free online access throughout the year for any or all of the WIREs titles. There is no obligation to subscribe in subsequent years if you opt for free access. Institutions retain online access to content published during the opt-in period, with or without a paid subscription in subsequent years. As a WIREs author *Your review will be published alongside other world-class contributions from leading researchers in the field All WIREs article topics and authors are selected by an internationally renowned Editorial Board, and all content is rigorously peer reviewed by experts. *Your article will have the highest possible visibility and usage All WIREs articles will initially be made available for free to online users. *Your review will attract full scientific and professional credit The WIREs are serial publications that qualify for full Abstracting and Indexing and an Impact Factor/ISI Ranking." . + NIFRID:synonym "Wiley Interdisciplinary Reviews series" ; + NIFRID:abbrev "WIREs" ; + definition: "Wiley Interdisciplinary Reviews series combines features of encyclopedic reference works and review journals in innovative online format. They are designed to promote cross-disciplinary research ethos while maintaining the highest scientific and presentational standards, but should be viewed first and foremost as evolving online databases of cutting-edge reviews." . SCR:000393 a NLX:63400, owl:NamedIndividual ; @@ -3055,13 +3042,13 @@ SCR:000394 a NLX:63400, NIFRID:synonym "microAnalyzer" ; definition: "Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems." . -SCR:000395 a NLX:152342, +SCR:000395 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-20877" ; rdfs:label "Molecular Connections NetPro" ; NIFRID:abbrev "MolCon", "NetPro" ; - definition: "A comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references. The strength of NetPro lies in the complete manual curation of literature. It covers several entities other than proteins as interacting partners, like RNA, DNA, processes, etc. with well defined, exhaustive interaction terms. NetPro has received several accolades for the quality and quantity of data it contains. It has become an important resource for target identification, validation and pathway research and has subscribers from all over the globe including 3 of the top 5 pharmas." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references. The strength of NetPro lies in the complete manual curation of literature. It covers several entities other than proteins as interacting partners, like RNA, DNA, processes, etc. with well defined, exhaustive interaction terms. NetPro has received several accolades for the quality and quantity of data it contains. It has become an important resource for target identification, validation and pathway research and has subscribers from all over the globe including 3 of the top 5 pharmas." . SCR:000396 a NLX:63400, owl:NamedIndividual ; @@ -3116,7 +3103,7 @@ SCR:000402 a NLX:63400, oboInOwl:hasDbXref "nlx_154743" ; rdfs:label "Polar Geospatial Center" ; NIFRID:abbrev "PGC" ; - definition: "A data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions. They can process and deliver imagery to federally-funded researchers, but most datasets are directly available for download from the satellite imagery page or aerial photography page. Included are the Alaskan High Altitude Aerial Photography (AHAP) Program, Antarctic TMA Aerial Photographs, Landsat and MODIS imagery, among others. The PGC also has staff trained in cartography and GIS to specifically create custom maps for your project. The PGC also holds a large collection of Antarctic maps in digital form. Included are series from the Antarctic and Arctic from many organizations and decades. In collaboration with the United States Geological Survey's Antarctic Resource Center, the PGC holds and digitally preserves the entire reconnaissance mapping series and satellite maps. The PGC also digitally stores geologic maps from the American Geographical Society, historic Antarctic nautical charts, and many others. If you cannot find a map of a specific region or time, it may still exist, especially since the PGC creates more than 100 maps per year and are still adding to the collection. Due to licensing and other restrictions, some of the maps are not be publicly available; send your request and they may be able to provide these maps to you. They also employ a remote sensing staff to assist in remote sensing analysis of your imagery. They provide analysis such as NDVI or land-use/land-cover. The PGC employs both full-time and student staff trained in the latest GIS software and techniques. Although not a primary data creator for the polar regions, they use and distribute many datasets for basemaps and operations. The GIS data page displays links to external resources or data direct for download. They provide analysis with geospatial data (raster and vector) including, but not limited to, imagery/spectral analysis, modeling, DEM creation and manipulation, raster processing, line-of-sight and transect analysis, and database creation and maintenance. In the past, the PGC has been a tremendous resource for researchers and logistics staff alike to make sense of their field or logistics data. Even if it's as simple as plotting coordinates on a map, the PGC can assist!" . + definition: "Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions." . SCR:000403 a NLX:63400, owl:NamedIndividual ; @@ -3125,7 +3112,7 @@ SCR:000403 a NLX:63400, NIFRID:synonym "Academic Seismic Portal (ASP) at UTIG" ; NIFRID:abbrev "ASP at UTIG", "ASP_UTIG" ; - definition: "Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links. The minimum requirements for data submission are: * unrestricted access to the navigation and small raster image (about 300 x 600 pixels) * file format is SEG-Y (they can help with this) * information relating geographic location to the traces in the file (this is often a big part of what they create) They also need basic descriptive information (metadata) about acquisition, navigation geometry, processing sequence and provenance (and pass some of our consistency tests). The submitted metadata is naturally highly variable but could include cruise reports, processing reports, important citations, etc." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links." . SCR:000404 a NLX:63400, owl:NamedIndividual ; @@ -3195,7 +3182,7 @@ SCR:000413 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_155661" ; rdfs:label "MIView" ; - definition: "An OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images." . + definition: "OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images." . SCR:000414 a NLX:63400, owl:NamedIndividual ; @@ -3209,7 +3196,7 @@ SCR:000415 a NLX:63400, rdfs:label "uManager" ; NIFRID:synonym "Micro Manager", "Micro-Manager" ; - definition: "Software package for control of automated microscopes. Cross-platform desktop application, to control a motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories." . + definition: "Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories." . SCR:000416 a NLX:63400, owl:NamedIndividual ; @@ -3224,7 +3211,7 @@ SCR:000417 a NLX:63400, oboInOwl:hasDbXref "OMICS_05545" ; rdfs:label "PSCBS" ; NIFRID:synonym "PSCBS: Analysis of Parent-Specific DNA Copy Numbers" ; - definition: "Software for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported." . + definition: "Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported." . SCR:000418 a NLX:63400, owl:NamedIndividual ; @@ -3255,7 +3242,7 @@ SCR:000422 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_155941" ; rdfs:label "RapidArt" ; - definition: "Software for detecting artifacts and performing individual region-of-interest (ROI) based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results." . + definition: "Software for detecting artifacts and performing individual region-of-interest based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results." . SCR:000423 a NLX:63400, owl:NamedIndividual ; @@ -3295,7 +3282,7 @@ SCR:000428 a NLX:152342, NIFRID:synonym "The Altmetric Explorer" ; definition: "Service to monitor, search and measure conversations about your publications and those of your competitors captured by Altmetric including tweets, blog posts, news stories and other content that mention scholarly articles. Use the Explorer to deliver insights, track mentions and measure levels of attention over time." . -SCR:000429 a NLX:152342, +SCR:000429 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156040" ; rdfs:label "Epistemio" ; @@ -3370,7 +3357,7 @@ SCR:000438 a NLX:63400, NIFRID:abbrev "MIP" ; definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. A database of molecular imaging probes for various diseases, such as Parkinson's disease, dopamine disorder and prion disorders." . -SCR:000439 a NLX:63400, +SCR:000439 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-24069" ; rdfs:label "PsychoGenics Inc" ; @@ -3447,7 +3434,7 @@ SCR:000448 a NLX:63400, rdfs:label "Talairach Daemon" ; NIFRID:synonym "Talairach Software" ; NIFRID:abbrev "talairach.org" ; - definition: "The Talairach software (client, applet and daemon) provide a 5 level hierarchy of label names created for the 1988 Talairach atlas. Labels can be accessed using talairach coordinates. It includes three components: * Talairach Client: a Java application for finding individual and batch labels as well as command-line tools for accessing the daemon. * Talairach Applet: a web application for the daemon which includes graphical overlays and nearest gray matter searches. * Talairach Daemon: a high-speed database server for querying and retrieving data about human brain structure over the internet. The Talairach Client reports Talairach labels for user-defined coordinates. Coordinate data can be manually input through the interface or read from a file. Input data files should be tab-, space-, or comma-delimited and arranged in x,y,z order. There are options to search for the single point, search range, or nearest gray matter. The results are shown on the interface or written to a file that can be viewed in a text editor or imported into a spreadsheet. The Talairach Applet provides a web application for the Talairach Daemon. Since it is an applet, it requires Java to run. In addition to providing label data and structural probability maps, the applet also displays graphical overlays of each region and can find nearest gray matter." . + definition: "Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas." . SCR:000449 a NLX:63400, owl:NamedIndividual ; @@ -3462,7 +3449,7 @@ SCR:000450 a NLX:63400, NIFRID:synonym "Bio-Formats Library", "BioFormats", "The Bio-Formats Library" ; - definition: "Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard. (Dec. 2013)" . + definition: "Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard." . SCR:000451 a NLX:63400, owl:NamedIndividual ; @@ -3621,7 +3608,7 @@ SCR:000472 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_02321" ; rdfs:label "RefFinder" ; - definition: "A web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking." . SCR:000473 a NLX:63400, owl:NamedIndividual ; @@ -3744,13 +3731,14 @@ SCR:000487 a NLX:63400, rdfs:label "PharmML" ; NIFRID:synonym "Pharmacometrics Markup Language" ; NIFRID:abbrev "pharmML" ; - definition: "A standard for encoding of models, associated tasks and their annotation as used in pharmacometrics." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Standard for encoding of models, associated tasks and their annotation as used in pharmacometrics." . -SCR:000488 a NLX:152342, +SCR:000488 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_158258" ; rdfs:label "sigma-tau" ; - NIFRID:synonym "sigma-tau s.p.a." ; + NIFRID:synonym "Leadiant Biosciences", + "sigma-tau s.p.a." ; definition: "Italian pharmaceutical company involved in research, manufacture and marketing of drugs. sigma-tau is present today in the most advanced research sectors, maintaining constant relations with scientific institutions with a world-wide reputation in the development of joint projects and in the implementation of original and innovative research programs." . SCR:000489 a NLX:152328, @@ -3824,6 +3812,7 @@ SCR:000497 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_158375" ; rdfs:label "Drug Design Data Resource" ; + NIFRID:synonym "Drug Design Data (D3R) Resource" ; NIFRID:abbrev "D3R" ; definition: "Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms." . @@ -3962,7 +3951,7 @@ SCR:000514 a NLX:63400, oboInOwl:hasDbXref "OMICS_01529" ; rdfs:label "ARNIE" ; NIFRID:synonym "AVEXIS Receptor Network with Integrated Expression" ; - definition: "Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided." . SCR:000515 a NLX:63400, owl:NamedIndividual ; @@ -4002,7 +3991,7 @@ SCR:000520 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_39837" ; rdfs:label "Quality of Medical Data" ; - definition: "A research resource about the issues surrounding the quality of medical data and its usage for secondary purposes. This portal serves as a resource to understand the current state of medical data quality and the factors that affect it. The information is gathered from anecdotal and empirical examples from peer-reviewed journals, popular media and author contributions. Issues of importance include understanding and measuring medical data quality, contributing factors, best practices, and the effects of data quality on secondary uses of medical data." . + definition: "Portal serves as resource to understand the current state of medical data quality and the factors that affect it. The information is gathered from anecdotal and empirical examples from peer-reviewed journals, popular media and author contributions. Issues of importance include understanding and measuring medical data quality, contributing factors, best practices, and the effects of data quality on secondary uses of medical data." . SCR:000521 a NLX:63400, owl:NamedIndividual ; @@ -4035,7 +4024,7 @@ SCR:000524 a NLX:63400, "Children's Cancer and Leukemia Group Tissue Bank" ; definition: "Tissue bank that provides access to tissue samples and an anonymized version of the tissue bank database.Bank has large collection of tumour, DNA and other tissue samples from childhood cancer patients." . -SCR:000525 a NLX:63400, +SCR:000525 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_51231" ; rdfs:label "CARTA" ; @@ -4049,7 +4038,7 @@ SCR:000526 a NLX:63400, rdfs:label "NERC Environmental Bioinformatics Centre" ; NIFRID:synonym "NERC Environmental Bioinformatics Center" ; NIFRID:abbrev "NEBC" ; - definition: "A data sharing platform based on the ISA software suite - including an annotation tool and a database - that holds environmental omic data in standards-compliant format. It uses various approaches to provide new discovery, interoperability and integration opportunities for environmental scientists, including the development of tools, databases, standard and ontologies. The main tool for collecting environmental omics data from researchers is the EnvBase data catalogue. The NEBC Toolbox contains a range of tools developed by NEBC to support environmental researchers. The data include next generation sequencing, microarray and ABI sequencing technologies. ISAconfigurator and ISAcreator ensure that the extensive information relating to environmental sampling is consistently collected by the NERC experimentalists, according to the appropriate MIBBI checklist(s), and then reported centrally to NEBC. A local instance of the BII runs as an internal prototype database that will soon provide public and private access to NERC research projects outputs, as appropriate. In accordance with the NERC Data Policy, and when data sets are declared ready for public release, the NEBC team will use the ISAconverter to perform (combined) submissions to the appropriate public repositories (ENA, or SRA, ArrayExpress and PRIDE) to ensure long term stewardship." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data sharing platform based on the ISA software suite - including an annotation tool and a database - that holds environmental omic data in standards-compliant format. It uses various approaches to provide new discovery, interoperability and integration opportunities for environmental scientists, including the development of tools, databases, standard and ontologies. The main tool for collecting environmental omics data from researchers is the EnvBase data catalogue. The NEBC Toolbox contains a range of tools developed by NEBC to support environmental researchers. The data include next generation sequencing, microarray and ABI sequencing technologies. ISAconfigurator and ISAcreator ensure that the extensive information relating to environmental sampling is consistently collected by the NERC experimentalists, according to the appropriate MIBBI checklist(s), and then reported centrally to NEBC. A local instance of the BII runs as an internal prototype database that will soon provide public and private access to NERC research projects outputs, as appropriate. In accordance with the NERC Data Policy, and when data sets are declared ready for public release, the NEBC team will use the ISAconverter to perform (combined) submissions to the appropriate public repositories (ENA, or SRA, ArrayExpress and PRIDE) to ensure long term stewardship." . SCR:000527 a NLX:63400, owl:NamedIndividual ; @@ -4118,7 +4107,7 @@ SCR:000534 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_01466" ; rdfs:label "SPHINX" ; - definition: "A hybrid binning tool that achieves high binning efficiency by utilizing both \"compositional\" and \"similarity\" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both \"compositional\" and \"similarity\" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms." . SCR:000535 a NLX:63400, owl:NamedIndividual ; @@ -4162,7 +4151,7 @@ SCR:000540 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_01459" ; rdfs:label "PhyloPythia" ; - definition: "Data analysis service for accurate phylogenetic classification of variable-length DNA fragments." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data analysis service for accurate phylogenetic classification of variable-length DNA fragments." . SCR:000541 a NLX:63400, owl:NamedIndividual ; @@ -4178,7 +4167,7 @@ SCR:000542 a NLX:63400, rdfs:label "University of Michigan Human Breast Cancer Cell Lines" ; NIFRID:synonym "University of Michigan Human Breast Cancer Cell Lines (SUM-LINES)", "University of Michigan SUM-LINES" ; - definition: "Asterand, Inc., the Detroit-based supplier of human tissue products and services, announces the distribution of eleven breast cancer cell lines, derived at the University of Michigan. The University has agreed to license the marketing of the breast cancer cell lines, known as the SUM lines, through Asterand in an effort to provide an exceptional tool to a broad base of researchers studying the disease. There are an estimated 1.2 million new diagnoses worldwide of breast cancer each year. The cell lines can be used to study all aspects of breast cancer biology, from new drug target identification to cell signaling to effects of novel drugs on cellular proliferation." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Asterand, Inc., the Detroit-based supplier of human tissue products and services, announces the distribution of eleven breast cancer cell lines, derived at the University of Michigan. The University has agreed to license the marketing of the breast cancer cell lines, known as the SUM lines, through Asterand in an effort to provide an exceptional tool to a broad base of researchers studying the disease. There are an estimated 1.2 million new diagnoses worldwide of breast cancer each year. The cell lines can be used to study all aspects of breast cancer biology, from new drug target identification to cell signaling to effects of novel drugs on cellular proliferation." . SCR:000543 a NLX:63400, owl:NamedIndividual ; @@ -4289,7 +4278,7 @@ SCR:000556 a NLX:63400, oboInOwl:hasDbXref "OMICS_00046" ; rdfs:label "Scaffold builder" ; NIFRID:abbrev "scaffold_builder" ; - definition: "Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome." . SCR:000557 a NLX:63400, owl:NamedIndividual ; @@ -4355,7 +4344,7 @@ SCR:000565 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_00194" ; rdfs:label "wANNOVAR" ; - definition: "A web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants." . SCR:000566 a NLX:63400, owl:NamedIndividual ; @@ -4367,9 +4356,8 @@ SCR:000566 a NLX:63400, SCR:000567 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_144218" ; - rdfs:label "A Lady Scientist" ; - NIFRID:abbrev "Lady Scientist" ; - definition: "A Lady Scientist chronicles the author's journey through grad school and navigating the so-called Two Body Problem. The author, Amanda (at) Lady Scientist, is a recent Ph.D. graduate in biochemistry and molecular biology." . + rdfs:label "Lady Scientist" ; + definition: "Lady Scientist chronicles the author's journey through grad school and navigating the so-called Two Body Problem. The author, Amanda (at) Lady Scientist, is a recent Ph.D. graduate in biochemistry and molecular biology." . SCR:000568 a NLX:63400, owl:NamedIndividual ; @@ -4459,7 +4447,7 @@ SCR:000579 a NLX:63400, "Jefferson Hospital for Neuroscience Alzheimer's Disease Dementia Center", "Jefferson Hospital for Neuroscience Alzheimers Disease Dementia Center" ; NIFRID:abbrev "Jefferson Alzheimer's Disease and Dementia Center" ; - definition: "If you or someone you love has been diagnosed with dementia caused by Alzheimer's disease, you'll be in good hands at Jefferson. Our neurologists and psychiatrists are dedicated to: Compassionate care for individuals with Alzheimer's disease; Supporting families; Advancing care through research into the epidemiology and treatment of neurodegenerative diseases. We interact with patients very early in the disease progression, when impairment is typically mild; deliver state-of-the-art care; provide information; build care-giving skills; and help caregivers connect with community support and plan for the future. Although there is no cure for Alzheimer's disease, our goal is to provide accurate diagnoses and state-of-the-art treatment. We are also involved in basic science research that is advancing fundamental knowledge of dementia-related disorders and paving the way for new methods of treatment. At Jefferson Hospital for Neuroscience, patients with Alzheimer's disease can participate in clinical trials with promising investigational treatments for the disease. Most of these studies are multicenter, multiyear trials that have already met a number of rigorous standards for safety and efficacy and have shown favorable effects on memory. For many patients and their families, participation not only offers the hope of slowing the disease but also represents a chance to share personal experience and contribute to new scientific knowledge. Patients who agree to participate must be able to assent to the study, and caregivers who support that participation act as surrogate decision-makers and provide informed consent." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. If you or someone you love has been diagnosed with dementia caused by Alzheimer's disease, you'll be in good hands at Jefferson. Our neurologists and psychiatrists are dedicated to: Compassionate care for individuals with Alzheimer's disease; Supporting families; Advancing care through research into the epidemiology and treatment of neurodegenerative diseases. We interact with patients very early in the disease progression, when impairment is typically mild; deliver state-of-the-art care; provide information; build care-giving skills; and help caregivers connect with community support and plan for the future." . SCR:000580 a NLX:63400, owl:NamedIndividual ; @@ -4481,7 +4469,7 @@ SCR:000582 a NLX:63400, oboInOwl:hasDbXref "nlx_144534" ; rdfs:label "Whole Brain Catalog Blog" ; NIFRID:abbrev "WBC Blog" ; - definition: "The blog of the Whole Brain Catalog." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog." . SCR:000583 a NLX:63400, owl:NamedIndividual ; @@ -4521,7 +4509,7 @@ SCR:000587 a NLX:63400, "OMICS_00670" ; rdfs:label "MPscan" ; NIFRID:synonym "MPscan: index free mapping of multiple short reads on a genome" ; - definition: "Tool for index free mapping of multiple short reads on a genome." . + definition: "Web tool for index free mapping of multiple short reads on a genome." . SCR:000588 a NLX:63400, owl:NamedIndividual ; @@ -4552,7 +4540,7 @@ SCR:000591 a NLX:63400, oboInOwl:hasDbXref "nlx_144623" ; rdfs:label "neurodudes" ; NIFRID:synonym "neurodudes - at the intersection of neuroscience and AI" ; - definition: "neurodudes is intended to be an open forum at the intersection of neuroscience and ai. regular readers are encouraged to post appropriate material. make sure to put your name somewhere in the post. The ultimate neurodudes RSS feed combines neuro/ai/cogsci-related RSS feeds from many sources, sometimes filtering along the way so as to minimize offtopic posts." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Neurodudes is intended to be an open forum at the intersection of neuroscience and ai. regular readers are encouraged to post appropriate material. make sure to put your name somewhere in the post. The ultimate neurodudes RSS feed combines neuro/ai/cogsci-related RSS feeds from many sources, sometimes filtering along the way so as to minimize offtopic posts." . SCR:000592 a NLX:63400, owl:NamedIndividual ; @@ -4571,7 +4559,7 @@ SCR:000594 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "OMICS_02257" ; rdfs:label "MutPred Splice" ; - definition: "Tool for identifying coding region variants which disrupt pre-mRNA splicing and the underlying mechanism." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool for identifying coding region variants which disrupt pre-mRNA splicing and the underlying mechanism." . SCR:000595 a NLX:63400, owl:NamedIndividual ; @@ -4593,7 +4581,7 @@ SCR:000597 a NLX:63400, rdfs:label "DDBJ Omics Archive" ; NIFRID:synonym "Ddbj Omics aRchive" ; NIFRID:abbrev "DOR" ; - definition: "Resource out of service. Documented on May,6th 2021.Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy." . SCR:000598 a NLX:152342, owl:NamedIndividual ; @@ -4613,13 +4601,13 @@ SCR:000600 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_149080" ; rdfs:label "NVM" ; - definition: "Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis." . SCR:000601 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_149109" ; rdfs:label "Onto-Design" ; - definition: "Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool" . SCR:000602 a NLX:63400, owl:NamedIndividual ; @@ -4629,7 +4617,7 @@ SCR:000602 a NLX:63400, NIFRID:synonym "Ontology Evolution Explorer", "Ontology Evolution Explorer (OnEx)" ; NIFRID:abbrev "OnEx" ; - definition: "Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released" . SCR:000603 a NLX:63400, owl:NamedIndividual ; @@ -4828,7 +4816,7 @@ SCR:000626 a NLX:63400, oboInOwl:hasDbXref "nlx_151739" ; rdfs:label "PredSL" ; NIFRID:synonym "PREDiction of Subcellular Location from the N-terminal Sequence" ; - definition: "A web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. Analysis of a non-redundant test set, consisting of plant protein sequences provides a ~90% accuracy, whereas analysis of a similar set of nonplant protein sequences provides a ~92% accuracy. As input PredSL requires the protein's sequence in fasta format. The algorithm cosists of 11 steps: # Initially the 100 N-terminal residues of the sequence are coded (see supplementary material-neural network training) and fed to a first layer of 2 neural networks which determine whether a residue belongs or not to a chloroplast transit peptide (cTP) or a mitochondrial transit peptide (mTP). From this step we get 100 scores (one per residue) from each network. # We have set a cutoff where the residues do not belong to a transit peptide any longer, and thus we calculate two approximate cleavage sites from the 100 scores we calculated in step 1.(One from each network) # We take a window of 40 positions around the approximate cleavage site we estimated in step 2, and we use a set of neural networks to predict the cleavage site. Therefore we have one prediction of the cleavage site of the hypothetical cTP and one for the mTP. # We calculate the average of the scores of the hypothetical peptides predicted from each network, and this results to two scores. # We feed the 100 scores from step 1 to two neural networks (one for the cTP and one for the mTP), and we get two more scores. These scores represent the probability that the sequence has an mTP or a cTP. # We use PrediSi to calculate one more score for each sequence. This score represents the probability of a sequence belonging to a secreted protein. # We use a program that uses Markov chains to discriminate between two categories to get 6 more scores for the plant proteins and 3 more for the nonplant. (See supplementary material-Markov chains) # We use HMMER to get two additional scores for each protein. One that shows the existence or not of a cTP and one that shows the existence or not of an mTP. # We feed all the scores we gathered (13 for the plant and 7 for the non-plant proteins) to a neural network that does the final prediction. # Finally, if a sequence is predicted to belong to a chloroplast protein, we use HMMER to determine the existence of a lumenal-transit peptide (lTP) # If the user requires it, PredSL provides the possibility to make a graph for each case. The graphs for the chloroplast and mitochondrial sequences are created using the scores from Step 1 and taking a window around the predicted cleavage site from Step 3. For the secreted proteins, the graphs are created usind the hydrophobicity index (Kytte-Doolittle, 1982) for a window around the predicted cleavage site from PrediSi." . + definition: "Web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. As input PredSL requires the protein's sequence in fasta format." . SCR:000627 a NLX:63400, owl:NamedIndividual ; @@ -4878,7 +4866,7 @@ SCR:000633 a NLX:63400, rdfs:label "Phosphor Antibody Array Data Analysis" ; NIFRID:synonym "PANDA: Phosphor Antibody Array Data Analysis" ; NIFRID:abbrev "PANDA" ; - definition: "A web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies." . SCR:000634 a NLX:63400, owl:NamedIndividual ; @@ -4892,7 +4880,7 @@ SCR:000635 a NLX:63400, oboInOwl:hasDbXref "nlx_151898" ; rdfs:label "Pathline" ; NIFRID:synonym "Pathline: A Tool For Comparative Genomics" ; - definition: "A visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species." . + definition: "Software visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species." . SCR:000636 a NLX:63400, owl:NamedIndividual ; @@ -4930,7 +4918,7 @@ SCR:000639 a NLX:63400, rdfs:label "University of Neurosurgery Webinar Series" ; NIFRID:synonym "CNS Webinar Series", "Congress of Neurological Surgeons Webinar Series" ; - definition: "A series of of webinars offered directly to users' computers. The webinars are offered in a variety of subjects, including neurotrauma, spine, tumor and vascular. Each webinars costs $35 US and offers CME credit." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. A series of of webinars offered directly to users' computers. The webinars are offered in a variety of subjects, including neurotrauma, spine, tumor and vascular. Each webinars costs $35 US and offers CME credit." . SCR:000640 a NLX:63400, owl:NamedIndividual ; @@ -4951,7 +4939,7 @@ SCR:000642 a NLX:63400, rdfs:label "UC3 Merritt" ; NIFRID:synonym "University of California Curation Center Merritt" ; NIFRID:abbrev "Merritt" ; - definition: "A data repository service from the University of California Curation Center (UC3) that lets the UC community manage, archive, and share its valuable digital content. Merritt provides long-term preservation of digital assets, allows researchers to share data with others, or meet the data sharing and preservation requirements of a grant-funded project." . + definition: "Data repository service from the University of California Curation Center (UC3) that lets the UC community manage, archive, and share its valuable digital content. Merritt provides long-term preservation of digital assets, allows researchers to share data with others, or meet the data sharing and preservation requirements of a grant-funded project." . SCR:000643 a NLX:63400, owl:NamedIndividual ; @@ -4962,14 +4950,14 @@ SCR:000643 a NLX:63400, "Quantitative traits" ; definition: "Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits." . -SCR:000644 a NLX:152342, +SCR:000644 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_149208", "OMICS_01120" ; rdfs:label "Avadis" ; NIFRID:synonym "Access Visualize Analyze Discover", "Avadis NGS" ; - definition: "An integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Genes can be clustered based on ontology terms to identify functional signatures in gene expression clusters. AVADIS platform has a rich collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible," . + definition: "Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible," . SCR:000645 a NLX:63400, owl:NamedIndividual ; @@ -6009,7 +5997,7 @@ SCR:000785 a NLX:63400, NIFRID:abbrev "EUMORPHIA" ; definition: "A portal documenting a project for the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. EUMORPHIA has developed a new robust primary screening platform for determining the phenotype of mice: EMPReSS - European Mouse Phenotyping Resource for Standardised Screens. The project is also focused on training new young scientists by funding them to work in a variety of laboratories to gain a broader swathe of techniques. The project has also identified the need for more trained mouse pathologists. To address this, they are setting up training courses in pathology and working at a European level to establish more training." . -SCR:000786 a NLX:152328, +SCR:000786 a NLX:152342, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-30523" ; rdfs:label "Eppendorf" ; @@ -7914,15 +7902,22 @@ SCR:001029 a NLX:63400, SCR:001030 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "SciEx_32" ; - rdfs:label "Washington University in St. Louis Genome Technology Access Center" ; + oboInOwl:hasDbXref "ABRF_279", + "SciEx_32", + "SCR_018204", + "SCR_018300" ; + rdfs:label "Washington University School of Medicine Genome Technology Access Center Core Facility" ; NIFRID:synonym "Genome Technology Access Center", - "GTAC", - "Washington University", - "Washington University in St. Louis", - "WUSTL" ; - NIFRID:abbrev "WUSTL GTAC" ; - definition: "Core provides sequencing and analysis technologies and services to local and external investigators. Services include sample preparation, data generation, bioinformatics analysis, and intellectual support for microarray, PCR, and high-throughput sequencing studies." . + "McDonnell Genome Institute Genome Technology Access Center", + "Washington University in St. Louis Genome Technology Access Center", + "Washington University in St. Louis McDonnell Genome Institute Genome Technology Access Center", + "Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility", + "Washington University McDonnell Genome Institute Genome Technology Access Center", + "Washington University School of Medicine GTAC", + "Washington University School of Medicine GTAC Core Facility" ; + NIFRID:abbrev "GTAC", + "WUSTL GTAC" ; + definition: "Genome Access Technology Center at the McDonnell Genome Institute offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms." . SCR:001031 a NLX:63400, owl:NamedIndividual ; @@ -11358,8 +11353,9 @@ SCR:001476 a NLX:63400, oboInOwl:hasDbXref "nlx_152707" ; rdfs:label "Harvard - Oxford Cortical Structural Atlas" ; NIFRID:synonym "Harvard Oxford Atlas", - "Harvard Oxford Cortical Structural Atlas" ; - NIFRID:abbrev "Harvard-Oxford cortical and subcortical structural atlases" ; + "Harvard Oxford Cortical Structural Atlas", + "Harvard-Oxford cortical and subcortical structural atlases" ; + NIFRID:abbrev "Atlases" ; definition: "Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School." . SCR:001477 a NLX:63400, @@ -11951,7 +11947,7 @@ SCR:001547 a NLX:63400, SCR:001548 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_41870" ; - rdfs:label "Karolinska Institutet; Stockholm; Sweden" ; + rdfs:label "Karolinska Institute; Stockholm; Sweden" ; NIFRID:synonym "Karolinska Institutet", "Karolinska University" ; NIFRID:abbrev "KI" ; @@ -12290,14 +12286,14 @@ SCR:001592 a NLX:63400, oboInOwl:hasDbXref "nlx_153838", "nlx_155839", "SCR_009594" ; - rdfs:label "Waxholm Space Atlas of the Sprague Dawley Rat Brain" ; - NIFRID:synonym "Waxholm Space", + rdfs:label "Waxholm Space" ; + NIFRID:synonym "Mouse WHS atlas", "Waxholm Space Atlas", "Waxholm Standard Space" ; NIFRID:abbrev "WHS", "WSA", "WSS" ; - definition: "Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files." . SCR:001593 a NLX:63400, owl:NamedIndividual ; @@ -15540,7 +15536,8 @@ SCR:002003 a NLX:63400, SCR:002004 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "nif-0000-10901" ; + oboInOwl:hasDbXref "nif-0000-10901", + "SCR_005058" ; rdfs:label "NeuronBank" ; NIFRID:synonym "NeuronBank wiki" ; definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. Platform for Neuroscientists to describe neurons and neural circuitry. Registered users may edit. The ultimate goal is advance the field of Neuromics by creating an encyclopedia of neurons and neural circuitry. NOTE: The database is no longer being maintained due to lack of funding." . @@ -15908,15 +15905,19 @@ SCR:002049 a NLX:63400, SCR:002050 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "nif-0000-12246", + oboInOwl:hasDbXref "ABRF_200", + "nif-0000-12246", "nif-0000-31997", "SCR_008627" ; - rdfs:label "Stanford University Functional Genomics Core Facility" ; + rdfs:label "Stanford Genomics Service Center Core Facility" ; NIFRID:synonym "Stanford Functional Genomics Facility", - "Stanford University Functional Genomics Facility" ; + "Stanford Genomics", + "Stanford Genomics Service Center", + "Stanford Medicine Stanford Functional Genomics Facility", + "Stanford School of Medicine Stanford Functional Genomics Facility", + "Stanford University Functional Genomics Core Facility" ; NIFRID:abbrev "SFGF" ; - definition: """Service center in Stanford School of Medicine providing genomics services:High-throughput Sequencing (Illumina), Library Generation for Illumina High-throughput Sequencing,Microarray Gene Expression (Affymetrix, Agilent, Illumina),QC for RNA, DNA, and High-throughput Sequencing Libraries,Whole Genome Genotyping (Illumina),Real-time PCR, gene expression, genotyping, melt, etc.Sample Preps,DNA and RNA extractions, Plasmid preps, NanoString, -Microarrays and Microarray Printing, Access to Instrumentation and Software. Supports all arrays based on microscope format including Agilent, Illumina, Nimblegen, and arrays produced by SFGF. Besides printing cDNA and oligonucliotide microarrays, facility can print arrays of your material in high throughput fashion, including proteins, peptides, antibodies, cell lysates, siRNAs, etc.""" . + definition: "Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field." . SCR:002051 a NLX:63400, owl:NamedIndividual ; @@ -16714,7 +16715,8 @@ SCR:002151 a NLX:63400, oboInOwl:hasDbXref "nlx_154662", "OMICS_02075" ; rdfs:label "STRUCTURE" ; - definition: "A software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and amplified fragment length polymorphisms (AFLPs)." . + NIFRID:synonym "Structure" ; + definition: "Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms." . SCR:002152 a NLX:63400, owl:NamedIndividual ; @@ -18003,7 +18005,7 @@ SCR:002313 a NLX:63400, rdfs:label "MAGE" ; NIFRID:synonym "MicroArray and Gene Expression", "MicroArray and Gene Expression - MAGE" ; - definition: "Group providing a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. Group providing a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems." . SCR:002314 a NLX:63400, owl:NamedIndividual ; @@ -19689,11 +19691,11 @@ SCR:002525 a NLX:63400, rdfs:label "Pythagorean Displacement and Motion Regressors" ; definition: "Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment." . -SCR:002526 a NLX:63400, - owl:NamedIndividual ; +SCR:002526 a owl:NamedIndividual ; oboInOwl:hasDbXref "SciRes_000114" ; rdfs:label "Stereo Investigator" ; - definition: "Stereo Investigator software includes computerized microscope control . Software and microscope hardware work together in stereology systems. Typical system includes microscope, computer, and Stereo Investigator software.Stereo Investigator system for stereology gives you accurate, unbiased estimates of number, length, area, and volume of cells or biological structures in tissue specimen." . + NIFRID:synonym "Stereo Investigator system" ; + definition: "Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology." . SCR:002527 a NLX:63400, owl:NamedIndividual ; @@ -20433,7 +20435,8 @@ SCR:002624 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156042" ; rdfs:label "eScholarship" ; - definition: "A suite of open access, scholarly publishing services and research tools that enable departments, research units, publishing programs, and individual scholars associated with the University of California to have direct control over the creation and dissemination of the full range of their scholarship. Content is delivered via a dynamic research platform and is available to scholars worldwide. eScholarship allows users to publish the following original scholarly works on a dynamic research platform available to scholars worldwide: Books, Journals, Working Papers, Previously Published Works, and Conferences. eScholarship also provides deposit and dissemination services for postprints, or previously published articles. Publications benefit from manuscript and peer-review management systems, as well as a full range of persistent access and preservation services." . + NIFRID:synonym "CDL eScholarship" ; + definition: "Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide." . SCR:002625 a NLX:63400, owl:NamedIndividual ; @@ -22011,7 +22014,8 @@ SCR:002823 a NLX:63400, "SCR_007368" ; rdfs:label "FSL" ; NIFRID:synonym "FMRIB Software Library", - "fMRIB Software Library" ; + "fMRIB Software Library", + "Functional Magnetic Resonance Imaging of the Brain Software Library" ; definition: "Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas." . SCR:002824 a NLX:63400, @@ -22765,13 +22769,6 @@ SCR:002913 a NLX:63400, NIFRID:abbrev "HMPDb" ; definition: "Database of mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. The mitochondrion plays a central role in cellular metabolism, and evidence of mitochondrial involvement in a number of different human diseases is increasing. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases. Mitochondrial DNA Sequence: A graphical tool was developed to visualize the human mitochondrial DNA sequences that highlight coding regions for RNAs and proteins. Disease susceptible mutations are also noted in the sequence. Mitochondrial DNA Polymorphism: Human mitochondrial sequences of different ethnic groups were obtained from the Human Mitochondrial Genome Database. A DNA sequence analysis tool was developed to compare polymorphisms of different human mitochondrial DNA sequences. This tool allows the user to select mitochondrial sequences from any two human populations and compare them for sequences variations. Mitochondrial proteins related diseases: Malfunction of mitochondrial proteins affect many cells from brain, heart, liver, skeletal muscles, kidney, and the endocrine and the respiratory systems which lead to many diseases. Relevant information for mitochondrial related diseases from OMIM, the Neuromuscular Disease Center and MITOMAP are gathered, and mitochondrion-associated diseases are grouped, categorized, and linked to OMIM. 3-D Structures of Mitochondrial proteins: The available 3D structures for mitochondrial proteins are presented through a custom-made interface. A concise HTML page is generated for reporting the structural details and the associated information obtained from relevant web sites (PDBREPORT, Interatomic Contacts of Structural Units (CSU), PROCHECK, Ligand Protein Contacts (LPC), PROMOTIF and CastP). References are linked to the PubMed site. The 3-D structures are presented through the use of a Kinemage." . -SCR:002914 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "nif-0000-30014" ; - rdfs:label "Kendrick Labs - Proteomic Services Including 2D Gel Electrophoresis Western Blotting and Mass Spectrometry" ; - NIFRID:synonym "Kendrick Labs" ; - definition: "Kendrick Labs has been carrying out protein electrophoresis as a service for academia, federal institutions and industry since 1987. It's mission is to help clients solve proteomic problems quickly and economically, especially problems which require 2-dimensional gel electrophoresis. The lab service functions nationwide via low-cost express mail, toll-free phone, and e-mail. It receive samples and return results to New York and Los Angeles as fast as labs based in these cities. It's goal is to help clients solve proteomic problems quickly and economically in a changing world. To that end it is now offering Phosphotyrosine Western Blotting with the PY20 monoclonal antibody and also Phosphoserine/Phosphothreonine Western Blotting with Qiagen antibodies." . - SCR:002915 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciRes_000188" ; @@ -23082,8 +23079,8 @@ SCR:002952 a NLX:63400, SCR:002953 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-00045" ; - rdfs:label "Mutant Mouse Regional Resource Center" ; - NIFRID:synonym "Mutant Mouse Resource and Research Center" ; + rdfs:label "Mutant Mouse Resource and Research Center" ; + NIFRID:synonym "Mutant Mouse Regional Resource Center" ; NIFRID:abbrev "MMRRC" ; definition: "National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics." . @@ -24048,6 +24045,7 @@ SCR:003070 a NLX:63400, oboInOwl:hasDbXref "2012ascl.soft06013R", "ascl:1206.013", "nif-0000-30467", + "Q1659584", "rid_000070", "SCR_018407" ; rdfs:label "ImageJ" ; @@ -24528,9 +24526,10 @@ SCR:003131 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156783" ; rdfs:label "NIH NeuroBioBank" ; - NIFRID:synonym "National Institutes of Health NeuroBioBank" ; - NIFRID:abbrev "NeuroBioBank" ; - definition: "A federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Brain tissue is a precious resource that enables scientists to better understand disorders affecting the brain in order to develop treatments and cures. The NIH NeuroBioBank also provides information to the public about the need for tissue donation and how to register as a donor." . + NIFRID:synonym "National Institutes of Health NeuroBioBank", + "NeuroBioBank" ; + NIFRID:abbrev "NBB" ; + definition: "National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor." . SCR:003132 a NLX:63400, owl:NamedIndividual ; @@ -25245,7 +25244,7 @@ SCR:003222 a NLX:63400, oboInOwl:hasDbXref "biotools:tab2mage", "nlx_157259" ; rdfs:label "MAGE-TAB" ; - definition: "A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML." . SCR:003223 a NLX:63400, owl:NamedIndividual ; @@ -26058,8 +26057,7 @@ SCR:003327 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-00064" ; rdfs:label "Brede Database" ; - NIFRID:abbrev "Brede" ; - definition: "A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments." . + NIFRID:abbrev "Brede" . SCR:003328 a NLX:63400, owl:NamedIndividual ; @@ -27670,9 +27668,11 @@ SCR:003523 a NLX:63400, SCR:003524 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "biotools:iDASH", - "nif-0000-38239" ; + "nif-0000-38239", + ; rdfs:label "iDASH" ; - NIFRID:synonym "Integrating Data for Analysis Anonymization and SHaring" ; + NIFRID:synonym "iDASH Repository", + "Integrating Data for Analysis Anonymization and SHaring" ; definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications." . SCR:003525 a NLX:63400, @@ -29938,12 +29938,10 @@ SCR:003812 a NLX:63400, NIFRID:synonym "Peer Library" ; definition: "Open source project providing a collaborative layer of knowledge over academic publications by allowing users to share real-time highlights and annotations. Participate in open discussion that drives ideas and academia forward. It provides a supportive space to learn about research and ask questions of peers and experts. Follow authors and other users to understand their perspectives, make connections, and discover new ideas." . -SCR:003813 a NLX:63400, - owl:NamedIndividual ; +SCR:003813 a owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_158114" ; - rdfs:label "Nephroseq" ; - NIFRID:synonym "Nephromine" ; - definition: "THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data.
Please note, Nepromie has become Nephroseq in 2016.. http://dx.doi.org/10.1016/j.kint.2016.01.015," . + rdfs:label "Nephromine" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data.
Please note, Nepromie has become Nephroseq in 2016.. http://dx.doi.org/10.1016/j.kint.2016.01.015." . SCR:003814 a NLX:152328, owl:NamedIndividual ; @@ -30091,16 +30089,7 @@ SCR:003832 a owl:NamedIndividual ; SCR:003833 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_158148" ; - rdfs:label "Elephant" ; - NIFRID:synonym "Electrophysiology Analysis Toolkit", - "Elephant - Electrophysiology Analysis Toolkit" ; - NIFRID:abbrev "ElePhAnT" ; - definition: """The Electrophysiology Analysis Toolkit (Elephant) is an open-source library for the analysis of electrophysiological data in the Python programming language. The focus of Elephant is on generic analysis functions for spike train data and time series recordings from electrodes, such as local field potentials (LFP) or intracellular voltages. In addition to providing a common platform for analysis code from different laboratories, the Elephant project aims to provide a consistent and homogeneous analysis framework built on a modular foundation. Elephant is built on the Neo data object model for electrophysiological data. - -Documentation: http://elephant.readthedocs.org -Support: https://github.com/NeuralEnsemble/elephant/issues -Source Code: https://github.com/NeuralEnsemble/elephant/ -Package Download: https://pypi.python.org/pypi/elephant/""" . + rdfs:label "Elephant" . SCR:003834 a owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_158149" ; @@ -30895,8 +30884,7 @@ SCR:003931 a NLX:63400, oboInOwl:hasDbXref "nlx_158300" ; rdfs:label "DataLad" ; NIFRID:synonym "Data Lad", - "DataGit" ; - definition: "Project to adapt model of open source software distributions to address technical limitations of data sharing and develop all components of data distribution. Builds on top of git-annex and extends it with intuitive command line interface. Enables users to operate on data using familiar concepts, such as files and directories, while transparently managing data access and authorization with underlying hosting providers. Can create DataLad datasets using any data files published on the web." . + "DataGit" . SCR:003932 a NLX:63400, owl:NamedIndividual ; @@ -31002,7 +30990,8 @@ SCR:003943 a NLX:63400, "ndex bio", "ndex biology", "Network Data Exchange", - "the Network Data Exchange" ; + "the Network Data Exchange", + "UCSD NDEx" ; definition: "Repository where scientists and organizations can share, store, manipulate, and publish biological network data. Users can also run their own copies of NDEx Server software in cases where stored networks must be kept in highly secure environment (such as for HIPAA compliance) or where high application load is incompatible with shared public resource. Open source software system that is part of Cytoscape family. Project of Cytoscape Consortium in conjunction with Ideker lab at UCSD School of Medicine. Public forum where biologists can exchange and publish computable network models in many types and formats. NDEx is based on REST web API which can be accessed by any application, including NDEx website and NDEx Cytoscape App. NDEx networks are assigned stable, globally unique URIs and so can be referenced by publications, by other networks, and by analytic applications." . SCR:003944 a NLX:152328, @@ -36252,17 +36241,6 @@ SCR:004575 a NLX:63400, NIFRID:synonym "Alien_hunter: Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA" ; definition: "Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer." . -SCR:004576 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "nlx_56885" ; - rdfs:label "NASC" ; - NIFRID:synonym "European Arabidopsis Stock Centre", - "NASC code", - "Nottingham Arabidopsis Stock Center", - "Nottingham Arabidopsis Stock Centre", - "uNASC" ; - definition: "Stock Centre provides seed and information resources to International Arabidopsis Genome Programme and research community. Maintains accessions of Arabidopsis thaliana (and small number of other related species), including Characterized lines, Mapping populations, and Insertion lines. You may browse or search catalog." . - SCR:004577 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_57488" ; @@ -39714,9 +39692,10 @@ SCR:004996 a NLX:152328, SCR:004997 a NLX:152328, owl:NamedIndividual ; - oboInOwl:hasDbXref "nlx_152318" ; - rdfs:label "BioXCell" ; - definition: "An Antibody supplier" . + oboInOwl:hasDbXref "nlx_152318", + "SCR_019248" ; + rdfs:label "Bio X Cell" ; + definition: "Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services." . SCR:004998 a NLX:63400, owl:NamedIndividual ; @@ -42192,7 +42171,9 @@ SCR:005309 a NLX:63400, oboInOwl:hasDbXref "biotools:maker", "nlx_144363" ; rdfs:label "MAKER" ; - definition: "MAKER is a portable and easily configurable genome annotation pipeline. It''s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER''s inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources. MAKER is available for academic use under either the Artistic License 2.0 developed by the Perl Foundation or the GNU General Public License developed by the Free Software Foundation. MAKER is not available for commercial use without a license. Those wishing to license MAKER for commercial use should contact Moj Eram to discuss your needs." . + NIFRID:synonym "maker", + "Maker2" ; + definition: "Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values." . SCR:005310 a NLX:152328, owl:NamedIndividual ; @@ -43792,9 +43773,9 @@ SCR:005505 a NLX:63400, SCR:005506 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_144606" ; - rdfs:label "MBL Pivot Collection" ; NIFRID:synonym "Mouse Brain Library Pivot Collection" ; - definition: "Mouse brains displayed in the Microsoft Silverlight PivotViewer from the Mouse Brain Library (MBL) which consist of high-resolution images of brains from many genetically characterized strains of mice. PivotViewer makes it easier to interact with massive amounts of data on the web in ways that are powerful, informative, and fun. By visualizing thousands of related items at once, users can see trends and patterns that would be hidden when looking at one item at a time. Because PivotViewer leverages Deep Zoom, it displays full, high-resolution content without long load times, while the animations and natural transitions provide context and prevent users from feeling overwhelmed by large quantities of information. This simple, inviting interaction model encourages exploration and longer audience engagement times, and applies broadly to a variety of content types." . + NIFRID:abbrev "MBL Pivot Collection" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. Mouse brains displayed in the Microsoft Silverlight PivotViewer from the Mouse Brain Library (MBL) which consist of high-resolution images of brains from many genetically characterized strains of mice. PivotViewer makes it easier to interact with massive amounts of data on the web in ways that are powerful, informative, and fun. By visualizing thousands of related items at once, users can see trends and patterns that would be hidden when looking at one item at a time. Because PivotViewer leverages Deep Zoom, it displays full, high-resolution content without long load times, while the animations and natural transitions provide context and prevent users from feeling overwhelmed by large quantities of information. This simple, inviting interaction model encourages exploration and longer audience engagement times, and applies broadly to a variety of content types." . SCR:005507 a NLX:63400, owl:NamedIndividual ; @@ -44607,7 +44588,8 @@ SCR:005608 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-00255" ; rdfs:label "CRCNS" ; - NIFRID:synonym "Collaborative Research in Computational Neuroscience - Data sharing", + NIFRID:synonym "Collaborative Research in Computational Neuroscience", + "Collaborative Research in Computational Neuroscience - Data sharing", "CRCNS - Data sharing", "CRCNS Data sharing" ; definition: "Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources." . @@ -45056,7 +45038,7 @@ SCR:005663 a NLX:63400, "SCR_002911", "SCR_007388" ; rdfs:label "GeneTools" ; - definition: "GeneTools is a collection of web-based tools that brings together information from a broad range of resources, and provides this in a manner particularly useful for genome-wide analyses. Today, the two main tools connected to this database are the NMC Annotation Database V2.0 and eGOn V2.0 (explore Gene Ontology). The NMC Annotation Database V2.0 provides information from UniGene, EntrezGene, SwissProt and Gene Ontology (GO). Major features are: * Single search/Batch search, extraction of data for single or batches of genes. * Manage reporter lists: in folders and share selected lists with other users. * Manual GO Annotation: add your own Gene Ontology (GO) annotations to genes of interest. * Export: to Excel, text or XML format. eGOn V2.0 facilitates interpretation of GO annotation. GO terms are retrieved in batch modus from EntrezGene and the GO database and displayed in the GO directed acyclic hierarchical graph (DAG). Essential features of eGOn V2.0 are: * Visualization: gene annotations are visualized in the GO DAG or as a table view. The granularity of the GO DAG can be edited freely by the user. * Filtering: GO annotations can be filtered on evidence codes. * Include user defined GO annotations: previously added to the Annotation database. * Statistical analysis: Several gene lists are analyzed simultaneously to compare the distribution of the annotated genes over the GO hierarchy. Statistical tests are implemented to allow the user to compute GO annotation dissimilarity within or between gene lists. * Connection to Annotation database: Links to Annotation database gene and protein information are offered directly from the GO DAG or in exported data. * Export: GO DAG information, statistical results and gene and protein information can be exported in excel, text or XML format. Platform: Online tool" . + definition: "Web-service providing access to database that brings together information from broad range of resources. Web application for functional annotation and statistical hypothesis testing. Provides tools for analysis of genomic and microarray data. Collection of tools include Bibliographic Information,Databases,Gene Annotation,Gene Regulation, Microarray,Proteins,Sequence Manipulation - Nucleic Acids,Sequence Manipulation - Protein, Systems Biology." . SCR:005664 a NLX:63400, owl:NamedIndividual ; @@ -47063,7 +47045,7 @@ SCR:005910 a NLX:63400, rdfs:label "Dryad Digital Repository" ; NIFRID:synonym "Dryad", "The Dryad Digital Repository" ; - definition: "International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies." . + definition: "International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository." . SCR:005911 a NLX:152328, owl:NamedIndividual ; @@ -48572,9 +48554,7 @@ SCR:006095 a NLX:63400, SCR:006096 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_151566" ; - rdfs:label "Web Platform Docs" ; - NIFRID:synonym "WebPlatform.org" ; - definition: "Web Platform Docs is a new community-driven site that aims to become a comprehensive and authoritative source for web developer documentation. Anyone can contribute and each person who does makes us stronger. Together we can continue to drive innovation on the Web to serve the greater good. It starts here, with you. Even though Web Platform Docs is still in alpha, you can already find lots of valuable content on the site, including information on: * How to use features of the open web, with syntax and examples * What platforms and devices you can use various technologies on * What is the current standardization, stability and implementation status of each technology specification In the future, Web Platform Docs will include even more content for you to explore such as live code examples, resources for educators and much more. To get there faster, we''d like to invite you to also contribute your knowledge. We hope you will join us!" . + definition: "Web Platform Docs is a new community-driven site that aims to become a comprehensive and authoritative source for web developer documentation. Anyone can contribute and each person who does makes us stronger. Together we can continue to drive innovation on the Web to serve the greater good. WebPlatform project, supported by various stewards between 2012 and 2015, has been discontinued. Static archived version of github is available." . SCR:006097 a NLX:63400, owl:NamedIndividual ; @@ -48628,7 +48608,7 @@ SCR:006102 a NLX:63400, oboInOwl:hasDbXref "nlx_151569" ; rdfs:label "MicrobeWorld" ; NIFRID:synonym "MicrobeWorld.org" ; - definition: "Interactive multimedia educational outreach resource promoting awareness and understanding of key microbiological issues to adult and youth audiences, and showcases the significance of microbes in our lives. It is an online community for sharing the latest news, blog posts, videos, podcasts, images, research and resources related to microbiology and the life sciences. Join today and help contribute to the fastest growing networks for science information on the web. The anthrax attacks of 2001 and the ensuing focus on bioterrorism, the potential of viral and bacterial infections for victims of Hurricane Katrina, the emergence of avian flu, and the public''s growing interest in alternative fuel sources have thrust microbes into unprecedented prominence in the headlines. MicrobeWorld informs the public about how science works. The various outreach methods feature the process of discovery, historical changes in research, and a variety of scientific careers in industry, academia, and government. One of the first MicrobeWorld Radio podcasts explained how microbes enter the initially sterile bodies of infants just hours after birth, establishing the microbial communities that stay with them for life. Other topics have included why the overuse of antibiotics is a growing problem, how microbes are key in the making of chocolate, and how microbiologists are on the front line in the war against infectious diseases that threaten human and animal health. Objectives * Leverage emerging communications technologies to promote the science of microbiology to the public and provide educational resources for all levels. * Repurpose the American Society for Microbiology''s resources for the wired generation. * Increase public understanding and appreciation of the vital role microbes play on our planet. * Use new technology to promote ASM''s resources to students, educators and other potential members of the Society. * Establish ASM as a leader in online science content." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 27,2023.Interactive multimedia educational outreach resource promoting awareness and understanding of key microbiological issues to adult and youth audiences, and showcases the significance of microbes in our lives. It is an online community for sharing the latest news, blog posts, videos, podcasts, images, research and resources related to microbiology and the life sciences. Join today and help contribute to the fastest growing networks for science information on the web. The anthrax attacks of 2001 and the ensuing focus on bioterrorism, the potential of viral and bacterial infections for victims of Hurricane Katrina, the emergence of avian flu, and the public''s growing interest in alternative fuel sources have thrust microbes into unprecedented prominence in the headlines. MicrobeWorld informs the public about how science works. The various outreach methods feature the process of discovery, historical changes in research, and a variety of scientific careers in industry, academia, and government. One of the first MicrobeWorld Radio podcasts explained how microbes enter the initially sterile bodies of infants just hours after birth, establishing the microbial communities that stay with them for life. Other topics have included why the overuse of antibiotics is a growing problem, how microbes are key in the making of chocolate, and how microbiologists are on the front line in the war against infectious diseases that threaten human and animal health. Objectives * Leverage emerging communications technologies to promote the science of microbiology to the public and provide educational resources for all levels. * Repurpose the American Society for Microbiology''s resources for the wired generation. * Increase public understanding and appreciation of the vital role microbes play on our planet. * Use new technology to promote ASM''s resources to students, educators and other potential members of the Society. * Establish ASM as a leader in online science content." . SCR:006103 a NLX:63400, owl:NamedIndividual ; @@ -51245,7 +51225,7 @@ SCR:006426 a NLX:63400, oboInOwl:hasDbXref "nif-0000-24356" ; rdfs:label "California National Primate Research Center" ; NIFRID:abbrev "CNPRC" ; - definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 21, 2022. Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice." . + definition: "Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice." . SCR:006427 a NLX:63400, owl:NamedIndividual ; @@ -51692,9 +51672,7 @@ SCR:006481 a NLX:152328, "ISNI: 0000 0001 1957 5136", "nlx_156041", "Wikidata: Q5020447" ; - rdfs:label "California Digital Library" ; - NIFRID:abbrev "CDL" ; - definition: "One of the world''s largest digital research libraries that changed the ways that faculty, students, and researchers discover and access information using innovative technology to connect content and communities in ways that enhance teaching, learning, and research. In partnership with the UC libraries, the CDL has continually broken new ground by developing systems linking their users to the vast print and online collections within UC and beyond. Building on the foundations of the Melvyl Catalog, they developed one of the largest online library catalogs in the country. They saved the University millions of dollars by facilitating the co-investment and sharing of materials and services used by libraries across the UC system. They work in partnership with campuses to bring the treasures of their libraries, museums, and cultural heritage organizations to the world. And they continue to explore how services such as digital curation, scholarly publishing, archiving and preservation support research throughout the information lifecycle." . + NIFRID:abbrev "CDL" . SCR:006482 a NLX:63400, owl:NamedIndividual ; @@ -56711,7 +56689,7 @@ SCR:007093 a NLX:63400, rdfs:label "CCHDO" ; NIFRID:synonym "CLIVAR & Carbon Hydrographic Data Office", "CLIVAR and Carbon Hydrographic Data Office" ; - definition: "High quality global CTD and hydrographic data from of decades of observations related to the physical characteristics of ocean waters carried out during WOCE, CLIVAR and numerous other oceanographic research programs. Whenever possible data are provided in three easy-to-use formats: WHP-Exchange (recommended for data submissions to the CCHDO), WOCE, and netCDF. The CCHDO also manages public and non-public CTD data to be used for the global Argo and OceanSITES programs." . + definition: "Supports oceanographic research by providing access to high quality, global, vessel-based CTD and hydrographic data from GO-SHIP, WOCE, CLIVAR and other repeat hydrography programs. These data are openly accessible and served in standardized community formats (WHP-Exchange, WOCE, and netCDF). CCHDO also manages public and non-public CTD data for use by the global Argo and OceanSITES programs." . SCR:007094 a NLX:63400, owl:NamedIndividual ; @@ -64551,6 +64529,7 @@ SCR:008161 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_152677" ; rdfs:label "Center for Computational Mass Spectrometry" ; + NIFRID:synonym "UCSD Center for Computational Mass Spectrometry" ; NIFRID:abbrev "CCMS" ; definition: "Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications." . @@ -64594,8 +64573,8 @@ SCR:008167 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nif-0000-24360" ; rdfs:label "Tulane National Primate Research Center" ; - NIFRID:synonym "TNPRC" ; - definition: "Center that is heavily focused on infectious disease research and also has a significant program in gene therapy that capitalizes on a unique colony of macaques with Krabbe disease. The major areas of infectious disease research at the Center are currently AIDS, Lyme disease, and biodefense-related agents, with additional programs involving tuberculosis, microsporidiosis, and malaria." . + NIFRID:abbrev "TNPRC" ; + definition: "Center focused on understanding human health problems, including infectious diseases that require the use of nonhuman primates to develop diagnostics, therapeutics and preventive strategies. Primary research interests include developing vaccines, treatments and diagnostic tools for infectious diseases such as AIDS, tuberculosis, CMV, COVID-19, Lyme disease, and malaria. TNPRC has both biosafety level 2 and biosafety level 3 laboratories facilities to accommodate various research needs, and is the only National Primate Research Center with Regional Biosafety Laboratory." . SCR:008168 a NLX:63400, owl:NamedIndividual ; @@ -65279,7 +65258,8 @@ SCR:008264 a NLX:63400, SCR:008265 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156487" ; - rdfs:label " Penn Diabetes Research Center Pancreatic Islet Cell Biology Core " ; + rdfs:label "University of Pennsylvania School of Medicine Penn Diabetes Research Center Pancreatic Islet Cell Biology Core Facility" ; + NIFRID:synonym "Penn Diabetes Research Center Pancreatic Islet Cell Biology Core" ; definition: "Core that gives support including experimental design, islet isolation, and performance of and training in an expansive range of assays for physiological and morphometric assessment of pancreatic islet function and growth. It contributes to the basic and translational research activities of the Institute of Diabetes, Obesity and Metabolism (IDOM) at the Perelman School of Medicine of the University of Pennsylvania. Its services include perform individual islet and single cell fluorescence imaging, respirometry with islet batches using a Seahorse Extracellular Flux Analyzer, perifusion coupled with respirometry, and closed respirometry experiments for our investigators." . SCR:008266 a NLX:63400, @@ -65483,7 +65463,8 @@ SCR:008292 a NLX:63400, SCR:008293 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156297" ; - rdfs:label " Boston Area Diabetes Endocrinology Research Center Metabolic Physiology " ; + rdfs:label "Boston Area Diabetes Endocrinology Research Center Metabolic Physiology and Energy Balance Core Facility" ; + NIFRID:synonym "Boston Area Diabetes Endocrinology Research Center Metabolic Physiology" ; definition: "Core in BADERC that provides services in consultation and teaching, use of DEXA scanner for determination of body fat and/or bone density, and use of Coulter Counter to measure cell number and cell size distribution." . SCR:008294 a NLX:152328, @@ -67978,7 +67959,7 @@ SCR:008643 a NLX:63400, oboInOwl:hasDbXref "nif-0000-32417" ; rdfs:label "LAMHDI: The Initiative to Link Animal Models to Human DIsease" ; NIFRID:synonym "LAMHDI" ; - definition: "LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal model for their research. LAMDHI is a free, Web-based, resource to help researchers bridge the gap between bench testing and human trials. It provides a free, unbiased resource that enables scientists to quickly find the best animal models for their research studies. LAMHDI includes mouse data from MGI, the Mouse Genome Informatics website; zebrafish data from ZFIN, the Zebrafish Model Organism Database; rat data from RGD, the Rat Genome Database; yeast data from SGD, the Saccharomyces Genome Database; and fly data from FlyBase. LAMHDI.org is operational today, and data is added regularly. Enhancements are planned to let researchers contribute their knowledge of the animal models available through LAMHDI. The LAMHDI goal is to allow researchers to share information about and access to animal models so they can refine research and testing, and reduce or replace the use of animal models where possible. LAMHDI Database Search: LAMHDI brings together scientifically validated information from various sources to create a composite multi-species database of animal models of human disease. To do this, the LAMHDI database is prepared from a variety of sources. The LAMHDI team takes publicly available data from OMIM, NCBI''s Entrez Gene database, Homologene, and WikiPathways, and builds a mathematical graph (think of it as a map or a web) that links these data together. OMIM is used to link human diseases with specific human genes, and Entrez provides universal identifiers for each of those genes. Human genes are linked to their counterpart genes in other species with Homologene, and those genes are linked to other genes tentatively or authoritatively using the data in WikiPathways. This preparatory work gives LAMHDI a web of human diseases linked to specific human genes, orthologous human genes, homologous genes in other species, and both human and non-human genes involved in specific metabolic pathways associated with those diseases. LAMHDI includes model data that partners provide directly from their data structures. For instance, MGI provides information about mouse models, including a disease for each model, as well as some genetic information (the ID of the model, in fact, identifies one or more genes). ZFIN provides genetic information for each zebrafish model, but no diseases, so zebrafish models are integrated by using the genes as the glue. For instance, a zebrafish model built to feature the zebrafish PKD2 gene would plug into the larger disease-gene map at the node representing the zebrafish PKD2 gene, which is connected to the node representing the human PKD2 gene, which in turn is connected to the node representing the human disease known as polycystic kidney disease. (Some of the partner data LAMHDI receives can even extend the base map. MGI provides a disease for every model, and in some cases this allows the creation of a disease-to-gene relationship in the LAMHDI database that might not already be documented in the OMIM dataset.) With curatorial and model information in hand, LAMHDI runs a lengthy automated process that exhaustively searches for every possible path between each model and each disease in the data, up to a set number of hops, producing for each disease-to-model pair a set of links from the disease to the model. The algorithm avoids circular paths and paths that include more than one disease anywhere in the middle of the path. At the end of this phase, LAMHDI has a comprehensive set of paths representing all the disease-to-model relationships in the data, varying in length from one hop to many hops. Each disease-to-model path is essentially a string of nodes in the data, where each node represents a disease, a gene, a linkage between genes (an orthologue, a homologue, or a pathway connection, referred to as a gene cluster or association), or a model. Each node has a human-friendly label, a set of terms and keywords, and - in most cases - a URL linking the node to the data source where it originated. When a researcher submits a search on the LAMHDI website, LAMHDI searches for the user''s search terms in its precomputed list of all known disease-to-model paths. It looks for the terms not only in the disease and model nodes, but also in every node along each path. The complete set of hits may include multiple paths between any given disease-to-model pair of endpoints. Each of these disease-to-model pair sets is ordered by the number of hops it involves, and the one involving the fewest hops is chosen to represent its respective disease-to-model pair in the search results presented to the user. Results are sorted by scores that represent their matches. The number of hops is one barometer of the strength of the evidence linking the model and the disease; fewer hops indicates the relationship is stronger, more hops indicates it may be weaker. This indicator works best for comparing models from a single partner dataset: MGI explicitly identifies a disease for each mouse model, so there can be disease-to-model hits for mice that involve just one hop. Because ZFIN does not explicitly identify a disease for each model, no zebrafish model will involve fewer than four hops to the nearest disease, from the zebrafish model to a zebrafish gene to a gene cluster to a human gene to a human disease." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE, it has been replaced by Monarch Initiative. LAMHDI, the initiative to Link Animal Models to Human DIsease, is designed to accelerate the research process by providing biomedical researchers with a simple, comprehensive Web-based resource to find the best animal model for their research. LAMDHI is a free, Web-based, resource to help researchers bridge the gap between bench testing and human trials. It provides a free, unbiased resource that enables scientists to quickly find the best animal models for their research studies. LAMHDI includes mouse data from MGI, the Mouse Genome Informatics website; zebrafish data from ZFIN, the Zebrafish Model Organism Database; rat data from RGD, the Rat Genome Database; yeast data from SGD, the Saccharomyces Genome Database; and fly data from FlyBase. LAMHDI.org is operational today, and data is added regularly. Enhancements are planned to let researchers contribute their knowledge of the animal models available through LAMHDI. The LAMHDI goal is to allow researchers to share information about and access to animal models so they can refine research and testing, and reduce or replace the use of animal models where possible. LAMHDI Database Search: LAMHDI brings together scientifically validated information from various sources to create a composite multi-species database of animal models of human disease. To do this, the LAMHDI database is prepared from a variety of sources. The LAMHDI team takes publicly available data from OMIM, NCBI''s Entrez Gene database, Homologene, and WikiPathways, and builds a mathematical graph (think of it as a map or a web) that links these data together. OMIM is used to link human diseases with specific human genes, and Entrez provides universal identifiers for each of those genes. Human genes are linked to their counterpart genes in other species with Homologene, and those genes are linked to other genes tentatively or authoritatively using the data in WikiPathways. This preparatory work gives LAMHDI a web of human diseases linked to specific human genes, orthologous human genes, homologous genes in other species, and both human and non-human genes involved in specific metabolic pathways associated with those diseases. LAMHDI includes model data that partners provide directly from their data structures. For instance, MGI provides information about mouse models, including a disease for each model, as well as some genetic information (the ID of the model, in fact, identifies one or more genes). ZFIN provides genetic information for each zebrafish model, but no diseases, so zebrafish models are integrated by using the genes as the glue. For instance, a zebrafish model built to feature the zebrafish PKD2 gene would plug into the larger disease-gene map at the node representing the zebrafish PKD2 gene, which is connected to the node representing the human PKD2 gene, which in turn is connected to the node representing the human disease known as polycystic kidney disease. (Some of the partner data LAMHDI receives can even extend the base map. MGI provides a disease for every model, and in some cases this allows the creation of a disease-to-gene relationship in the LAMHDI database that might not already be documented in the OMIM dataset.) With curatorial and model information in hand, LAMHDI runs a lengthy automated process that exhaustively searches for every possible path between each model and each disease in the data, up to a set number of hops, producing for each disease-to-model pair a set of links from the disease to the model. The algorithm avoids circular paths and paths that include more than one disease anywhere in the middle of the path. At the end of this phase, LAMHDI has a comprehensive set of paths representing all the disease-to-model relationships in the data, varying in length from one hop to many hops. Each disease-to-model path is essentially a string of nodes in the data, where each node represents a disease, a gene, a linkage between genes (an orthologue, a homologue, or a pathway connection, referred to as a gene cluster or association), or a model. Each node has a human-friendly label, a set of terms and keywords, and - in most cases - a URL linking the node to the data source where it originated. When a researcher submits a search on the LAMHDI website, LAMHDI searches for the user''s search terms in its precomputed list of all known disease-to-model paths. It looks for the terms not only in the disease and model nodes, but also in every node along each path. The complete set of hits may include multiple paths between any given disease-to-model pair of endpoints. Each of these disease-to-model pair sets is ordered by the number of hops it involves, and the one involving the fewest hops is chosen to represent its respective disease-to-model pair in the search results presented to the user. Results are sorted by scores that represent their matches. The number of hops is one barometer of the strength of the evidence linking the model and the disease; fewer hops indicates the relationship is stronger, more hops indicates it may be weaker. This indicator works best for comparing models from a single partner dataset: MGI explicitly identifies a disease for each mouse model, so there can be disease-to-model hits for mice that involve just one hop. Because ZFIN does not explicitly identify a disease for each model, no zebrafish model will involve fewer than four hops to the nearest disease, from the zebrafish model to a zebrafish gene to a gene cluster to a human gene to a human disease." . SCR:008644 a NLX:63400, owl:NamedIndividual ; @@ -73777,11 +73758,11 @@ SCR:009432 a NLX:63400, NIFRID:abbrev "ATID" ; definition: "A database of publicly available genes, alternatively translational isoforms and their detailed annotation. Alternative translational initiation is one of mechanisms to increase the complexity level of an organism by alternative gene expression pathways. The use of alternative translation initiation codons in a singe mRNA contributes to the generation of protein diversity. The genes produce two or more versions of the encoded proteins, and the shorter version, initiated from a downstream in-frame start codon, lacks the N-terminal amino acids fragment of the full-length isoform version. Since the first discovery of alternative translation initiation, a small, yet growing, number of mRNAs initiating translation from alternative start codons have been reported. Various studies began to emerge focusing on this new field in gene expression and revealed the biological significance of the use of alternative initiation. In response to the need for systematic studies on genes involving alternative translational initiation, Alternative Translational Initiation Database(ATID) is established to provide data of publicly available genes, alternatively translational isoforms and their detailed annotation." . -SCR:009433 a NLX:152342, +SCR:009433 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_155525" ; rdfs:label "iGen" ; - definition: "A certified clinical laboratory (ISO15189). To clinicians in oncology we offer genetic and epigenetic analyses together with interpretation. iGen also provides professional genetic counseling ?????????????????? a healthcare service, which advises people who are at the risk of hereditary cancer. In the research field iGen performs assay development and genotyping services. Our customers are clinical laboratories, research groups and genetic tests distributors. To improve molecular diagnostics in cancer treatment iGen is continuously carrying out research and applied science projects. Currently, our main cooperation partners are the Competence Centre of Cancer Research and North Estonian Medical Centre. We are looking for other cooperation opportunities, and are interested in participating in national and international cooperative research projects, to which we can contribute with our expertise in molecular diagnostics. Our laboratory and office are situated in Tehnopol Tallinn Science Park territory, next to the campus of Tallinn University of Technology. Prices quoted are highly dependable on the number of samples and are given based on full plate/machine, please contact us for pricing for smaller projects." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Certified clinical laboratory (ISO15189). To clinicians in oncology we offer genetic and epigenetic analyses together with interpretation. iGen also provides professional genetic counseling ?????????????????? a healthcare service, which advises people who are at the risk of hereditary cancer. In the research field iGen performs assay development and genotyping services. Our customers are clinical laboratories, research groups and genetic tests distributors. To improve molecular diagnostics in cancer treatment iGen is continuously carrying out research and applied science projects. Currently, our main cooperation partners are the Competence Centre of Cancer Research and North Estonian Medical Centre. We are looking for other cooperation opportunities, and are interested in participating in national and international cooperative research projects, to which we can contribute with our expertise in molecular diagnostics. Our laboratory and office are situated in Tehnopol Tallinn Science Park territory, next to the campus of Tallinn University of Technology. Prices quoted are highly dependable on the number of samples and are given based on full plate/machine, please contact us for pricing for smaller projects." . SCR:009434 a NLX:63400, owl:NamedIndividual ; @@ -74856,9 +74837,14 @@ SCR:009593 a NLX:63400, SCR:009594 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_155839" ; - rdfs:label "Waxholm Space Atlas" ; - NIFRID:abbrev "WHS Atlas" ; - definition: "Downloadable image volumes representing the canonical Waxholm Space (WHS) mouse brain. These images include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel), and a label volume describing 37 structures. All volumes are represented at 21.5? isotropic resolution." . + rdfs:label "Waxholm Space" ; + NIFRID:synonym "Mouse WHS atlas", + "Waxholm Space Atlas", + "Waxholm Standard Space" ; + NIFRID:abbrev "WHS", + "WSA", + "WSS" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023.Downloadable image volumes representing the canonical Waxholm Space (WHS) mouse brain. These images include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel), and a label volume describing 37 structures. All volumes are represented at 21.5? isotropic resolution." . SCR:009595 a NLX:63400, owl:NamedIndividual ; @@ -75389,7 +75375,7 @@ SCR:009668 a NLX:63400, NIFRID:abbrev "BIDMC Genomics", "Bioinformatics and Systems Biology Center", "Proteomics" ; - definition: "Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics." . SCR:009669 a NLX:63400, owl:NamedIndividual ; @@ -75555,7 +75541,7 @@ SCR:009694 a NLX:63400, SCR:009695 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156155" ; - rdfs:label "Clark Atlanta University Collaborative Center for Cancer Genomics and Bioinformatics Core" ; + rdfs:label "Clark Atlanta University Collaborative Center for Cancer Genomics and Bioinformatics Core Facility" ; NIFRID:synonym "assay", "Bioinformatics Core", "Cancer Genomics", @@ -75563,7 +75549,7 @@ SCR:009695 a NLX:63400, "Clark Atlanta University", "Collaborative Center", "sequencing" ; - definition: "Core provides next generation sequencing service. Collaborative effort between the CCRTD and the Ovarian Cancer Institute at Georgia Tech University (OCIGT). CCRTD provides laboratory to prepare libraries and to operate the instrument, while OCIGT contributes bioinformatics support for processing the data and additional services to complement genomics data including hardware, software, and personnel. OCIGT contributes patients sample procurement and complementary technologies including Affymetrix microarray technology and mass spectroscopy analysis." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core provides next generation sequencing service. Collaborative effort between the CCRTD and the Ovarian Cancer Institute at Georgia Tech University (OCIGT). CCRTD provides laboratory to prepare libraries and to operate the instrument, while OCIGT contributes bioinformatics support for processing the data and additional services to complement genomics data including hardware, software, and personnel. OCIGT contributes patients sample procurement and complementary technologies including Affymetrix microarray technology and mass spectroscopy analysis." . SCR:009696 a NLX:63400, owl:NamedIndividual ; @@ -75900,8 +75886,8 @@ SCR:009746 a NLX:63400, SCR:009747 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156208" ; - rdfs:label "DFCI Biospecimen Repository Core" ; - definition: "Core facility that provides the following services: Storage services for -80 degrees C and -190 degrees C in secure facility.

The Biospecimen Repository provides long-term storage of clinical and research material in -80 degrees C and liquid nitrogen freezers located at Dana Farber''s Harbor Campus. Transportation of samples to and from Harbor Campus is provided by the facility for a small fee. Competitive prices are available on per box or per freezer basis in both segregated or non-segregated environments." . + rdfs:label "DFCI Biospecimen Repository Core Facility" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core facility that provides the following services: Storage services for -80 degrees C and -190 degrees C in secure facility.

The Biospecimen Repository provides long-term storage of clinical and research material in -80 degrees C and liquid nitrogen freezers located at Dana Farber''s Harbor Campus. Transportation of samples to and from Harbor Campus is provided by the facility for a small fee. Competitive prices are available on per box or per freezer basis in both segregated or non-segregated environments." . SCR:009748 a NLX:63400, owl:NamedIndividual ; @@ -75941,9 +75927,14 @@ SCR:009753 a NLX:63400, SCR:009754 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "nlx_156214" ; - rdfs:label "DFCI Molecular Biology Core Facilities" ; - definition: "Core facility that provides the following services: Mass spectrometry service, Automated DNA sequencing service, Peptide synthesis service, Protein sequencing service, BIAcore ligand assays service, Genotyping service, Next Generation DNA Sequencing using three Illumina MiSeq DNA Sequencers.

The Molecular Biology Core Facilities (MBCF) was created in 1986 to allow investigators at the Dana-Farber Cancer Institute access to cutting edge molecular biology tools which would be tested and developed in a shared setting. Collaborations can be set up with anyone in the world. Although these services are primarily focused on cancer and AIDS research, there is a broad spectrum of research that uses these resources." . + oboInOwl:hasDbXref "ABRF_57", + "nlx_156214", + "SCR_018264" ; + rdfs:label "Dana-Farber Cancer Institute Molecular Biology Core Facility" ; + NIFRID:synonym "Dana-Farber Cancer Institute Molecular Biology Core Facilities", + "DFCI Molecular Biology Core Facilities" ; + NIFRID:abbrev "MBCF at DFCI" ; + definition: "Core offers services for genomic next-generation sequencing library preparation, sequencing and analysis applications including RNAseq, ChIPseq, ATACseq, CRISPR screening, whole genome methylation profiling, targeted resequencing, single-cell RNAseq, exome sequencing, and more. Performs bioinformatics analysis such as integration of multi-omics datasets or specialized analyses. Genomics core technology platforms include Illumina NovaSeq6000, NextSeq500s, MiSeqs, MiniSeq. High throughput sample preparation is performed on Beckman Coulter Biomek FX and i7 systems. Low throughput samples are prepared by technical staff." . SCR:009755 a NLX:63400, owl:NamedIndividual ; @@ -76394,7 +76385,7 @@ SCR:009822 a NLX:63400, "Environmental Statistics", "Harvard School of Public Health", "HSPH" ; - definition: "Core provides intellectual guidance for quantitative aspects of the design and analysis of center studies and expertise in biostatistical methods, environmental risk assessment, Geographic Information System (GIS) , spatial statistics, molecular biology, bioinformatics and statistical genetics. Core runs a regular seminar series and often sponsors short courses on specialized topics of interest to the community." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core provides intellectual guidance for quantitative aspects of the design and analysis of center studies and expertise in biostatistical methods, environmental risk assessment, Geographic Information System (GIS) , spatial statistics, molecular biology, bioinformatics and statistical genetics. Core runs a regular seminar series and often sponsors short courses on specialized topics of interest to the community." . SCR:009823 a NIFSTD:NEMO_0569000, owl:NamedIndividual ; @@ -76665,13 +76656,13 @@ SCR:009863 a NLX:63400, SCR:009864 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156335" ; - rdfs:label "Howard University Center for Computational Biology and Bioinformatics" ; + rdfs:label "Howard University Center for Computational Biology and Bioinformatics Core Facility" ; NIFRID:synonym "CCBB", "Howard", "Laboratory of Molecular Computations and Bioinformatics", "LMCB" ; NIFRID:abbrev "Howard CCBB" ; - definition: "Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University." . SCR:009865 a NLX:63400, owl:NamedIndividual ; @@ -76725,8 +76716,8 @@ SCR:009872 a NLX:63400, SCR:009873 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156350" ; - rdfs:label " Joslin Diabetes Center Advanced Genomics and Genetics Core " ; - definition: "Core that provides services for genetic and genomic analysis, including DNA extraction from blood, access to DNA collections from the Core?s repository, SNP genotyping, and support for gene expression studies based on both high-density oligonucleotide arrays and real-time quantitative PCR." . + rdfs:label "Joslin Diabetes Center Advanced Genomics and Genetics Core Facility" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides services for genetic and genomic analysis, including DNA extraction from blood, access to DNA collections from the Core?s repository, SNP genotyping, and support for gene expression studies based on both high-density oligonucleotide arrays and real-time quantitative PCR." . SCR:009874 a NLX:152328, owl:NamedIndividual ; @@ -76743,14 +76734,14 @@ SCR:009874 a NLX:152328, SCR:009875 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156345" ; - rdfs:label " Joslin Diabetes Center Advanced Microscopy Core " ; - definition: "Core that provides services for performing specific morphological procedures, providing training and access to equipment, maintaining the specialized microscopes, and giving advice and interpretation." . + rdfs:label "Joslin Diabetes Center Advanced Microscopy Core Facility" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides services for performing specific morphological procedures, providing training and access to equipment, maintaining the specialized microscopes, and giving advice and interpretation." . SCR:009876 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156346" ; - rdfs:label " Joslin Diabetes Center Animal Physiology Core " ; - definition: "Core that provides technically advanced physiological evaluation of metabolism in diabetes, obesity, and their associated complications in rodents for DRC investigators and outside users. It also provides training of investigators and trainees in several physiological procedures." . + rdfs:label "Joslin Diabetes Center Animal Physiology Core Facility" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides technically advanced physiological evaluation of metabolism in diabetes, obesity, and their associated complications in rodents for DRC investigators and outside users. It also provides training of investigators and trainees in several physiological procedures." . SCR:009877 a NLX:63400, owl:NamedIndividual ; @@ -76761,8 +76752,8 @@ SCR:009877 a NLX:63400, SCR:009878 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156348" ; - rdfs:label " Joslin Diabetes Center Flow Cytometry Core " ; - definition: "Core that provides cell sorting and flow cytometry services. Specific services include cell analysis, large object sorting,magnetic cell enrichment, and automatic cell counting." . + rdfs:label "Joslin Diabetes Center Flow Cytometry Core Facility" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core that provides cell sorting and flow cytometry services. Specific services include cell analysis, large object sorting,magnetic cell enrichment, and automatic cell counting." . SCR:009879 a NLX:63400, owl:NamedIndividual ; @@ -76795,7 +76786,7 @@ SCR:009882 a NLX:63400, SCR:009883 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156352" ; - rdfs:label "Joslin Diabets Center Proteomics Core" ; + rdfs:label "Joslin Diabets Center Proteomics Core Facility" ; NIFRID:abbrev "JDC Proteomics Core" ; definition: "THIS RESOURCE IS NO LONGER IN SERVCE, documented January 24, 2019. Core provides the following services: Trypsinization service. Core provides a full range of services to the Joslin research community spanning from consulting on proteomic experimental design to data acquisition and analysis. The core operates a high throughput nano liquid chromatography, nanospray ionization, LTQ 2D ion trap tandem mass spectrometer system. This system is used for two routine proteomic services, including Targeted Protein Analysis and Protein Inventory. Targeted Protein Analysis is used to identify and provide in depth characterization, including phosphorylation site mapping, of proteins isolate by SDS-PAGE. Protein Inventory is used to catalogue the protein composition in a sample separated by 1D SDS-PAGE. This service provides information on protein identification, molecular weight (gel mobility), and spectral/peptide counts, a semi-quantitative measure of protein abundance. In addition, the Core works with investigators on specialized analyses involving tandem mass spectrometry, including specialized enzymatic digests (peptide preparation), selective reaction monitoring (SRM), and targeted peptide detection. The Proteomic Core provides in house database resources and analysis tools and also coordinates with Joslin's Bioinformatics Core to provide further assistance with data organization and interpretation. The Core hosts seminars on proteomic topics and provides instruction on practical and theoretical aspects of mass spectrometry-based proteomics." . @@ -77142,7 +77133,7 @@ SCR:009937 a NLX:63400, "core facility", "Montana State University", "MSU" ; - definition: "Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research." . SCR:009938 a NLX:63400, owl:NamedIndividual ; @@ -77772,7 +77763,8 @@ SCR:010027 a NLX:63400, SCR:010028 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156498" ; - rdfs:label " Penn Diabetes Research Center Radioimmunoassay and Biomarkers Core " ; + rdfs:label "Penn Diabetes Research Center Radioimmunoassay and Biomarkers Core Facility" ; + NIFRID:synonym "Penn Diabetes Research Center Radioimmunoassay and Biomarkers Core" ; definition: "Core which offers high quality immunoassay services to basic, translational, and clinical investigators performing diabetes and related metabolic disease research. The core also provides consultation and training and education services." . SCR:010029 a NLX:63400, @@ -77826,7 +77818,8 @@ SCR:010035 a NLX:63400, SCR:010036 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156507" ; - rdfs:label " Penn Diabetes Research Center Transgenic and Chimeric Mouse Core " ; + rdfs:label "Penn Diabetes Research Center Transgenic and Chimeric Mouse Core Facility" ; + NIFRID:synonym "Penn Diabetes Research Center Transgenic and Chimeric Mouse Core" ; definition: "Mouse core which generates transgenic and gene-targeted mouse lines for diabetes research." . SCR:010037 a NLX:63400, @@ -77838,9 +77831,9 @@ SCR:010037 a NLX:63400, SCR:010038 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156509" ; - rdfs:label " University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core " ; + rdfs:label "University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core Facility" ; NIFRID:synonym "University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core" ; - definition: "Core whose main aim is to provide vector technology for preclinical studies and other basic research applications. Its services include rovision of AAV, adenoviral and lentiviral based vectors, consultation and advice in the design of custom vectors and in vector serotype/pseudotype selection, and design, cloning and production of plasmid DNA for the production of custom vectors." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core whose main aim is to provide vector technology for preclinical studies and other basic research applications. Its services include rovision of AAV, adenoviral and lentiviral based vectors, consultation and advice in the design of custom vectors and in vector serotype/pseudotype selection, and design, cloning and production of plasmid DNA for the production of custom vectors." . SCR:010039 a NLX:63400, owl:NamedIndividual ; @@ -78020,7 +78013,7 @@ SCR:010065 a NLX:63400, "TU", "Tuskegee University" ; NIFRID:abbrev "TU BIMS" ; - definition: "Core provides services and training in computational biology, bioinformatics, experimental design and statistical analysis to the RCMI researchers and the biomedical research community at Tuskegee University." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core provides services and training in computational biology, bioinformatics, experimental design and statistical analysis to the RCMI researchers and the biomedical research community at Tuskegee University." . SCR:010066 a NLX:63400, owl:NamedIndividual ; @@ -78180,7 +78173,7 @@ SCR:010089 a NLX:63400, "UH", "UHM", "University of Hawaii" ; - definition: "Core provides access to high speed computer hardware and bioinformatics consultation. Research at the facility includes studying of evolutionary change in emergent dengue viruses associated with increasingly severe epidemics and confirm the impact of these changes in experimental models." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core provides access to high speed computer hardware and bioinformatics consultation. Research at the facility includes studying of evolutionary change in emergent dengue viruses associated with increasingly severe epidemics and confirm the impact of these changes in experimental models." . SCR:010090 a NLX:63400, owl:NamedIndividual ; @@ -78242,7 +78235,7 @@ SCR:010099 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156568" ; rdfs:label "University of Hawaii at Manoa INBRE Bioinformatics Core Facility" ; - definition: "Core to provide bioinformatics analysis and consulting service, to increase the research capacity in bioinformatics in the State of Hawaii, to provides software applications, hardware, access, and support to researchers who utilize genomic and proteomic data. Undertake collaborative project with INBRE researchers to develop novel tools or applications that address specific needs. Develop an academic program in bioinformatics with the John A. Burns School of Medicine (JABSOM). Recruit a full-time junior faculty member to lead the academic program. Conduct training workshops and courses, and run a user support help desk." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core to provide bioinformatics analysis and consulting service, to increase the research capacity in bioinformatics in the State of Hawaii, to provides software applications, hardware, access, and support to researchers who utilize genomic and proteomic data. Undertake collaborative project with INBRE researchers to develop novel tools or applications that address specific needs. Develop an academic program in bioinformatics with the John A. Burns School of Medicine (JABSOM). Recruit a full-time junior faculty member to lead the academic program. Conduct training workshops and courses, and run a user support help desk." . SCR:010100 a NLX:63400, owl:NamedIndividual ; @@ -78689,8 +78682,9 @@ SCR:010164 a NLX:63400, SCR:010165 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156644" ; - rdfs:label " Vanderbilt Diabetes Research and Training Center Cell Imaging Shared Resource " ; - definition: "Core facility that provides any Vanderbilt researcher with access to imaging equipment and expert technical support for microscopy and analysis of tissue and cellular physiology." . + rdfs:label "Vanderbilt Diabetes Research and Training Center Cell Imaging Shared Resource Core Facility" ; + NIFRID:synonym "Vanderbilt Diabetes Research and Training Center Cell Imaging Shared Resource" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that provides any Vanderbilt researcher with access to imaging equipment and expert technical support for microscopy and analysis of tissue and cellular physiology." . SCR:010166 a NLX:63400, owl:NamedIndividual ; @@ -78799,9 +78793,10 @@ SCR:010180 a NLX:63400, SCR:010181 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156660" ; - rdfs:label " Vanderbilt Diabetes Research and Training Center Hormone Assay and Analytical Services Core " ; - NIFRID:synonym "Vanderbilt Hormone Assay & Analytical Services Core" ; - definition: "Core facility that supports diabetes, endocrine, and metabolic research across a range of species. Its objective is to provide sensitive, reproducible, and inexpensive analyses of hormones, amino acids, and other relevant chemicals." . + rdfs:label "Vanderbilt Diabetes Research and Training Center Hormone Assay and Analytical Services Core Facility" ; + NIFRID:synonym "Vanderbilt Diabetes Research and Training Center Hormone Assay and Analytical Services Core", + "Vanderbilt Hormone Assay & Analytical Services Core" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that supports diabetes, endocrine, and metabolic research across a range of species. Its objective is to provide sensitive, reproducible, and inexpensive analyses of hormones, amino acids, and other relevant chemicals." . SCR:010182 a NLX:63400, owl:NamedIndividual ; @@ -78861,8 +78856,9 @@ SCR:010190 a NLX:63400, SCR:010191 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_156670" ; - rdfs:label " Vanderbilt Diabetes Research and Training Center Vanderbilt Diet Body Composition and Metabolism Core " ; - definition: "Core facility that provides training and expertise in nutrition/diet methodology to obtain valid and reliable assessment and analyses of dietary intakes, nutritional status, body composition and metabolism." . + rdfs:label "Vanderbilt Diabetes Research and Training Center Vanderbilt Diet Body Composition and Metabolism Core Facility" ; + NIFRID:synonym "Vanderbilt Diabetes Research and Training Center Vanderbilt Diet Body Composition and Metabolism Core" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility that provides training and expertise in nutrition/diet methodology to obtain valid and reliable assessment and analyses of dietary intakes, nutritional status, body composition and metabolism." . SCR:010192 a NLX:63400, owl:NamedIndividual ; @@ -82221,9 +82217,10 @@ SCR:010653 a NLX:63400, SCR:010654 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_68401" ; - rdfs:label "Computational Biology Research Center" ; - NIFRID:synonym "CBRC" ; - definition: "Core performs research activities to create a wide array of industrial technologies using genomes and the other biological information to fulfill their mission. CBRC hosts research staff experts in diverse fields spanning computer science, mathematics, physics, chemistry, and biology and scientists affiliated with other institutions, with whom they work closely on joint, collaborative projects. Core offers internally developed and maintained software applications and databases, with corresponding external resources." . + rdfs:label "Computational Biology Research Center Core Facility" ; + NIFRID:synonym "CBRC", + "Computational Biology Research Center" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core performs research activities to create a wide array of industrial technologies using genomes and the other biological information to fulfill their mission. CBRC hosts research staff experts in diverse fields spanning computer science, mathematics, physics, chemistry, and biology and scientists affiliated with other institutions, with whom they work closely on joint, collaborative projects. Core offers internally developed and maintained software applications and databases, with corresponding external resources." . SCR:010655 a NLX:63400, owl:NamedIndividual ; @@ -83121,7 +83118,7 @@ SCR:010778 a NLX:63400, oboInOwl:hasDbXref "biotools:mutpred", "OMICS_00154" ; rdfs:label "MutPred" ; - definition: "A web application tool developed to classify an amino acid substitution as disease-associated or neutral in human." . + definition: "Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human." . SCR:010779 a NLX:63400, owl:NamedIndividual ; @@ -85111,7 +85108,7 @@ SCR:011050 a NLX:63400, oboInOwl:hasDbXref "SciEx_9764" ; rdfs:label "Babraham Institute Labs and Facilities" ; NIFRID:abbrev "Babraham Institute Labs & Facilities" ; - definition: "An Portal, Core facility" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Portal, Core facility." . SCR:011051 a NLX:63400, owl:NamedIndividual ; @@ -88349,7 +88346,8 @@ SCR:011379 a NIFSTD:SIO_000688, "Max-Planck-Institut fur Entwicklungsbiologie", "Max-Planck-Institute for Molecular Genetics" . -SCR:011380 a owl:NamedIndividual ; +SCR:011380 a NLX:152328, + owl:NamedIndividual ; oboInOwl:hasDbXref "nlx_97833" ; rdfs:label "Max Planck Institute of Biochemistry; Martinsried; Germany" ; NIFRID:synonym "Max Planck Institute of Biochemistry", @@ -88506,20 +88504,16 @@ SCR:011395 a NLX:152328, "Ministry of Science and Technology of China of the Peoples Republic of China" ; definition: "Formerly the State Science and Technology Commission, is the central government ministry which coordinates science and technology activities in the country. It succeeded the State Science and Technology Commission in 1998." . -SCR:011396 a NLX:152328, - owl:NamedIndividual ; +SCR:011396 a owl:NamedIndividual ; oboInOwl:hasDbXref "Crossref funder ID:100006531", "grid.260128.f", "ISNI:0000 0000 9364 6281", "nlx_144159", "Wikidata:Q4380853" ; - rdfs:label "Missouri University of Science and Technology; Missouri; USA" ; NIFRID:synonym "Missouri S and T", "Missouri University of Science and Technology", "Missouri University of Science Technology", - "University of Missouri-Rolla" ; - NIFRID:abbrev "Missouri S andT" ; - definition: "Founded in 1870 as one of the first technological schools west of the Mississippi, Missouri S&T is one of the nation''s top technological research universities. Missouri S&T produced the engineers, scientists and innovators who helped drive the Industrial Revolution and launch the Space Age. Today, our graduates are poised to lead the new global, green economy." . + "University of Missouri-Rolla" . SCR:011397 a NIFSTD:birnlex_2431, owl:NamedIndividual ; @@ -90782,8 +90776,12 @@ SCR:011624 a NLX:152328, SCR:011625 a NLX:152328, owl:NamedIndividual ; - oboInOwl:hasDbXref "nlx_71933", - "SCR_016626" ; + oboInOwl:hasDbXref "Crossref Funder ID 100007911", + "GRID grid.266100.3", + "ISNI 0000 0001 2107 4242", + "nlx_71933", + "SCR_016626", + "Wikidata Q622664" ; rdfs:label "University of California at San Diego; California; USA" ; NIFRID:synonym "UC San Diego", "UC San Diego; California; USA", @@ -93439,10 +93437,12 @@ SCR:011935 a NLX:63400, SCR:011936 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "OMICS_01493" ; + oboInOwl:hasDbXref "OMICS_01493", + "SCR_021246" ; rdfs:label "Prodigal" ; - NIFRID:synonym "Prokaryotic Dynamic Programming Genefinding Algorithm" ; - definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Microbial (bacterial and archaeal) gene finding software program developed at Oak Ridge National Laboratory and the University of Tennessee." . + NIFRID:synonym "PROkaryotic DYnamic programming Gene-finding ALgorithm", + "Prokaryotic Dynamic Programming Genefinding Algorithm" ; + definition: "Software tool for protein coding gene prediction for prokaryotic genomes." . SCR:011937 a NLX:63400, owl:NamedIndividual ; @@ -94844,10 +94844,10 @@ SCR:012142 a NLX:63400, SCR:012143 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_11940" ; - rdfs:label "Universite de Sherbrooke Najmanovich Research Group" ; + rdfs:label "Universite de Sherbrooke Najmanovich Research Group Core Facility" ; NIFRID:synonym "Najmanovich Research Group", - "Universite de Sherbrooke" ; - definition: "Core facility provides consultancy services as well as contract work in all areas of bioinformatics, chemoinformatics and systems biology." . + "Universite de Sherbrooke Najmanovich Research Group" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core facility provides consultancy services as well as contract work in all areas of bioinformatics, chemoinformatics and systems biology." . SCR:012144 a NLX:63400, owl:NamedIndividual ; @@ -94982,10 +94982,11 @@ SCR:012160 a NLX:63400, NIFRID:abbrev "MQAAAstro" ; definition: "he Macquarie University Research Centre for Astronomy, Astrophysics, and Astrophotnics (MQAAAstro) grew out of our Concentration of Research Excellence (CORE) and is now one of the largest and fastest growing astronomy groups in Australia. We are a highly active centre of astronomical research excellence. We have close ties to the Australian Astronomical Observatory (AAO) and CSIRO Astronomy & Space Science (CASS), both of which are close to campus. These strong links offer valuable synergies and opportunities for collaborations in observational astronomy, theoretical astrophysics, astrophotonics, science education, and Aboriginal astronomy." . -SCR:012161 a NLX:152342, +SCR:012161 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10114" ; rdfs:label "Trenzyme" ; + NIFRID:synonym "Trenzyme service resource" ; definition: "Trenzyme is a privately owned German contract research organization offering highly individualized scientific services. As your life science service partner, we offer more than 11 years of experience and a continuously growing staff of highly skilled employees. Connected with our outstanding collection of state-of-the-art laboratory equipment this guarantees a flexible high-quality service to accommodate your needs. From the very first beginning of Trenzyme in 2000, we offered molecular biology services. In this field, we provide you with every service from gene to plasmid. Custom cloning, gene synthesis, mutagenesis and plasmid purification are only the main services in our baseline business domain. Whether expressed in microbials or mammalian cells, our protein services department delivers the exact proteins for your downstream applications. To keep your budget in balance, we offer standardized Fixed-Price-Protein-Manufactures. Cell culture is one of the most time-consuming and challenging life science branch of the last years. We understand the importance of your work and take pride in freeing you of valuable time, always keeping track of our mission: accelerating your innovation!" . SCR:012162 a NLX:63400, @@ -94995,7 +94996,7 @@ SCR:012162 a NLX:63400, NIFRID:synonym "Virginia Commonwealth University Nanomaterials Characterization Center" ; definition: "The Nanomaterials Characterization Center at Virginia Commonwealth University is a state of the art 4000 sq. ft. facility located within the new Health and Life Science Engineering Facility. The Center provides an academic structure for students in natural sciences, mathematics, engineering, and medicine to participate in nanoscience and nanotechnology research to acquire the skills necessary to pursue such careers. In the past year, VCU received two National Science Foundation major research instrumentation grants totaling more than $1.6 million to expand its capabilities for research in materials science. Combining these federal awards with state instrumentation grants and private donations, the facility has been able to build a state of the art facility with over $5 million in new equipment. This new equipment will allow faculty and student researchers from both VCU campuses, as well as other universities along the East Coast to use state_����of_����the_����art instrumentation for nanomaterials characterization." . -SCR:012163 a NLX:152342, +SCR:012163 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10051" ; rdfs:label "PerkinElmer Discovery Services" ; @@ -95003,18 +95004,18 @@ SCR:012163 a NLX:152342, NIFRID:abbrev "PDS" ; definition: "Preclinical contract research company performing CLIA-certified DNA Next Gen Sequencing Services." . -SCR:012164 a NLX:152342, +SCR:012164 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10052" ; rdfs:label "Lonza Viral Based Therapeutics" ; NIFRID:abbrev "Lonza Viral-Based Therapeutics" ; definition: "Contract research organization for gene therapy product development. Services include adenoviral vectors, AAV vectors and lentiviral vectors and range from cell line optimization and vector development to process development and cGMP manufacturing through product release testing." . -SCR:012165 a NLX:152342, +SCR:012165 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10150" ; rdfs:label "Flow Paradigm" ; - definition: "ICCE certified instructors with 20 years experience in flow cytometry and assay development can deliver basic, intermediate, and advanced training tailored to your needs. We can ensure rapid assay development and implementation, using theoretical and hands-on training conducted at your site, using your assays and your instruments." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. ICCE certified instructors with 20 years experience in flow cytometry and assay development can deliver basic, intermediate, and advanced training tailored to your needs. We can ensure rapid assay development and implementation, using theoretical and hands-on training conducted at your site, using your assays and your instruments." . SCR:012166 a NLX:63400, owl:NamedIndividual ; @@ -95066,12 +95067,12 @@ SCR:012171 a NLX:63400, NIFRID:abbrev "UTHSCSA OIF" ; definition: "Service resource which makes imaging technology available to investigators on UTHSCSA campus and neighboring scientific community. Core Optical Imaging Facility offers access to technology for imaging of living cells, tissues, and animals, consultation, education and assistance regarding theory and application of optical imaging techniques, technical advice on specimen preparation techniques and probe selection." . -SCR:012172 a NLX:152342, +SCR:012172 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10155" ; rdfs:label "SCIPAC" ; NIFRID:synonym "SCIPAC Ltd" ; - definition: "Our contract antibody service is designed to be highly flexible to ensure we meet the individual needs of our customers. Whether you are looking for a complete start to finish service or simply one aspect such as clone yield optimisation, then SCIPAC can meet your needs. Our service caters for both monoclonal antibodies as well as recombinant antibodies. Why chose SCIPAC? * Over 25 years???????????? experience serving the diagnostics industry * Totally flexible service allowing customers to choose exactly what they need * Small scale and large scale capabilities ranging from 1mg to 1kg + batches * Antibodies manufactured under ISO 9001 quality systems * Tried and tested ??????????????????design control and review???????????? project management system to ensure best communication practices and streamlined projects" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Our contract antibody service is designed to be highly flexible to ensure we meet the individual needs of our customers. Whether you are looking for a complete start to finish service or simply one aspect such as clone yield optimisation, then SCIPAC can meet your needs. Our service caters for both monoclonal antibodies as well as recombinant antibodies." . SCR:012173 a NLX:63400, owl:NamedIndividual ; @@ -95099,7 +95100,7 @@ SCR:012175 a NLX:63400, NIFRID:synonym "University of Colorado Denver Labs & Facilities" ; NIFRID:abbrev "CU Denver Labs & Facilities", "CU Denver Labs and Facilities" ; - definition: "An Portal, Core facility" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Portal, Core facility" . SCR:012176 a NLX:63400, owl:NamedIndividual ; @@ -95125,7 +95126,7 @@ SCR:012178 a NLX:63400, NIFRID:synonym "University of Chicago Labs & Facilities" ; NIFRID:abbrev "UChicago Labs & Facilities", "UChicago Labs and Facilities" ; - definition: "An Portal, Core facility" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Portal, Core facility" . SCR:012179 a NLX:63400, owl:NamedIndividual ; @@ -95135,12 +95136,12 @@ SCR:012179 a NLX:63400, NIFRID:abbrev "MMC Proteomics Core" ; definition: "Core facility that aids investigators and trainees with high performance computation in proteomics, as well as other omics type applications needing efficient analysis of large-scale biological data sets. The ability to incorporate proteomics into translational and clinical biomedical research is critical for the discovery of therapeutic interventions and high fidelity biomarkers of disease and response to therapy. The Core provides state-of-the-art services, training, and bioinformatics-driven data analysis to the Meharry translational research community." . -SCR:012180 a NLX:152342, +SCR:012180 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10255" ; rdfs:label "AKESOgen Inc." ; NIFRID:abbrev "AKESOgen" ; - definition: "AKESOgen is a biomarker, genomics and pharmacogenomics contract research organization that services the academic, pharmaceutical, biotechnology and agricultural sectors. AKESOgen performs biomarker profiling and genomics services utilizing different types of markers (e.g. DNA, RNA, methylation) for the R&D market. AKESOgen establishes and validates biomarkers in the Clinical Trials arena. AKESOgen provides expertise in biobanking. AKESOgen is CLIA certified." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30, 2023. AKESOgen is a biomarker, genomics and pharmacogenomics contract research organization that services the academic, pharmaceutical, biotechnology and agricultural sectors. AKESOgen performs biomarker profiling and genomics services utilizing different types of markers (e.g. DNA, RNA, methylation) for the R&D market. AKESOgen establishes and validates biomarkers in the Clinical Trials arena. AKESOgen provides expertise in biobanking. AKESOgen is CLIA certified." . SCR:012181 a NLX:63400, owl:NamedIndividual ; @@ -95150,14 +95151,14 @@ SCR:012181 a NLX:63400, NIFRID:abbrev "Oxford CPF" ; definition: "The Central Proteomics Facility (CPF) of Oxford University offers proteomics mass spectrometry services and expertise to academic and commercial organisations. The facility is quipped with state-of-the-art Orbitrap and Q Exactive Orbitrap mass spectrometers. The facility routinely perfroms idenitification, post-translational modification and protein quantitation work using SILAC." . -SCR:012182 a NLX:152342, +SCR:012182 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10286" ; rdfs:label "Molecule Inc." ; NIFRID:abbrev "Molecule" ; - definition: "Molecule serves the needs of your businesses, both large and small. We are based in Silicon Valley with local and international labs. We are a team of experts who have worked for world-class companies over 2 decades and provide service in a wide range of chemistry, formulation and new technology development areas of medical device and drug control release products. We provide both contract work and consulting service in wet chemistries (customer design and synthesis) and formulation development. We have spent so much time to accumulate experience so your work can be developed in the shortest amount of time." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Molecule serves the needs of your businesses, both large and small. We are based in Silicon Valley with local and international labs. We are a team of experts who have worked for world-class companies over 2 decades and provide service in a wide range of chemistry, formulation and new technology development areas of medical device and drug control release products. We provide both contract work and consulting service in wet chemistries (customer design and synthesis) and formulation development. We have spent so much time to accumulate experience so your work can be developed in the shortest amount of time." . -SCR:012183 a NLX:152342, +SCR:012183 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10291" ; rdfs:label "Richman Chemical" ; @@ -95179,12 +95180,12 @@ SCR:012185 a NLX:63400, NIFRID:synonym "DNASU Core Facility at Arizona State University" ; definition: "Core Facility within the Center For Personalized Diagnostics offers both Sanger DNA sequencing and Illumina NGS services (HiSeq 2000). DNASU is also a central repository for plasmid clones and collections. We currently store and distribute over 191,000 plasmids including over 75,000 human and mouse plasmids, full genome collections from numerous organisms, the protein expression plasmids from the Protein Structure Initiative as the PSI:Biology-Materials Repository (PSI:Biology-MR), and both small and large collections from individual researchers." . -SCR:012186 a NLX:152342, +SCR:012186 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10307" ; rdfs:label "Integrated Technology Enterprise Inc" ; NIFRID:abbrev "Integrated Technology Enterprise" ; - definition: "We will design and produce DNA constructs for any purpose: Mutations/Deletions Knockout/Transgenic constructs Epitope tags & Fusion proteins Protein expression constructs Viral gene delivery constructs RNAi & related constructs Cost is generally about $300 per construct Turnaround time usually 5 business days" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. We will design and produce DNA constructs for any purpose: Mutations/Deletions Knockout/Transgenic constructs Epitope tags & Fusion proteins Protein expression constructs Viral gene delivery constructs RNAi & related constructs Cost is generally about $300 per construct Turnaround time usually 5 business days" . SCR:012187 a NLX:63400, owl:NamedIndividual ; @@ -95200,13 +95201,13 @@ SCR:012188 a NLX:63400, NIFRID:abbrev "C-CAMP" ; definition: "Centre for Cellular and Molecular Platforms (C-CAMP), is a Dept. of Biotechnology (Govt. of India) initiative and a not for profit organisation, that also forms an important part of the Bangalore Bio-cluster. We are acting as an enabler of bioscience research and entrepreneurship by providing research, development, training and service in state of the art technology platforms." . -SCR:012189 a NLX:152342, +SCR:012189 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10312" ; rdfs:label "Frontier Scientific Services" ; NIFRID:synonym "Frontier Scientific Services Inc." ; NIFRID:abbrev "FSSI" ; - definition: "Since 1988, Frontier Scientific Services, Inc. (FSSI) has functioned as a specialty CRO, working to enable dramatic cost reductions via outsourced compound management, reformatting, sample procurement, liquid handling, and compound library management. Our infrastructure and distribution capabilities empower smaller groups with logistics capabilities that would often not be available in-house, as well as offering the same services to larger groups, which maximizes their capital efficiency." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Since 1988, Frontier Scientific Services, Inc. (FSSI) has functioned as a specialty CRO, working to enable dramatic cost reductions via outsourced compound management, reformatting, sample procurement, liquid handling, and compound library management. Our infrastructure and distribution capabilities empower smaller groups with logistics capabilities that would often not be available in-house, as well as offering the same services to larger groups, which maximizes their capital efficiency." . SCR:012190 a NLX:63400, owl:NamedIndividual ; @@ -95232,7 +95233,7 @@ SCR:012192 a NLX:63400, NIFRID:synonym "University of Louisville Labs & Facilities" ; NIFRID:abbrev "UL Labs & Facilities", "UL Labs and Facilities" ; - definition: "An Portal, Core facility" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Portal, Core facility" . SCR:012193 a NLX:63400, owl:NamedIndividual ; @@ -95241,18 +95242,18 @@ SCR:012193 a NLX:63400, NIFRID:abbrev "UL MNTC" ; definition: "More than 40 research scientists and engineers from diverse disciplines work together at the MNTC Center at the University of Louisville. Scientists with specialties in MEMS, bioMEMS, nanotechnology, electrooptics, biomechanics, bioengineering, microfabrication, and theoretical and applied physics, work along side scientists from the College of Arts and Sciences with expertise in molecular, cellular and structural biology and medicinal and combinatorial chemistry, and with cancer and genetic researchers from the Schools of Medicine and Dentistry." . -SCR:012194 a NLX:152342, +SCR:012194 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_11420" ; rdfs:label "SeqMatic" ; NIFRID:synonym "SeqMatic LLC" ; definition: "SeqMatic provides comprehensive next generation sequencing services for DNA, RNA, and miRNA sequencing. We are proud to offer high quality sequencing with very fast turnaround time. We also offer customized experiment solutions including library generation, sequencing, and data analysis tailored to each customer''s needs." . -SCR:012195 a NLX:152342, +SCR:012195 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10371" ; rdfs:label "IBT Bioservices" ; - definition: "IBT Bioservices is a research organization offering R&D services to identify and develop vaccines and therapeutics for infectious diseases. As a division of Integrated BioTherapeutics, Inc., IBT is a small business as defined by the SBA and meets the US Government''s requirements for small business subcontracting. IBT''s principals Dr. M. Javad Aman and Dr. Kelly Warfield have a long track record of accomplishments in the filovirus field including highly productive tenures at USAMRIID. Our business is focused on a collaborative ????????????????????????????????????scientist-to-scientist???????????????????????? model where creativity, client interaction, and expertise are emphasized. This focus allows us to keep our costs down with non-GLP preclinical studies that play an integral role in making go, no-go decisions in drug development. We offer the core functions of early R&D including initial screens in vitro and in vivo, animal model development, assay development, immunogenicity testing, and serology testing" . + definition: "Research organization offering R&D services to identify and develop vaccines and therapeutics for infectious diseases." . SCR:012196 a NLX:63400, owl:NamedIndividual ; @@ -95261,7 +95262,7 @@ SCR:012196 a NLX:63400, NIFRID:synonym "University of Illinois at Chicago Labs & Facilities" ; NIFRID:abbrev "UIC Labs & Facilities", "UIC Labs and Facilities" ; - definition: "An Portal, Core facility" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Portal, Core facility" . SCR:012197 a NLX:63400, owl:NamedIndividual ; @@ -95278,20 +95279,20 @@ SCR:012198 a NLX:63400, NIFRID:synonym "Peter MacCallum Cancer Centre Translational Research Laboratory" ; definition: "The Translational Research Laboratory at the Peter MacCallum Cancer Centre offers oncology focused, small animal PET imaging services to both academic and commercial investigators. Using the wide range of mouse models of cancer available at Peter Mac, experiments are tailored to investigators_������_ needs and performed in state of the art facilities. Infrastructure available includes 2 Philips Mosaic PET scanners, on-site radiotracer production, fully trained imaging staff and a dedicated animal facility. Digital autoradiography using the Biospace BetaImager and MicroImager allows high resolution ex-vivo imaging of labelled compounds in whole animal or tissue sections. The VisualSonics Vevo 770 small animal ultrasound is available for detection and monitoring of in vivo tumor growth. Ex-vivo correlative biomarker studies are also available." . -SCR:012199 a NLX:152342, +SCR:012199 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10494" ; rdfs:label "Aeirtec Limited" ; NIFRID:synonym "Aeirtec", "Aeirtec Ltd." ; - definition: "Core provides a biomarker service activity for both large pharma and biotech. Core does not subcontract any of its activities." . + definition: "Provides biomarker service activity for both large pharma and biotech." . -SCR:012200 a NLX:152342, +SCR:012200 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10567" ; rdfs:label "Acellera" ; NIFRID:synonym "Acellera Ltd" ; - definition: "Acellera is a high-technology company focused on developing high-throughput molecular dynamics techniques that deliver solutions for estimating common physico-chemical properties such as binding affinities, kinetics, poses and pathways with validated accuracy." . + definition: "Acellera is company focused on developing high-throughput molecular dynamics techniques that deliver solutions for estimating common physico-chemical properties such as binding affinities, kinetics, poses and pathways with validated accuracy.Company mission is to accelerate transition to rational, computerized drug discovery via simulations and machine learning." . SCR:012201 a NLX:63400, owl:NamedIndividual ; @@ -95321,12 +95322,11 @@ SCR:012203 a NLX:63400, SCR:012204 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10586" ; - rdfs:label "University of California Los Angeles Technology Center for Genomics & Bioinformatics" ; - NIFRID:synonym "TCGB", - "Technology Center for Genomics and Bioinformatics", - "UCLA", - "University of California Los Angeles" ; - NIFRID:abbrev "UCLA TCGB" ; + rdfs:label "University of California Los Angeles Technology Center for Genomics and Bioinformatics Core Facility" ; + NIFRID:synonym "University of California Los Angeles", + "University of California Los Angeles Technology Center for Genomics & Bioinformatics" ; + NIFRID:abbrev "TCGB", + "UCLA TCGB" ; definition: "Core is a fully automated, high-throughput genomic Center equipped with next generation sequencing and microarray platforms. TCGB provides genomics technologies, comprehensive services, specialized expertise and a wide range of trainings, enabling these services to serve basic science and translational/clinical research. In addition, TCGB provides pre-experiment consultation and post-experiment support, including preparation of grant applications, publications, and strategic planning for additional research steps. TCGB also provides educational training to faculty, staff, and students to raise awareness of new directions and major discoveries in the areas of genomics and bioinformatics." . SCR:012205 a NLX:63400, @@ -95346,22 +95346,22 @@ SCR:012206 a NLX:63400, NIFRID:abbrev "UIC" ; definition: "The UCLA Immunogenetics Center (UIC) provides comprehensive testing for organ and tissue transplantation. Transplant testing has a long history at UCLA. HLA typing was pioneered here in the 1960' '''s. The development of the microcytoxicity test in 1964 marked the beginning of international testing and standardization of HLA typing. The UCLA Immunogenetics Center has retained its leadership position in HLA research, and in the development of accompanying diagnostic testing. In the intervening years, laboratory and scientific personnel, from the US and abroad, have learned HLA typing through courses and workshops at the UCLA Immunogenetics laboratory. The center provides immunogenetics and histocompatibility testing services to a wide range of physicians, patients, pharmaceutical companies and other medical facilities. The laboratory is a World Health Organization reference laboratory for HLA, and is licensed by the State of California, New York, Maryland, Pennsylvania and Rhode Island, is CMS certified and accredited by the American Society for Histocompatibility and Immunogenetics." . -SCR:012207 a NLX:152342, +SCR:012207 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10618" ; rdfs:label "Affina Biotechnologies" ; NIFRID:synonym "Affina Biotechnologies Inc." ; - definition: "Affina Biotechnologies is dedicated to excellence in helping our customers develop measurements of activities, kinetics and affinities of interactions and concentrations of biomolecules. We offer a unique mix of label-free and label-dependent assay technologies supported by scientific and technical expertise and a wide range of instrumentation." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Affina Biotechnologies is dedicated to excellence in helping our customers develop measurements of activities, kinetics and affinities of interactions and concentrations of biomolecules. We offer a unique mix of label-free and label-dependent assay technologies supported by scientific and technical expertise and a wide range of instrumentation." . SCR:012208 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10624" ; - rdfs:label "Sanford-Burnham Applied Bioinformatics Core" ; + rdfs:label "Sanford-Burnham Applied Bioinformatics Core Facility" ; NIFRID:synonym "Applied Bioinformatics Core", - "Lake Nona", "Medical Research Institute", "Sanford-Burnham" ; - definition: "THIS RESOURCE IS NO LONGER IN SERVCE, documented January 23, 2019. Core supports SBMRI investigators in exploring, understanding and analyzing complex biological data. Core is equipped with cutting-edge computational infrastructure and a selective collection of bioinformatics software. Core's services include consultation, data analysis and management, software development, and accessing to large computing resources. To meet various demands from the investigators, we provide services at multiple levels, from full service to cost-effective limited service as well as collaborative projects requiring longer-term commitment of time and effort." . + NIFRID:abbrev "Sanford-Burnham Applied Bioinformatics Core" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE, documented January 23, 2019. Core supports SBMRI investigators in exploring, understanding and analyzing complex biological data. Core is equipped with cutting-edge computational infrastructure and a selective collection of bioinformatics software. Core's services include consultation, data analysis and management, software development, and accessing to large computing resources. To meet various demands from the investigators, we provide services at multiple levels, from full service to cost-effective limited service as well as collaborative projects requiring longer-term commitment of time and effort." . SCR:012209 a NLX:63400, owl:NamedIndividual ; @@ -95372,7 +95372,7 @@ SCR:012209 a NLX:63400, "USF Center for Drug Discovery and Innovation Labs & Facilities" ; NIFRID:abbrev "USF CDDI Labs & Facilities", "USF CDDI Labs and Facilities" ; - definition: "The Center for Drug Discovery and Innovation (CDDI) is a Florida Center of Excellence serving the research community at USF and south Florida. From concept to clinical trials there are significant challenges in the successful development of new pharmaceuticals. It is the mission of CDDI to assist research groups at USF in overcoming some of the critical bottlenecks in early phase drug discovery." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. The Center for Drug Discovery and Innovation (CDDI) is a Florida Center of Excellence serving the research community at USF and south Florida. From concept to clinical trials there are significant challenges in the successful development of new pharmaceuticals. It is the mission of CDDI to assist research groups at USF in overcoming some of the critical bottlenecks in early phase drug discovery." . SCR:012210 a NLX:63400, owl:NamedIndividual ; @@ -95390,11 +95390,11 @@ SCR:012211 a NLX:63400, NIFRID:abbrev "IUSM TVC" ; definition: "The Therapeutic Validation core (TVC) assists clinical investigators to develop and perform correlative biological assays needed to validate mechanism(s) of action of candidate drugs/therapies and to develop and test new hypotheses. The TVC also provides technical and intellectual support in the development, implementation, and validation of predictive and pharmacodynamic biomarkers for novel, molecularly-targeted anticancer agents." . -SCR:012212 a NLX:152342, +SCR:012212 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_10715" ; rdfs:label "GeneWake" ; - definition: "GeneWake GmbH is a pharmacogenomics company with a sound scientific background in biomarker analysis in the field of oncology. Our mission is to realize a personalized and tailor-made cancer treatment by targeted analysis of relevant gene expression levels in tumour tissue and in circulating tumour cells in blood. By employing bioinformatical algorithms based on our knowledge in pathway structure and microarray data from public sources, biomarker screening can be limited to a low-density scale. The output of 10-20 potential genes can be used for ptient stratification or therapy tracking. In addition, GeneWake offers contract research like DNA and RNA sequencing and annotation, SNP genotyping, mutation detection, multiplex PCR, kit development, immune histology and genotyping for clinical studies." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. GeneWake GmbH is a pharmacogenomics company with a sound scientific background in biomarker analysis in the field of oncology. Our mission is to realize a personalized and tailor-made cancer treatment by targeted analysis of relevant gene expression levels in tumour tissue and in circulating tumour cells in blood. By employing bioinformatical algorithms based on our knowledge in pathway structure and microarray data from public sources, biomarker screening can be limited to a low-density scale. The output of 10-20 potential genes can be used for ptient stratification or therapy tracking. In addition, GeneWake offers contract research like DNA and RNA sequencing and annotation, SNP genotyping, mutation detection, multiplex PCR, kit development, immune histology and genotyping for clinical studies." . SCR:012213 a NLX:63400, owl:NamedIndividual ; @@ -95955,15 +95955,6 @@ SCR:012279 a NLX:63400, "CSISP Labs and Facilities" ; definition: "A portal and core facility. Contains the FISABIO sequencing and bioinformatics service." . -SCR:012280 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "SciEx_11307" ; - rdfs:label "Dartmouth DartLab" ; - NIFRID:synonym "DartLab (Dartmouth)", - "Dartmouth College Geisel School of Medicine DartLab" ; - NIFRID:abbrev "DartLab" ; - definition: "Core facility that provides the following services: Whole blood processing service, Cell surface staining, Cell subset enrichment service, Flow cytometry service, ELISPOT service, CFSE lymphoproliferation analysis service, Regulatory T cell conversion service, Multi-plex cytokine assay service, Flow cytometry assay service, Cell separation service. They are committed to assisting at all stages in the scientific process - from experimental design to data analysis - to meet the needs of faculty and other investigators.

DartLab is a Shared Resource that is used both by basic scientists and by clinicians carrying out mechanistic studies for clinical trials. Services are also available to non-Dartmouth clients. The consolidated Shared Resource moves beyond the simple provisioning of technical services to making complex experiments possible by providing scientific and technological support for implementing advanced, high-complexity assays in a cost-effective way, and by providing a mechanism for the acquisition of new methodologies. They carry out a spectrum of immunoassays and can develop customized immunoassays to suit your studies. They provide dedicated instruments for your use including cell sorters, flow cytometers, an ELISPOT reader, a Bio-Plex array reader and a Sector Imager, an autoMACS and a Robosep. Whole Blood Services * Flow Cytometry * Whole blood processing * Cell Subset Enrichment * Education * Clinical Trial Studies" . - SCR:012281 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_11324" ; @@ -96121,8 +96112,7 @@ SCR:012299 a NLX:63400, NIFRID:abbrev "JDC Islet Isolation Core" ; definition: "Core facility that provides the following services: Rodent and Porcine Islet Isolation Services, Training Services. The main objective of the Islet Isolation Core is to provide Islets of Langerhans to investigators in the Boston area and beyond. By receiving islets from the Core one is assured of consistent high quality and purity of islets for experiments. The Core can isolate rodent and neonatal porcine islets. This leaves the investigator to concentrate on experiments rather than the complexity of islet isolation. The Core can buy the animals or the investigator can provide their own, such as special transgenic mice. Over the last five years the Core has isolated more than 10 million islets. They also provide training and advice. The Core can provide training not only for the isolation procedure but islet viability, islet size measurement, GSIS (Glucose Stimulated Insulin Secretion), STZ-induced diabetes, transplantation under the kidney capsule, and islet graft retrieval." . -SCR:012300 a NLX:63400, - owl:NamedIndividual ; +SCR:012300 a owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_11655" ; rdfs:label "New York University Center for Health Informatics and Bioinformatics" ; NIFRID:synonym "Bioinformatics", @@ -96132,9 +96122,7 @@ SCR:012300 a NLX:63400, "Health Informatics", "Langone Medical Center", "New York University", - "NYU" ; - NIFRID:abbrev "NYU CHIBI" ; - definition: "Core handles both low-level (instrument-specific, or upstream) informatics as well as higher-level (hypothesis testing and generation oriented, or downstream informatics). CHIBI also has the scientific responsibility for the high-end computing needed to process the genomic data." . + "NYU" . SCR:012301 a NLX:63400, owl:NamedIndividual ; @@ -97740,10 +97728,13 @@ SCR:012486 a NLX:63400, SCR:012487 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "SciEx_254" ; - rdfs:label "Ohio University Genomics Facility" ; - NIFRID:abbrev "Ohio Genomics Facility" ; - definition: "The Ohio University Genomics Facility was established in 2007 by funds secured through a NSF award to Drs. Sarah Wyatt & Morgan Vis for major instrumentation. The Ohio University Genomics Facility has been instrumental in increasing the researcher' '''s potential by providing services like DNA sequencing, fragment analysis, RNA, DNA, protein and cell cytometry services through various equipment. Various new equipment and software have been added since 2007." . + oboInOwl:hasDbXref "ABRF_498", + "SciEx_254", + "SCR_018268" ; + rdfs:label "Ohio University Genomics Core Facility" ; + NIFRID:synonym "Ohio Genomics Facility", + "Ohio University Genomics Facility" ; + definition: "Facility offers Next-Generation Sequencing services, Sanger sequencing, Fragment Analysis, qPCR, data analysis. Provided services include DNA sequencing, fragment analysis, RNA, DNA, protein and cell cytometry through various equipment." . SCR:012488 a NLX:63400, owl:NamedIndividual ; @@ -97982,15 +97973,6 @@ SCR:012513 a NLX:63400, NIFRID:abbrev "QFAB" ; definition: "Core facility providing support in bioinformatics, biostatistics and biodata to life sciences and health researchers across Queensland and beyond. Services include microarrays, next generation sequencing and proteomics profiling, biostatistical support from design of experiments, to analysis and interpretation, help High Degree Research students and Early Career Researchers in management, mining and visualization of small and big data, leveraging the cloud and hpc research infrastructure powered by the Queensland Cyber Infrastructure Foundation." . -SCR:012514 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "SciEx_41" ; - rdfs:label "New York University Genome Technology Center" ; - NIFRID:synonym "New York University Langone Medical Center Genome Technology Center" ; - NIFRID:abbrev "GTC", - "NYU GTC" ; - definition: "The mission of GTC is to enable and foster institutional science by providing expertise in genomics, resources, and the training necessary to promote basic and clinical research through dedicated collaborative effort. GTC assists with the presentation and publication of investigator data." . - SCR:012515 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_4165" ; @@ -98761,12 +98743,12 @@ SCR:012607 a NLX:152342, rdfs:label "Aptagen" ; definition: "Supplier of aptamers, RNA or DNA that binds with high affinity and specificity to targets such as small organics, peptides, proteins, cells, and tissues. Unlike antibodies, some aptamers exhibit stereoselectivity. In addition, aptamers have been generated that exhibit greater than 10,000-fold binding affinity for theophylline over caffeine, which differ from one another in structure by only a single methyl group." . -SCR:012608 a NLX:152342, +SCR:012608 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SciEx_535" ; rdfs:label "NanoRacks" ; NIFRID:synonym "Nanoracks U.S. National Lab" ; - definition: "NanoRacks provides the ultimate ??????????????????Plug and Play???????????? microgravity research facilities allowing small standardized payloads to be plugged into any of our platforms, providing interface with the International Space Station power and data capabilities. NanoRacks???????????? low-cost model puts microgravity research projects within the budgetary realm of hundreds of universities, smaller organizations and first-time commercial space research users. Our U.S. National Lab facilities provide turnkey opportunities for your choice of experimentation and currently includes two NanoLab Platforms, NanoRacks Plate Reader, NanoRacks Microscope and NanoRacks MixStix, providing repeatable microgravity research opportunities onboard the International Space Station." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10th,2023. NanoRacks provides microgravity research facilities and currently includes NanoLab Platforms, NanoRacks Plate Reader, NanoRacks Microscope and NanoRacks MixStix." . SCR:012609 a NLX:63400, owl:NamedIndividual ; @@ -99810,7 +99792,7 @@ SCR:012728 a NLX:63400, NIFRID:synonym "Rutgers University Waksman Institute of Microbiology Labs & Facilities", "Rutgers University Waksman Institute of Microbiology Labs and Facilities" ; NIFRID:abbrev "Rutgers Waksman Institute of Microbiology Labs & Facilities" ; - definition: "Our mission is to conduct research in microbial molecular genetics, developmental molecular genetics, plant molecular genetics, and structural and computational biology. We also provide a catalyst for general university initiatives, a life science infrastructure, undergraduate and graduate education, and a public service function for the State of New Jersey. The Institute employs faculty teams that concentrate on certain classes of organisms amenable to genetic analysis such as bacteria and fungi (E. coli and yeast), animal systems (e.g., Drosophila), and plants (Arabidopsis, tobacco, and maize). Although the Institute focuses on basic questions in microbial, animal, and plant research, it continues to engage in extensive technology transfer of its basic discoveries." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 10, 2023. Our mission is to conduct research in microbial molecular genetics, developmental molecular genetics, plant molecular genetics, and structural and computational biology. We also provide a catalyst for general university initiatives, a life science infrastructure, undergraduate and graduate education, and a public service function for the State of New Jersey. The Institute employs faculty teams that concentrate on certain classes of organisms amenable to genetic analysis such as bacteria and fungi (E. coli and yeast), animal systems (e.g., Drosophila), and plants (Arabidopsis, tobacco, and maize). Although the Institute focuses on basic questions in microbial, animal, and plant research, it continues to engage in extensive technology transfer of its basic discoveries." . SCR:012729 a NLX:63400, owl:NamedIndividual ; @@ -100115,7 +100097,7 @@ SCR:012765 a NLX:63400, oboInOwl:hasDbXref "rid_000030" ; rdfs:label "BCube A Broker Framework for Next Generation Geoscience" ; NIFRID:abbrev "BCube" ; - definition: "Project that brings together an internationally recognized team of geo- and social-scientists, cyberinfrastructure experts and educators to explore how expert systems can mediate interactions and improve access between scientific fields. To address complex Earth system issues such as climate change and water resources, geoscientists must work across disciplinary boundaries, which requires them to access data outside of their fields. The initial focus is on hydrology, oceans, polar and weather, with the intent to make the technology applicable and available to all the geosciences. The team''s social scientists and educators will research how technology can improve knowledge exchange between scientific communities." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 17,2023. Project that brings together an internationally recognized team of geo- and social-scientists, cyberinfrastructure experts and educators to explore how expert systems can mediate interactions and improve access between scientific fields. To address complex Earth system issues such as climate change and water resources, geoscientists must work across disciplinary boundaries, which requires them to access data outside of their fields. The initial focus is on hydrology, oceans, polar and weather, with the intent to make the technology applicable and available to all the geosciences. The team''s social scientists and educators will research how technology can improve knowledge exchange between scientific communities." . SCR:012766 a NLX:63400, owl:NamedIndividual ; @@ -101914,6 +101896,7 @@ SCR:012986 a NLX:63400, "Non-human Primate Reagent Resources", "Non-human primate repository", "Nonhuman Primate Reagent Resources" ; + NIFRID:abbrev "NHPRR" ; definition: "Center that facilitates the optimal use of nonhuman primate models in biomedical research by identifying, developing, characterizing and producing reagents for monitoring or modulating immune responses. They distribute non-human primate-specific antibodies for in vitro diagnostics, as well as develop and produce primate recombinant antibodies for in vivo cell depletion or modulating immune responses." . SCR:012987 a NLX:63400, @@ -106700,7 +106683,7 @@ SCR:013656 a NLX:63400, oboInOwl:hasDbXref "nif-0000-00528" ; rdfs:label "Center for Cell Analysis and Modeling" ; NIFRID:synonym "CCAM - Computational Facility" ; - definition: "CCAM is one of five National Technology Centers for Networks and Pathways, NTCNP, funded throught the NIH Technology Center for Networks and Pathways, TCNP. CCAM integrates new microscope technologies for making quantitative in vivo live cell measurements with new physical formulations and computational tools that will produce spatially realistic quantitative models of intracellular dynamics. :The overarching rationale for CCAMs research as a TCNP is that polarity in networks and pathways is determined by the spatial organization, subcellular distribution, dynamic behavior, interactions and functions of specific molecules within the cell. To investigate these relationships, we use a tripartite approach described as: :1) Measure - develop new tools for measuring spatially resolved dynamic behavior of molecules in cells, :2) Model - develop new methods for spatial modeling of biological systems. :3) Manipulate - develop new techniques for manipulating the spatial distribution of molecules in living cells. :Microscopy contrast enhancement protocol, biophotonics, subcellular :" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 26,2023. CCAM is one of five National Technology Centers for Networks and Pathways, NTCNP, funded throught the NIH Technology Center for Networks and Pathways, TCNP. CCAM integrates new microscope technologies for making quantitative in vivo live cell measurements with new physical formulations and computational tools that will produce spatially realistic quantitative models of intracellular dynamics. :The overarching rationale for CCAMs research as a TCNP is that polarity in networks and pathways is determined by the spatial organization, subcellular distribution, dynamic behavior, interactions and functions of specific molecules within the cell. To investigate these relationships, we use a tripartite approach described as: :1) Measure - develop new tools for measuring spatially resolved dynamic behavior of molecules in cells, :2) Model - develop new methods for spatial modeling of biological systems. :3) Manipulate - develop new techniques for manipulating the spatial distribution of molecules in living cells. :Microscopy contrast enhancement protocol, biophotonics, subcellular :" . SCR:013657 a NLX:63400, owl:NamedIndividual ; @@ -106801,12 +106784,14 @@ SCR:013672 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SCR_014248", "SCR_015958" ; - rdfs:label "ZEN Digital Imaging for Light Microscopy" ; + rdfs:label "ZEISS ZEN Microscopy Software" ; NIFRID:synonym "ZEISS Efficient Navigation", "ZEISS Efficient Navigation (ZEN)", - "ZEN Blue" ; + "ZEN Blue", + "ZEN Digital Imaging for Light Microscopy", + "ZEN Microscopy Software" ; NIFRID:abbrev "ZEN" ; - definition: "User interface software for Carl Zeiss light microscopy imaging systems. After selecting a fluorophore, ZEN applies the necessary settings to collect and organize data." . + definition: "User interface software for Carl Zeiss light microscopy imaging systems. ZEN is the universal user interface you will see on every imaging system from ZEISS. After selecting fluorophore, ZEN applies the necessary settings to collect and organize data." . SCR:013673 a NLX:63400, owl:NamedIndividual ; @@ -107036,9 +107021,7 @@ SCR:013715 a NLX:63400, "Image Studio Lite version 3.1", "LI-COR Image Studio Lite Software", "LICOR Image Studio Lite Software" ; - definition: """Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. - -freeware for analyzing, quantifying, and exporting scanned using the LiCOR Odyssey infrared imaging system.""" . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2023. Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. Image Studio Lite has been discontinued and replaced with Empiria Studio Software." . SCR:013716 a NLX:63400, owl:NamedIndividual ; @@ -107487,8 +107470,8 @@ SCR:013793 a NLX:63400, SCR:013794 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "biotools:Metabolomics_Workbench" ; - rdfs:label "Metabolomics Workbench (MetWB)" ; - NIFRID:synonym "Metabolomics Workbench", + rdfs:label "Metabolomics Workbench" ; + NIFRID:synonym "Metabolomics Workbench (MetWB)", "MetWB", "UCSD Metabolomics Workbench" ; definition: "Repository for metabolomics data and metadata which provides analysis tools and access to various resources. NIH grantees may upload data and general users can search metabolomics database. Provides protocols for sample preparation and analysis, information about NIH Metabolomics Program, data sharing guidelines, funding opportunities, services offered by its Regional Comprehensive Metabolomics Resource Cores (RCMRC)s, and training workshops." . @@ -107835,8 +107818,9 @@ SCR:013861 a NLX:63400, SCR:013869 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "nif-0000-30108" ; rdfs:label "Cellosaurus" ; - definition: "Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, the NCI Thesaurus entry code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples." . + definition: "Database of all cell lines used in biomedical research which include immortalized cell lines, naturally immortal cell lines (stem cells), widely used and distributed finite life cell lines, vertebrate cell lines (majority being human, mouse, and rat), and invertebrate (insects and ticks) cell lines, as well as cell line synonyms. Each cell line is provided with the following information: the recommended name (the name which appears in the original publication), a list of synonyms, a unique accession number, comments on a number of topics including misspellings and gene transfection, information on the tissue/organ origin with the UBERON code, the NCI Thesaurus or Orphanet ORDO code for the disease(s) the individual suffered from (for cancer and human genetic disease lines only), the species of origin, the parent cell line, cross-references of sister cell lines, the sex of the individual, the category in which the cell line belongs (Adult stem cell; Cancer cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type), web links, publication references, and/or cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources, and to databases that list cell lines as samples." . SCR:013955 a NLX:63400, owl:NamedIndividual ; @@ -109517,8 +109501,10 @@ SCR:014289 a NLX:63400, SCR:014290 a NLX:63400, owl:NamedIndividual ; rdfs:label "GeneMapper " ; - NIFRID:synonym "GeneMapper Software" ; - definition: "A genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment." . + NIFRID:synonym "GeneMapper Software", + "GeneMapper Software 5", + "GeneMapper Software 6" ; + definition: "Genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems. GeneMapper specializes in multiapplication functionality, including amplified fragment length polymorphism, loss of heterozygosity, microsatellite, and SNP genotyping analysis. The software provides remote auto-analysis and command line operation, and allows for multiuser, client-server deployment." . SCR:014291 a NLX:63400, owl:NamedIndividual ; @@ -110993,7 +110979,7 @@ SCR:014586 a NLX:63400, "Brain Extraction Tool (BET)" ; NIFRID:abbrev "BET", "BET2" ; - definition: "A tool which deletes non-brain tissue from an image of the whole head and estimates both the internal and external skull surfaces." . + definition: "Software tool which deletes non-brain tissue from image of the whole head and estimates both internal and external skull surfaces." . SCR:014587 a NLX:63400, owl:NamedIndividual ; @@ -111238,11 +111224,12 @@ SCR:014626 a NLX:63400, SCR:014627 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "biotools:i-tasser" ; + oboInOwl:hasDbXref "biotools:i-tasser", + "SCR_018803" ; rdfs:label "I-TASSER" ; NIFRID:synonym "Iterative Threading ASSEmbly Refinement", "Iterative Threading Assembly Refinement" ; - definition: "Web server used to generate automated, full-length 3D protein structural and function predictions. Users can copy and paste sequences in FASTA format or upload the sequence from a file." . + definition: "Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation." . SCR:014628 a NLX:63400, owl:NamedIndividual ; @@ -112035,10 +112022,10 @@ SCR:014772 a NLX:152342, rdfs:label "Radiometer" ; definition: "Commercial organizations which develops, manufactures, and sells solutions and equipment for blood sampling, blood gas analysis, transcutaneous monitoring, and IT management systems under certain brand names." . -SCR:014773 a NLX:152342, +SCR:014773 a NLX:152328, owl:NamedIndividual ; rdfs:label "EcoCyte Bioscience" ; - definition: "Supplier and servicer of products for experiments involving Xenopus laevis. Their products include laboratory equipment, media, and oocytes, and their services for pharmacological studies include heterologous expression and in vitro electrophysiology." . + definition: "Supplier and servicer of products for expression studies in Xenopus laevis oocytes. Products include overnight delivery of freshly prepared Xenopus laevis oocytes, Cell & Tissue Media necessary during preparation, maintenance, and recording of Xenopus oocytes and lab chemicals. Services for pharmacological studies include heterologous expression and in vitro electrophysiology." . SCR:014774 a NLX:152342, owl:NamedIndividual ; @@ -112201,7 +112188,7 @@ SCR:014807 a NLX:152342, rdfs:label "Diagenode" ; definition: "Commercial provider of equipment and resources for epigenetics research, biological sample preparation, and diagnostic assays. The products Diagenode provides include automation and semi-automation software, antibodies, reagents, kits, and shearing technologies." . -SCR:014808 a NLX:152328, +SCR:014808 a NLX:152342, owl:NamedIndividual ; oboInOwl:hasDbXref "grid.470425.0" ; rdfs:label "Sage Science" ; @@ -113523,11 +113510,13 @@ SCR:015017 a NLX:63400, SCR:015018 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "SCR_018408" ; rdfs:label "SourceData" ; NIFRID:synonym "Source Data", "source data", "sourcedata" ; - definition: "Platform for researchers and publishers that mines text from figures and figure legends in scientific papers in a machine-readable manner. The main goal of SourceData is to make scientific papers discoverable based on data content, to enable researchers to find specific data, to test or generate new hypotheses, and to share and connect data." . + definition: """Software semantic platform for curating and searching figures. Allows to share scientific figures and underlying data in way that is machine readable and findable. Platform for researchers and publishers to make their papers discoverable based on their data content. +Used to make scientific papers discoverable based on data content, to enable researchers to find specific data, to test or generate new hypotheses, and to share and connect data. Openly accessible and easily applicable data discovery tool as initiative by EMBO.""" . SCR:015019 a NLX:63400, owl:NamedIndividual ; @@ -113992,11 +113981,6 @@ SCR:015104 a NLX:63400, rdfs:label " University of California San Francisco Diabetes Research Center Lentiviral RNAi Core " ; definition: "Core that provides reagents, equipment, training, supervision, and monitoring of investigators wishing to ensure the proper compliance with biosafety containment required for lentiviral-based research, lentiviral preparation services for investigators, and education on RNAi experimentation, through the lentiviral core website, and through protocols available at the facility." . -SCR:015105 a NLX:63400, - owl:NamedIndividual ; - rdfs:label " University of California San Francisco Diabetes Research Center Cytometry and Cell Sorting Core " ; - definition: "Core that assists investigators whose research requires molecular marker characterization of cells in suspension as well as the isolation of cells based on those markers. Experts in the core perform advanced cell sorting and cytometric analyses." . - SCR:015106 a NLX:63400, owl:NamedIndividual ; rdfs:label " University of California San Francisco Diabetes Research Center Islet Production Core " ; @@ -115331,11 +115315,6 @@ SCR:015365 a NLX:63400, rdfs:label " MMPC-University of Massachusetts Medical School Analytical Core " ; definition: "Core that provides analysis of hormones, cytokines, chemokines, metabolites, and electrolytes across multiple platforms (serum, tissues, homogenates, and cells) as well as liver function analysis through instrumentation." . -SCR:015366 a NLX:63400, - owl:NamedIndividual ; - rdfs:label " MMPC-University of Massachusetts Medical School " ; - definition: "Research center which provides various research techniques for investigating mouse models of human disease to advance medical and biological research by providing the scientific community with comprehensive, standardized, and high quality metabolic phenotyping services for mouse models of diabetes, diabetic complications, obesity and related disorders." . - SCR:015367 a NLX:63400, owl:NamedIndividual ; rdfs:label " MMPC-University of Cincinnati Medical Center " ; @@ -117842,9 +117821,10 @@ SCR:015820 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "SCR_017266" ; rdfs:label "BICCN" ; - NIFRID:synonym "BRAIN Initiative Cell Census Network", + NIFRID:synonym "BICCN 2.0", + "BRAIN Initiative Cell Census Network", "BRAIN Initiative Cell Census Network (BICCN)" ; - definition: "Consortium for the cell census in the brain. It is funded by the BRAIN Initiative Cell Census Network (BICCN) grants." . + definition: "Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains." . SCR:015821 a NLX:63400, owl:NamedIndividual ; @@ -120697,14 +120677,6 @@ SCR:016326 a NLX:63400, rdfs:label "ANNOgesic" ; definition: "Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data." . -SCR:016327 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_643", - "SCR_017847" ; - rdfs:label "Rockefeller University Antibody and Bioresource Core Facility" ; - NIFRID:synonym "Antibody and Bioresource Core Facility" ; - definition: "Core used to develop custom monoclonal antibodies and obtain large scale quantities of existing ones for experiments. Core provides cell line distribution service and tests samples for mycoplasma contamination." . - SCR:016328 a NLX:63400, owl:NamedIndividual ; rdfs:label "The Pancreatic Beta-Cell Consortium" ; @@ -120980,28 +120952,37 @@ SCR:016376 a NLX:63400, SCR:016377 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_iSeq 100", + "SCR_020125" ; rdfs:label "Illumina iSeq 100 Sequencing System" ; NIFRID:synonym "iSeq100", "iSeq 100" ; - definition: "Next-generation sequencer. Designed for simplicity. Allows labs of all sizes to sequence DNA and RNA." . + definition: "Benchtop next-generation sequencer to sequence DNA and RNA." . SCR:016378 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_MiniSeq", + "SCR_020136" ; rdfs:label "Illumina MiniSeq System" ; - NIFRID:synonym "MiniSeq" ; - definition: "The MiniSeq System delivers the power and confidence of proven Illumina next-generation sequencing (NGS) technology in an accessible sequencing solution. It features cost-efficient sequencing, even for low numbers of samples. Its streamlined workflow enables rapid sequencing of both DNA and RNA. The small footprint allows it to fit seamlessly into laboratories, with no need for specialized, ancillary equipment." . + NIFRID:synonym "MiniSeq", + "MiniSeq System" ; + definition: "MiniSeq System to perform range of targeted DNA and RNA applications for low numbers of samples." . SCR:016379 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_MiSeq", + "SCR_020134" ; rdfs:label "Illumina MiSeq System" ; NIFRID:synonym "MiSeq" ; - definition: "The MiSeq System facilitates your research with a wide range of sequencing applications. It is capable of automated paired-end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits that it uses are optimized for a variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics, and more." . + definition: "MiSeq System offers wide range of sequencing applications. Capable of automated paired end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits are optimized for variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics." . SCR:016380 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_MiSeqDx", + "SCR_020137" ; rdfs:label "Illumina MiSeqDx System" ; NIFRID:synonym "MiSeqDx" ; - definition: "Leverage the power of next-generation sequencing (NGS) in your clinical laboratory. The MiSeqDx System is the first FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing." . + definition: "MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes." . SCR:016381 a NLX:63400, owl:NamedIndividual ; @@ -121012,19 +120993,26 @@ SCR:016381 a NLX:63400, SCR:016382 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Illumina MiSeq FGx Forensic Genomics System" ; + oboInOwl:hasDbXref "Model_Number_MiSeq FGx", + "SCR_020133" ; + rdfs:label "Illumina MiSeq FGx System" ; NIFRID:synonym "MiSeq FGx", - "MiSeq FGx Forensic Genomics" ; - definition: "The MiSeq FGx Forensic Genomics System is the first fully validated, next-generation sequencing (NGS) solution designed for forensic science. Dedicated library kits and analytical software take you from DNA-to-answer with streamlined efficiency." . + "MiSeq FGx Forensic Genomics", + "MiSeq FGx Forensic Genomics System" ; + definition: "MiSeq FGx Forensic Genomics System is the first fully validated, next-generation sequencing (NGS) solution designed for forensic science. Dedicated library kits and analytical software take you from DNA-to-answer with streamlined efficiency." . SCR:016383 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_HiSeq 2500", + "SCR_020123" ; rdfs:label "Illumina HiSeq 2500 System" ; NIFRID:synonym "HiSeq 2500" ; - definition: "High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023." . SCR:016384 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_NextSeq 550Dx", + "SCR_020138" ; rdfs:label "Illumina NextSeq 550Dx System" ; NIFRID:synonym "NextSeq 550Dx", "NextSeq 550Dx System" ; @@ -121032,14 +121020,17 @@ SCR:016384 a NLX:63400, SCR:016385 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Illumina HiSeq X Ten" ; - NIFRID:synonym "HiSeq X", - "HiSeq X Ten" ; - definition: "Sequencer machine for whole-genome sequencing (WGS). The system consists of a set of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year." . + oboInOwl:hasDbXref "Model_Number_HiSeq X", + "SCR_020131" ; + rdfs:label "Illumina HiSeq X" ; + NIFRID:synonym "HiSeq X" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year." . SCR:016386 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Illumina HiSeq 3000/HiSeq 4000 System" ; + oboInOwl:hasDbXref "Model_Number_HiSeq 3000/4000", + "SCR_020127" ; + rdfs:label "Illumina HiSeq 3000/HiSeq 4000 Sequencing System" ; NIFRID:synonym "HiSeq 3000", "HiSeq 3000/4000", "HiSeq 4000" ; @@ -122035,7 +122026,7 @@ SCR:016552 a NLX:63400, owl:NamedIndividual ; rdfs:label "iMITS" ; NIFRID:synonym "international Micro Injection Tracking System" ; - definition: "Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products." . + definition: "This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products." . SCR:016553 a NLX:63400, owl:NamedIndividual ; @@ -122747,6 +122738,7 @@ SCR:016672 a NLX:63400, SCR:016673 a "Research", owl:NamedIndividual ; rdfs:label "Open Data Commons for Spinal Cord Injury" ; + NIFRID:synonym "Open Data Commons at UCSD FDI Lab" ; NIFRID:abbrev "ODC-SCI", "odc-sci" ; definition: "Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research." . @@ -124245,8 +124237,10 @@ SCR:016996 a NLX:63400, SCR:016999 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Linnarsson lab Mouse Brain Atlas" ; - definition: "Single cell gene expression atlas of mouse nervous system." . + oboInOwl:hasDbXref "SCR_018356" ; + rdfs:label "mousebrain.org" ; + NIFRID:synonym "Linnarsson lab Mouse Brain Atlas" ; + definition: "Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system." . SCR:017000 a NLX:63400, owl:NamedIndividual ; @@ -124502,7 +124496,8 @@ SCR:017041 a NLX:63400, owl:NamedIndividual ; rdfs:label "SPARC Project" ; NIFRID:synonym "SPARC Portal", - "SPARC Repository" ; + "SPARC Repository", + "Stimulating Peripheral Activity to Relieve Conditions" ; NIFRID:abbrev "SPARC.science" ; definition: "The SPARC data repository as of 2023 is an open data repository developed as part of the NIH SPARC initiative and has been used by SPARC funded investigator groups to curate and publish high quality datasets related to the autonomic nervous system. We are thrilled that as of August 2022, SPARC is accepting datasets from investigators that are not funded through the NIH SPARC program. The NIH's Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) program aims to transform our understanding of these nerve-organ interactions and ultimately advance neuromodulation field toward precise treatment of diseases and conditions for which conventional therapies fall short." . @@ -125057,7 +125052,10 @@ SCR:017141 a NLX:63400, SCR:017142 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Ultima In Vitro Multiphoton Microscope System" ; + oboInOwl:hasDbXref "Model_Number_Ultima_In_Vitro", + "SCR_019800" ; + rdfs:label "Bruker Ultima In Vitro Multiphoton Microscope System" ; + NIFRID:synonym "Bruker Ultima In Vitro Multiphoton Microscope" ; definition: "Fluorescence microscopy system by Bruker. Multiphoton imaging system for intravital imaging applications in neuroscience, oncology and immunology using Bruker Prairie View software to provide turnkey operation for imaging as well as synchronizing Ultima system with external stimulus and experimental control devices." . SCR:017143 a NLX:63400, @@ -125147,15 +125145,6 @@ SCR:017154 a owl:NamedIndividual ; "University of Cambridge" ; definition: "Provides assistance in characterization and analysis of genomic variants, next generation sequencing data processing and analysis, computational systems biology, HPC and big data software development for genome scale data analysis, machine learning and data mining, cloud based solutions to process and manage large amounts of data, databases and genome scale data visualization." . -SCR:017155 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_769", - "SCR_017894" ; - rdfs:label "Massachusetts Institute of Technology Koch Institute Bioinformatics and Computing Core Facility" ; - NIFRID:synonym "Barbara K. Ostrom Bioinformatics Facility", - "The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility" ; - definition: "Core provides support, assistance and training in wide range of bioinformatics topics. Maintains high-performance computing resource offering many bioinformatics applications, substantial processing power and secure storage. Provides support for desktop computing and poster printing. Services include Data Analysis, Software Support (access to proprietary bioinformatics resources Ingenuity Pathway Analysis and GeneGO MetaCore, Training sessions covering various bioinformatics topics, Linux compute cluster, data storage." . - SCR:017156 a NLX:152328, owl:NamedIndividual ; oboInOwl:hasDbXref "grid.13648.38", @@ -125588,8 +125577,10 @@ SCR:017205 a NLX:63400, SCR:017206 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_2565CA", + "SCR_019384" ; rdfs:label "Agilent G2565CA Microarray Scanner" ; - definition: "Part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays." . + definition: "Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays." . SCR:017207 a NLX:63400, owl:NamedIndividual ; @@ -125952,7 +125943,7 @@ SCR:017272 a NLX:63400, "DOI:10.35077" ; rdfs:label "Brain Image Library" ; NIFRID:abbrev "BIL" ; - definition: "Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University." . + definition: "Repository for confocal microscopy brain imaging data. Data archives that have been established by BRAIN Initiative Data Sharing. National public resource enabling researchers to deposit, analyze, mine, share and interact with large brain image datasets. Operated as partnership between Biomedical Applications Group at Pittsburgh Supercomputing Center, Center for Biological Imaging at University of Pittsburgh and Molecular Biosensor and Imaging Center at Carnegie Mellon University. Provides persistent centralized repository for brain microscopy data." . SCR:017273 a NLX:63400, owl:NamedIndividual ; @@ -126197,8 +126188,11 @@ SCR:017318 a NLX:63400, SCR:017319 a NLX:63400, owl:NamedIndividual ; rdfs:label "Biomethane Potential Test" ; - NIFRID:synonym "Biomethane Potential Test System" ; - NIFRID:abbrev "BMP", + NIFRID:synonym "Automatic Methane Potential Test System", + "Automatic Methane Potential Test System (AMPTS) II", + "Biomethane Potential Test System" ; + NIFRID:abbrev "AMPTS", + "BMP", "BMP Test" ; definition: "Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry." . @@ -126217,9 +126211,11 @@ SCR:017321 a NLX:63400, SCR:017322 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "SCR_019005" ; rdfs:label "TissueMaker" ; - NIFRID:synonym "TissueMakerTM" ; - definition: "Software for generation of high resolution 3D volume reconstructions from serial sections imaged with whole slide scanners and research microscopes by MBF Bioscience. Used to assist with cell mapping, cytoarchitectonics and other areas to create comprehensive anatomical reference." . + NIFRID:synonym "MBF Bioscience TissueMaker", + "TissueMakerTM" ; + definition: "Software tool to automatically align serial sections and visualize entire 3D organ. Generates full resolution 3D reconstructions from serial sections imaged with whole slide scanners and research microscopes. Used to assist with cell mapping, cytoarchitectonics, and other measures that require visualizing neuronal circuitry to create comprehensive anatomical reference." . SCR:017323 a NLX:63400, owl:NamedIndividual ; @@ -126623,7 +126619,7 @@ SCR:017386 a "Software", SCR:017387 a NLX:63400, owl:NamedIndividual ; rdfs:label "SSA-II sperm analysis system" ; - definition: "System developed under guidance of experts in reproduction and andrology from Andrological Branch of Chinese Medical Association and Research Institute of National Health Planning Commission. Designed according to standard of 5th edition of World Health Organization laboratory manual for examination and processing of human semen." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 1, 2023. System developed under guidance of experts in reproduction and andrology from Andrological Branch of Chinese Medical Association and Research Institute of National Health Planning Commission. Designed according to standard of 5th edition of World Health Organization laboratory manual for examination and processing of human semen." . SCR:017388 a NLX:63400, owl:NamedIndividual ; @@ -127991,10 +127987,13 @@ SCR:017636 a NLX:63400, SCR:017637 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "biotools:structure" ; + oboInOwl:hasDbXref "biotools:structure", + "SCR_002151", + "SCR_021634" ; rdfs:label "STRUCTURE" ; - NIFRID:synonym "Structure software" ; - definition: "Software tool to perform analysis for population genetics. Software package for using multi locus genotype data to investigate population structure. Its uses include inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs." . + NIFRID:synonym "Structure", + "structure" ; + definition: "Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms." . SCR:017638 a NLX:63400, owl:NamedIndividual ; @@ -128135,9 +128134,9 @@ SCR:017660 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "biotools:pybel" ; rdfs:label "PyBEL" ; - NIFRID:synonym "Python Biological Expression Language" ; - definition: """Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language. -Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language.""" . + NIFRID:synonym "pybel", + "Python Biological Expression Language" ; + definition: "Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J." . SCR:017661 a NLX:63400, owl:NamedIndividual ; @@ -128331,14 +128330,6 @@ SCR:017691 a NLX:63400, NIFRID:abbrev "ABCF" ; definition: "ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University." . -SCR:017692 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_105", - "SCR_017713" ; - rdfs:label "NYU School of Medicine Rodent Genetic Engineering Laboratory Core Facility" ; - NIFRID:synonym "NYU Langone Rodent Genetic Engineering Laboratory" ; - definition: "Core to apply advanced molecular genetic techniques in rodent models of physiology and disease. Generates novel mutant mouse strains by using gene targeting in embryonic stem cells (ESCs) and by developing novel methods of modifying rodent genomes and assaying genetically modified cells in vivo.Offers sperm and embryo cryopreservation and storage technologies for strain preservation and recovery." . - SCR:017693 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_111", @@ -128916,11 +128907,12 @@ SCR:017769 a NLX:63400, SCR:017770 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_311", - "ABRF_726" ; + "ABRF_726", + "SCR_017884" ; rdfs:label "Northwestern University Center for Atom Probe Tomography Core Facility" ; NIFRID:synonym "Northwestern University Center for Atom-Probe Tomography" ; NIFRID:abbrev "NUCAPT" ; - definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 26,2023.Facility specializes in high resolution chemical imaging by three dimensional atom probe tomography. APT used to study nano- or nanostructured materials." . + definition: "Facility specializes in high resolution chemical imaging by three dimensional atom probe tomography. APT produces three-dimensional (3D) atom-by-atom elementally and isotopically resolved image with sub-nanometer spatial resolution of sample volume typically 100 x 100 x 300 nm^3, by simultaneous high resolution direct-space imaging and atom-by-atom time of flight mass spectrometry. APT is particularly suited to study nano- or nanostructured materials." . SCR:017771 a NLX:63400, owl:NamedIndividual ; @@ -128985,10 +128977,12 @@ SCR:017778 a NLX:63400, SCR:017779 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_329" ; - rdfs:label "Northwestern University Macro/Nano Fabrication Core Facility" ; - NIFRID:synonym "Northwestern University micro/nano fabrication facility" ; + rdfs:label "Northwestern University Micro/Nano Fabrication Core Facility" ; + NIFRID:synonym "Micro/nano fabrication facility", + "Northwestern University micro/nano fabrication facility", + "NUFAB Northwestern University micro/nano fabrication facility" ; NIFRID:abbrev "NUFAB" ; - definition: "Provides range of nanofabrication equipment and technical expertise. Supports research in all areas of science, engineering, medicine, and interdisciplinary fields." . + definition: "Central micro/nano fabrication facility of Northwestern University. Provides range of nanofabrication equipment and technical expertise. Supports research in all areas of science, engineering, medicine, and interdisciplinary fields." . SCR:017780 a NLX:63400, owl:NamedIndividual ; @@ -129488,7 +129482,8 @@ Lentivirus prep from shRNA and CRSPR constructs can be obtained from our Gene Th SCR:017847 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_643" ; + oboInOwl:hasDbXref "ABRF_643", + "SCR_016327" ; rdfs:label "Rockefeller University Antibody and Bioresource Core Facility" ; NIFRID:synonym "Antibody and Bioresource Core Facility" ; definition: "Core used to develop custom monoclonal antibodies and obtain large scale quantities of existing ones for experiments. Core provides cell line distribution service and tests samples for mycoplasma contamination." . @@ -129742,13 +129737,6 @@ SCR:017879 a NLX:63400, NIFRID:abbrev "NU-HTA" ; definition: "Core provides expertise and resources for large scale biology. Helps to set up, run, gather data and perform analysis in drug discovery research, biochemistry, cell and organismal biology, functional genomic screening, and synthetic genetic. Works with proteins, nucleic acids, small model organisms, and microbial strains. Provides tissue culture,produces and uses lentivirus particles, screens compound libraries, does experiments for investigators,generates preliminary data to figure out if idea is workable, discusses project development. Services include Macromolecular binding, biochemical, and cell-based assays,High content screening with widefield or confocal optics,Nanoliter liquid handling up to 1536-well density,Whole-plate kinetic assays (ion currents, GPCR signaling),Compound library screening,CRISPR/Cas9 screening (multiplexed libraries),Analysis of large data sets,Fluorescence Thermal Shift assay (measures protein melting),Complex liquid handling work flows." . -SCR:017880 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_738" ; - rdfs:label "Northwestern University Proteomics Core Facility" ; - NIFRID:synonym "Northwestern Proteomics" ; - definition: "Core offers multiple types of experiments from simple protein identification to protein quantitation (both relative and absolute), performs both traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Core proteomics specialists help guide your project to completion." . - SCR:017881 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_737" ; @@ -129777,12 +129765,12 @@ SCR:017884 a NLX:63400, rdfs:label "Northwestern University Center for Atom Probe Tomography Core Facility" ; NIFRID:synonym "Northwestern University Center for Atom-Probe Tomography" ; NIFRID:abbrev "NUCAPT" ; - definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 26,2023.Core specializes in high-resolution chemical imaging by three-dimensional atom-probe tomography (APT). APT produces three-dimensional (3D) atom-by-atom elementally and isotopically resolved image with sub-nanometer spatial resolution of sample volume typically 100 x 100 x 300 nm^3, by simultaneous high resolution direct-space imaging and atom-by-atom time of flight mass spectrometry. APT is particularly suited to study nano- or nanostructured materials." . + definition: "Facility specializes in high resolution chemical imaging by three dimensional atom probe tomography. APT produces three-dimensional (3D) atom-by-atom elementally and isotopically resolved image with sub-nanometer spatial resolution of sample volume typically 100 x 100 x 300 nm^3, by simultaneous high resolution direct-space imaging and atom-by-atom time of flight mass spectrometry. APT is particularly suited to study nano- or nanostructured materials." . SCR:017885 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_748" ; - rdfs:label "New England University Histology and Imaging Core Facility" ; + rdfs:label "University of New England COBRE Histology and Imaging Core Facility" ; NIFRID:synonym "Histology and Imaging Core" ; definition: "Core provides access to expertise, training and specialized instrumentation related to tissue processing, sectioning, staining, immunohistochemistry and microscopy. Offers services and training related to image analysis and image analysis software to guide investigators in choosing best methods for presenting their data.Services include Trimming of wet tissues,Tissue processing into paraffin, OCT and paraffin embedding, Sectioning of paraffin-embedded/frozen tissues, Routine and special histochemical staining, Immunohistochemistry/Immunofluorescence, Antibody optimization, Brightfield/ widefield/ confocal microscopy, Image capture and image analysis.Core has cryostats, microtomes and microscopes available for reservation." . @@ -129848,9 +129836,11 @@ SCR:017893 a NLX:63400, SCR:017894 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_769" ; + oboInOwl:hasDbXref "ABRF_769", + "SCR_017155" ; rdfs:label "Massachusetts Institute of Technology Koch Institute Bioinformatics and Computing Core Facility" ; - NIFRID:synonym "Barbara K. Ostrom (1978) Bioinformatics Facility" ; + NIFRID:synonym "Barbara K. Ostrom Bioinformatics Facility", + "The Barbara K. Ostrom (1978) Bioinformatics and Computing Facility" ; definition: "Core provides support, assistance and training in wide range of bioinformatics topics. Maintains high-performance computing resource offering many bioinformatics applications, substantial processing power and secure storage. Provides support for desktop computing and poster printing. Services include Data Analysis, Software Support (access to proprietary bioinformatics resources Ingenuity Pathway Analysis and GeneGO MetaCore, Training sessions covering various bioinformatics topics, Linux compute cluster, data storage." . SCR:017895 a NLX:63400, @@ -129972,10 +129962,12 @@ SCR:017910 a NLX:63400, SCR:017911 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_796" ; - rdfs:label "Iowa State University W M. Keck Metabolomics Research Laboratory Core Facility" ; - NIFRID:synonym "W. M. Keck Metabolomics Research Laboratory" ; - NIFRID:abbrev "MRL Facility" ; - definition: "Core services include non-targeted complete metabolite profiling,Targeted metabolite profiling,Mass spectrometry imaging, Direct sample analysis for small molecules with no or little sample preparation using DART-MS,Direct infusion,Consultation. Laboratory is equipped with two GC/MS instruments, HPLC system coupled to combination of different detectors, Capillary Electrophoresis System, and two LC/MS/MS instruments.Services for on Campus Users include Consultations for custom design and methods development to detect and quantify metabolite of interest (Instruments), Training to develop custom libraries with in-house libraries and NIST database,Instrument Training,Training in sample preparation,Protocols for metabolite extractions,Help with basic data analysis,Access to libraries and software for data analysis.Services for off Campus Users include Consultations regarding metabolomics experimental design, protocol and methods development for analysis of metabolite of interest, Training in sample preparation,Assistance with data acquisition and data analysis,Protocols for metabolite extractions,Access to libraries and software for data analysis." . + rdfs:label "Iowa State University W.M. Keck Metabolomics Research Laboratory Core Facility" ; + NIFRID:synonym "Iowa State University Metabolomics Research Laboratory", + "Iowa State University W.M. Keck Metabolomics Research Laboratory", + "W. M. Keck Metabolomics Research Laboratory" ; + NIFRID:abbrev "MRL" ; + definition: "Core facility that conducts fee for service mass spectrometry-based non-targeted and targeted metabolomic studies. The facility serves and partners with both on- and off-campus clients." . SCR:017912 a NLX:63400, owl:NamedIndividual ; @@ -130051,12 +130043,10 @@ SCR:017921 a NLX:63400, NIFRID:synonym "CRI Mouse Genome Engineering Core" ; definition: "Core provides production of mouse models to support fundamental and translational research. Provides transgenic, gene targeting,DNA microinjection services, CRISPR/Cas9 microinjection, ES cell manipulation and other microinjection services to generate transgenic mice, knock-in/knock-out mice and chimeric mice harboring select genetic mutations. Other services include mouse sperm cryopreservation and recovery, in vitro fertilization (IVF), rederivation of pathogen free mouse lines and derivation of mouse embryonic stem cell lines. Provides general consultations on experimental designs and vectors for gene modification-related projects, DNA preparation, recombinant ES clones, mouse genotyping, colony breeding and husbandry, customize services as requested to support development of animal models for modeling human diseases." . -SCR:017922 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_815" ; +SCR:017922 a owl:NamedIndividual ; rdfs:label "Florida State University X-Ray Crystallography Core Facility" ; - NIFRID:synonym "X-Ray Crystallography Facility" ; - definition: "Core is multi-user macromolecular x-ray crystallography facility (XRF). Provides instrument and expertise for collecting and processing x-ray diffraction data from macromolecular single crystals.Coordinates additional data collection at third generation synchrotron x-ray source using FSU membership in SER-CAT Beamline 22 in Advanced Photon Source in Argonne National Laboratory, Argonne, IL. XRF also offers Protein Crystal Screening Service to users." . + NIFRID:abbrev "XRF" ; + definition: "Shared macromolecular x-ray crystallography facility provides instruments and expertise for screening, optimizing, imaging, growing, and storing crystals of biological macromolecules. Core coordinates single crystal x-ray diffraction data collection at third generation synchrotron x-ray source using FSU's membership at the National Synchrotron Light Source II at Brookhaven National Lab, Upton, NY. XRF also offers custom buffer preparation, optimization, and crystal set-up using multi-well format crystallization blocks and plates." . SCR:017923 a NLX:63400, owl:NamedIndividual ; @@ -130075,11 +130065,15 @@ SCR:017924 a NLX:63400, SCR:017925 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_822" ; - rdfs:label "New York University School of Medicine Langone Health Rodent Genetic Engineering Laboratory Core Facility" ; + oboInOwl:hasDbXref "ABRF_105", + "ABRF_822", + "SCR_017692", + "SCR_017713" ; + rdfs:label "NYU School of Medicine Rodent Genetic Engineering Laboratory Core Facility" ; NIFRID:synonym "New York University School of Medicine Langone Health Rodent Genetic Engineering Laboratory", + "New York University School of Medicine Langone Health Rodent Genetic Engineering Laboratory Core Facility", "Rodent Genetic Engineering Laboratory" ; - definition: "Core to apply advanced molecular genetic techniques in rodent models. Experienced at generating novel mutant mouse strains by using gene targeting in embryonic stem cells (ESCs) and by developing novel methods of modifying rodent genomes and assaying genetically modified cells in vivo. Customizes technologies to meet individual project needs, including specialized expertise in use clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) systems and other approaches for direct genome editing in vivo.Services include CRISPR/Cas9,proprietary rapid strain-creation method known as EZ-Mouse Model, tetraploid complementation systems, GEMMs-ESC Speedy Models, regulated gene expression by high-throughput RNA interference assay in mice, safe-harbor knock-in gene editing using Rosa26 and other loci, recombinase-mediated cassette exchange, Inducible Tet-On and Tet-Off Gene Expression Systems, homologous recombination, induced pluripotent stem cells, assisted reproductive technologies, and vitrification systems,production of transgenic mice by pronuclear injection of plasmid DNA or bacterial artificial chromosome DNA and the production of ESC chimeras by blastocyst injection. Production of fully ESC-derived mice by tetraploid complementation, including following, isolating, and manipulating novel ESC lines from existing mouse strains.Offers sperm and embryo cryopreservation and storage technologies for strain preservation and recovery. Highly efficient in vitro fertilization technologies using fresh or cryopreserved sperm are available, facilitating import of novel mouse strains without quarantine and recovery of poorly breeding strains.Offers traditional embryo rederivation technologies for animal import into barrier vivaria through quarantine." . + definition: "Core to apply advanced molecular genetic techniques in rodent models of physiology and disease. Generates novel mutant mouse strains by using gene targeting in embryonic stem cells (ESCs) and by developing novel methods of modifying rodent genomes and assaying genetically modified cells in vivo.Offers sperm and embryo cryopreservation and storage technologies for strain preservation and recovery." . SCR:017926 a NLX:63400, owl:NamedIndividual ; @@ -130109,10 +130103,15 @@ Services include tissue preparation, processing, and sectioning, as well as hist SCR:017929 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_824" ; + oboInOwl:hasDbXref "ABRF_824", + "SciEx_41", + "SCR_012514" ; rdfs:label "New York University School of Medicine Langone Health Genome Technology Center Core Facility" ; - NIFRID:synonym "New York University School of Medicine Langone Health Genome Technology Center", + NIFRID:synonym "New York University School of Medicine Genome Technology Center", + "New York University School of Medicine Langone Health Genome Technology Center", "NYU Langone's Genome Technology Center" ; + NIFRID:abbrev "GTC", + "NYU GTC" ; definition: "Core provides range of services related to genome, epigenome, and transcriptome analysis. Offers technologies including Illumina deep sequencing and sample preparation for variety of applications, including DNA and RNA sequencing (DNA- and RNA-seq), exome sequencing, targeted capture, chromatin immunoprecipitation sequencing (ChIP-seq), methylation sequencing (Methyl-seq), metagenomics, and many others;Automation of Illumina library and targeted capture preps, including 16S ribosomal RNA (rRNA) sequencing;Oxford Nanopore sequencing (long reads);Bio-Rad Droplet Digita polymerase chain reaction (PCR);Nanostring nCounter;Single-cell RNA- and DNA-seq using the C1 Auto Prep System from Fluidigm, and 10x Genomics Chromium System.Provides expertise on strategies to achieve research goals in any field related to genomics, and can tailor bioinformatics analysis to individual project. If you supply us with nucleic acids, we can perform every step required to help you achieve your desired results." . SCR:017930 a NLX:63400, @@ -130224,16 +130223,19 @@ SCR:017943 a NLX:63400, SCR:017944 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_940" ; - rdfs:label "Northwestern University Micro/Nano Fabrication Facility" ; - NIFRID:synonym "Micro/nano fabrication facility" ; + rdfs:label "Northwestern University Micro/Nano Fabrication Core Facility" ; + NIFRID:synonym "Micro/nano fabrication facility", + "Northwestern University micro/nano fabrication facility" ; NIFRID:abbrev "NUFAB" ; - definition: "Facility provides nanofabrication equipment and technical expertise.Supports research in all areas of science, engineering, medicine, and interdisciplinary fields. Equipment is located in clean room with laminar airflow and includes 3D Optical Profiler Zygo,Atomic Force Microscope Bruker Edge,Contact Angle Measurement VCA Optima XE,Electrical Test Station,Microscope Nikon LV150,Reflectometer Filmetrics F20,Spectroscopic Ellipsometer J.A. Woollam alpha-SE,Stylus Profilometer Veeco Dektak-8,Atomic Layer Deposition Arradiance GEMStar XT-P,E-beam Evaporator AJA,Parylene Coater SCS Labcoter2 Parylene Deposition System,Plasma Enhanced Chemical Vapor Deposition (PECVD) STS LpX CVD,Sputter I AJA Orion,Sputter II AJA Orion,Thermal Evaporator, Denton Vacuum Explorer 14,ETCHING ASHING,Deep Reactive Ion Etcher (DRIE) ,STS LpX Pegasus,Plasma Cleaner ,Samco PC-300,Reactive Ion Etcher (RIE) ,Samco RIE-10NR,Xenon Difluoride Etcher ,Xactix,Furnace ,Tystar,Rapid Thermal Processor ,AW-610,Laser Cutter, LPKF ProtoLaser R,Wire Bonder -Ball- iBond5000,Wire Bonder ,Wedge West Bond 747677E,Convection Ovens Blue M DCC-146-C-ST35,Mask Aligner ,Suss MABA6,Mask Aligner ,Suss MJB4,Maskless Aligner , Heidelberg MLA150,Maskless Aligner ,Heidelberg uPG501,Microscope Nikon LV150,Polyimide/SU8 Hood,Spinner Hood,Ultraviolet Flood Exposure System , Inpro Technologies F300S,Vacuum Oven,Acid Hoods,Critical Point Dryer ,Tousimis Automegasamdri 915B, Series C,Ultrasonic and Megasonic Cleaners." . + definition: "Central micro/nano fabrication facility of Northwestern University. Provides range of nanofabrication equipment and technical expertise. Supports research in all areas of science, engineering, medicine, and interdisciplinary fields." . SCR:017945 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_944" ; - rdfs:label "Northwestern University Proteomics Center of Excellence Core Facility" ; - NIFRID:synonym "Northwestern Proteomics" ; + oboInOwl:hasDbXref "ABRF_944", + "SCR_017880" ; + rdfs:label "Northwestern University Proteomics Core Facility" ; + NIFRID:synonym "Northwestern Proteomics", + "Northwestern University Proteomics Center of Excellence Core Facility" ; definition: "Core offers multiple types of experiments from simple protein identification to protein quantitation. Performs traditional bottom-up proteomics, where proteins are digested with enzyme prior to analysis and intact, top-down proteomics analyses. Services include proteins identification after in-gel or in-solution digestion, top-down mass spectrometry to preserve post-translationally modified forms of proteins present in vivo by measuring them intact, IP-MS Pulldown,BioID service to identify target of biotin ligase that has been tagged onto their protein via traditional cloning methods,Untargeted Quantitative Peptide Proteomics,Targeted Quantitative Peptide Proteomics,Epiproteomic Histone Modification Panel A,Epiproteomic Histone Modification Panel B,Untargeted Metabolomics,Phosphoproteomics,PTM Scan,ChIP-MS." . SCR:017946 a NLX:63400, @@ -130375,7 +130377,7 @@ SCR:017964 a NLX:152328, "grid.4367.6", "ISNI:0000 0001 2355 7002", "Wikidata:Q777403" ; - rdfs:label "Washington University in St. Louis" ; + rdfs:label "Washington University in St. Louis; Missouri; USA" ; NIFRID:abbrev "WashU" ; definition: "Private research university in Greater St. Louis with its main campus mostly in unincorporated St. Louis County, Missouri and Clayton, Missouri." . @@ -130765,11 +130767,12 @@ SCR:018028 a NLX:63400, SCR:018029 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_212" ; - rdfs:label "Bruker BioSpin Gel Logic 212 PRO" ; - NIFRID:synonym "CareStream Gel Pro 212 Imager", + oboInOwl:hasDbXref "SCR_018601" ; + rdfs:label "Carestream Gel Logic 212 PRO Imaging System" ; + NIFRID:synonym "Bruker BioSpin Gel Logic 212 PRO", + "Carestream Gel Pro 212 Imager", "Gel Logic 212 PRO" ; - definition: "Fully automated laboratory preparation system that images fluorescence or colorimetric data in sample formats such as gels (DNA, Coomassie, Silver stain), membranes, and 96 well plates. Features include autofocusing and directed autoexposure." . + definition: "Automated gel imaging system for imaging fluorescence or colorimetric data in sample formats such as gels (DNA/Coomassie/Silver stain) membranes, and 96 well plates. Features include autofocusing and directed autoexposure." . SCR:018030 a NLX:63400, owl:NamedIndividual ; @@ -130782,7 +130785,8 @@ SCR:018031 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_840" ; rdfs:label "Molecular Dynamics Storm 840 Molecular Imager" ; - NIFRID:synonym "Storm 840 Molecular Imager", + NIFRID:synonym "Molecular Dynamics Storm 840 Phosphorimager Scanner", + "Storm 840 Molecular Imager", "Storm Gel and Blot Imaging System" ; definition: "Molecular imager system for performing gel and blot analysis. This system provides both PhosphorImager capabilities along with non-radioactive fluorescent labeling techniques-direct fluorescence and chemifluorescence. It can be used for non-radioactive gel and blot analysis methods or radioisotope techniques. Storm 840 scans storage phosphor screens plus fluorescent gels and chemifluorescent blots in the 35 x 43 cm scanning area." . @@ -130878,11 +130882,12 @@ SCR:018043 a NLX:63400, SCR:018044 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_3000" ; + oboInOwl:hasDbXref "Model_Number_3000", + "SCR_019676" ; rdfs:label "Biacore 3000 Real Time Biomolecular Interaction Analyzer" ; NIFRID:synonym "BIACORE 3000 GOLDSEAL", "BiaCore 3000 Surface Plasmon Resonance" ; - definition: "Label free system that performs detailed studies of biomolecular interactions. System delivers comprehensive characterization of interaction, answers questions about rate constants, affinity, specificity, and determines active concentration of components. Ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes system highly applicable to fast identification of unknown interactants." . + definition: "Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants." . SCR:018045 a NLX:63400, owl:NamedIndividual ; @@ -130915,7 +130920,8 @@ SCR:018048 a NLX:63400, SCR:018049 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_4000B" ; + oboInOwl:hasDbXref "Model_Number_4000B", + "SCR_019955" ; rdfs:label "Molecular Devices GenePix 4000B Microarray Scanner" ; NIFRID:synonym "GenePix 4000B Scanner" ; definition: "Microarray scanner that performs genetic and compound analysis. Coupled with GenePix ProMicroarray Image Analysis Software and Acuity Microarray Informatics Software for acquisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells. Scanner flexibility allows to configure scanning and analysis of one slide or many, whether they are all alike or each is different. Slide loader accommodates low- and high-density, opaque, mirrored, or translucent, plastic or glass, commercial or homebrew slides." . @@ -130978,12 +130984,14 @@ SCR:018057 a NLX:63400, SCR:018058 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_AATI FemtoPulse" ; - rdfs:label "AATI FEMTO Pulse Fragment Analyzer" ; - NIFRID:synonym "AATI FemtoPulse", + oboInOwl:hasDbXref "Model_Number_Femto Pulse", + "SCR_019498" ; + rdfs:label "Agilent Femto Pulse System" ; + NIFRID:synonym "AATI FEMTO Pulse Fragment Analyzer", + "AATI FemtoPulse", "Advanced Analytical Technologies", "Inc. FEMTO Pulse Fragment Analyzer" ; - definition: "Fragment analyzer that provides pulsed field power supply which allows large molecular weight DNA fragments to be separated and nucleic acids detected into femtogram range. Ability to separate high molecular weight DNA up to 165 kb and detect nucleic acids down to 50 fg per uL input concentration makes system ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low concentration samples." . + definition: "Femto Pulse System separates large molecular weight DNA fragments and detects nucleic acids into femtogram range.Fragment analyzer that provides pulsed field power supply which allows large molecular weight DNA fragments to be separated and nucleic acids detected into femtogram range. Ability to separate high molecular weight DNA up to 165 kb and detect nucleic acids down to 50 fg per uL input concentration makes system ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low concentration samples." . SCR:018059 a NLX:63400, owl:NamedIndividual ; @@ -131772,11 +131780,18 @@ SCR:018203 a NLX:63400, SCR:018204 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_279" ; - rdfs:label "Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility" ; - NIFRID:synonym "McDonnell Genome Institute at Washington University in St. Louis", - "Missouri Sequencing Center" ; - definition: "GTAC offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users to ensure maximum data value. Full service facility, from hypothesis to publication." . + oboInOwl:hasDbXref "ABRF_279", + "SciEx_32" ; + rdfs:label "Washington University School of Medicine Genome Technology Access Center Core Facility" ; + NIFRID:synonym "Genome Technology Access Center", + "McDonnell Genome Institute Genome Technology Access Center", + "Washington University in St. Louis Genome Technology Access Center", + "Washington University in St. Louis McDonnell Genome Institute Genome Technology Access Center", + "Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility", + "Washington University School of Medicine McDonnell Genome Institute" ; + NIFRID:abbrev "GTAC", + "WUSTL GTAC" ; + definition: "GTAC offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms." . SCR:018205 a NLX:63400, owl:NamedIndividual ; @@ -131788,9 +131803,13 @@ SCR:018205 a NLX:63400, SCR:018206 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_1007" ; + oboInOwl:hasDbXref "ABRF_1007", + "SCR_015105" ; rdfs:label "University of California San Francisco Parnassus Flow Cytometry Core Facility" ; - NIFRID:synonym "UCSF Parnassus Flow CoLab" ; + NIFRID:synonym "UCSF Parnassus Flow CoLab", + "University of California San Francisco Diabetes Research Center Cytometry and Cell Sorting Core", + "University of California San Francisco Diabetes Research Center Parnassus Flow Cytometry CoLab" ; + NIFRID:abbrev "PFCC" ; definition: "Core assists investigators whose research requires molecular marker characterization of cells in suspension as well as isolation of cells based on those markers. Advanced cell sorting and cytometric analyses by Flow or Mass Cytometry are provided." . SCR:018207 a NLX:63400, @@ -131975,10 +131994,11 @@ SCR:018250 a NLX:63400, SCR:018251 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "SCR_018318" ; + oboInOwl:hasDbXref "SCR_018279", + "SCR_018318" ; rdfs:label "Global Initiative on Sharing All Influenza Data" ; NIFRID:abbrev "GISAID" ; - definition: "Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy." . + definition: "Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data." . SCR:018252 a NLX:63400, owl:NamedIndividual ; @@ -132107,11 +132127,7 @@ SCR:018268 a NLX:63400, oboInOwl:hasDbXref "ABRF_498" ; rdfs:label "Ohio University Genomics Core Facility" ; NIFRID:synonym "Ohio University Genomics Facility" ; - NIFRID:abbrev "OUGF" ; - definition: """Core provides equipment and services.Equipment available includes AB 3130xl Genetic Analyzer 16 capillary array,Nanodrop 1000 -Agilent 2100 Bioanalyzer, Agilent 3100 Off Gel Fractionator, Sage Science Pippin Prep, Aria Mx Real Time PCR machine, Illumina MiSeq, Ion Torrent PGM. Research services include DNA sequencing, fragment and microsatellite analysis, AFLP, SNP screening -RNA/DNA quantification, quality control, size distribution, RIN analysis, Protein fraction sizing and quanitification, QA/QC purified protein/antibodies, Low cell consumption two-color flow cytometry analysis, Isoelectric focusing prior to Mass Spec, DIGE analysis, or SDS-PAGE, Automated nucleic acid separation and size collection (90 bp to 1.5 kbp), Relative and Absolute qPCR quantification (SYBR, TaqMan probe), End-point PCR genotyping, fragment melt analysis, copy number determination. Provides Next-Generation Sequencing including total RNA, small RNA, exosome and rRNA-depleted RNAseq, SHAPE-seq, 5-end mapping, de novo genome sequencing and targeted DNA sequencing, ChIP-seq, Methyl-seq, Bioinformatic analysis of NGS data, Custom experimental design, optimization, and consulting. Educational services include Hands on training for any basic lab technique or service used at OUGF, -Classroom and research lab lectures and informational seminars, Class and small group tours of facility.""" . + definition: "Facility offers Next-Generation Sequencing services, Sanger sequencing, Fragment Analysis, qPCR, data analysis. Provided services include DNA sequencing, fragment analysis, RNA, DNA, protein and cell cytometry through various equipment." . SCR:018269 a NLX:63400, owl:NamedIndividual ; @@ -132133,11 +132149,13 @@ SCR:018270 a NLX:63400, SCR:018271 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_514" ; + oboInOwl:hasDbXref "ABRF_514", + "nif-0000-30014", + "SCR_002914" ; rdfs:label "Kendrick Labs Core Facility" ; NIFRID:synonym "Kendrick Labs", "Private Company - Kendrick Labs" ; - definition: "Contract Research Org. specializing in custom protein analysis.Services Provided include SDS PAGE analysis, Western Blotting, Mass Spectrometry, protein staining ( silver, coomassie)." . + definition: "Contract Research Org. specializing in custom protein analysis. Services Provided include SDS PAGE analysis, Western Blotting, Mass Spectrometry, protein staining ( silver,coomassie) for academia, federal institutions and industry." . SCR:018272 a NLX:63400, owl:NamedIndividual ; @@ -132187,9 +132205,9 @@ SCR:018278 a NLX:63400, SCR:018279 a NLX:63400, owl:NamedIndividual ; - rdfs:label "GISAID" ; - NIFRID:synonym "Global Initiative on Sharing All Influenza Data" ; - definition: "International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data." . + rdfs:label "Global Initiative on Sharing All Influenza Data" ; + NIFRID:abbrev "GISAID" ; + definition: "Portal to share hCoV-19 genome sequences. Collection of genome sequences and related clinical and epidemiological data associated with coronavirus hCoV-19. Global repository of SARS-CoV-2 genomes. Initiative involves public-private-partnerships between Freunde of GISAID and governments of Federal Republic of Germany, Singapore and United States of America, with support from private and corporate philanthropy.International database of hCoV-19 genome sequences and related clinical and epidemiological data. Resource for influenza and hCoV-19 data." . SCR:018280 a NLX:63400, owl:NamedIndividual ; @@ -132320,10 +132338,15 @@ SCR:018300 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_279" ; rdfs:label "Washington University School of Medicine Genome Technology Access Center Core Facility" ; - NIFRID:synonym "Washington University School of Medicine Genome Technology Access Center" ; - NIFRID:abbrev "GTAC" ; - definition: """Core provides Nextgen sequencing, Microarray, PCR and Bioinformatic services.Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. -NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms.""" . + NIFRID:synonym "Genome Technology Access Center", + "McDonnell Genome Institute Genome Technology Access Center", + "Washington University in St. Louis Genome Technology Access Center", + "Washington University in St. Louis McDonnell Genome Institute Genome Technology Access Center", + "Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility", + "Washington University School of Medicine McDonnell Genome Institute" ; + NIFRID:abbrev "GTAC", + "WUSTL GTAC" ; + definition: "GTAC offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms." . SCR:018301 a NLX:63400, owl:NamedIndividual ; @@ -132472,8 +132495,8 @@ SCR:018323 a NLX:63400, SCR:018324 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Compilor" ; - NIFRID:synonym "Complior Analyse" ; + rdfs:label "Complior Analyse" ; + NIFRID:synonym "Alam Medical Complior Analyse" ; definition: "System for arterial assessment and diagnosis by Alam Medical. Device measuring pulse wave velocity and central pressure analysis in single acquisition." . SCR:018325 a NLX:63400, @@ -132657,7 +132680,7 @@ SCR:018355 a NLX:63400, SCR:018356 a NLX:63400, owl:NamedIndividual ; rdfs:label "mousebrain.org" ; - definition: "Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more." . + definition: "Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system." . SCR:018358 a NLX:63400, owl:NamedIndividual ; @@ -132912,9 +132935,10 @@ SCR:018405 a NLX:63400, SCR:018406 a NLX:63400, owl:NamedIndividual ; - rdfs:label "RUMP" ; - NIFRID:synonym "Reproducible Untargeted Metabolomics data processing Pipeline" ; - definition: "Software tool as reproducible untargeted metabolomics data processing pipeline." . + rdfs:label "Nextflow4Metabolomics Suite" ; + NIFRID:synonym "Reproducible Untargeted Metabolomics Data Processing Workflow" ; + NIFRID:abbrev "N4M" ; + definition: "Computational workflows for reproducible untargeted metabolomics data processing pipeline." . SCR:018407 a owl:NamedIndividual ; rdfs:label "ImageJ" ; @@ -132922,8 +132946,9 @@ SCR:018407 a owl:NamedIndividual ; SCR:018408 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Source Data" ; - definition: "Software semantic platform for curating and searching figures. Allows to share scientific figures and underlying data in way that is machine readable and findable. Platform for researchers and publishers to make their papers discoverable based on their data content. Openly accessible and easily applicable data discovery tool as initiative by EMBO." . + rdfs:label "SourceData" ; + definition: """Software semantic platform for curating and searching figures. Allows to share scientific figures and underlying data in way that is machine readable and findable. Platform for researchers and publishers to make their papers discoverable based on their data content. +Used to make scientific papers discoverable based on data content, to enable researchers to find specific data, to test or generate new hypotheses, and to share and connect data. Openly accessible and easily applicable data discovery tool as initiative by EMBO.""" . SCR:018409 a NLX:63400, owl:NamedIndividual ; @@ -133063,27 +133088,35 @@ SCR:018432 a owl:NamedIndividual ; rdfs:label "ABI Voyager DE Pro MALDI-Mass Spectrometer" ; definition: "Benchtop MALDI TOF mass spectrometer that has linear and reflector analyzer. It is used to analyze organic and inorganic compounds, protein identification, synthetic peptide validation, and polymer analysis." . -SCR:018433 a owl:NamedIndividual ; +SCR:018433 a NLX:63400, + owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_3100", - "SCR_018442" ; + "SCR_018442", + "SCR_019388" ; rdfs:label "Agilent 3100 OFFGEL Fractionator" ; - definition: "Fractionator that performs isoelectric focusing of proteins or peptides in immobilized pH gradient IPG gel strips. It recovers sample components from liquid phase." . + definition: "Agilent 3100 OFFGEL Fractionator performs isoelectric focusing of proteins or peptides in immobilized pH gradient (IPG) gel strips." . SCR:018434 a owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_860", - "SCR_018451" ; + "SCR_018451", + "SCR_019570" ; rdfs:label "American Optical 860 Sliding Microtome" ; - definition: "Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns." . + definition: "THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome used for cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns." . -SCR:018435 a owl:NamedIndividual ; +SCR:018435 a NLX:63400, + owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_4200", - "SCR_018444" ; - rdfs:label "Agilent 4200 Tapestation Genetic Analyzer" ; + "SCR_018444", + "SCR_019398" ; + rdfs:label "Agilent 4200 TapeStation System" ; + NIFRID:synonym "Agilent 4200 Tapestation Genetic Analyzer" ; definition: "Benchtop genetic analyzer electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow." . -SCR:018436 a owl:NamedIndividual ; +SCR:018436 a NLX:63400, + owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_9700", - "SCR_018448" ; + "SCR_018448", + "SCR_019577" ; rdfs:label "Applied Biosystems GeneAmp 9700 PCR Thermocycler System" ; definition: "Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C." . @@ -133095,11 +133128,13 @@ SCR:018437 a NLX:63400, rdfs:label "API 5000 Triple Quadrupole Liquid Chromatography Mass Spectrometer System" ; definition: "Triple quadrupole liquid chromatography mass spectrometer for analysis of bioanalytical samples. It can be used for DMPK and ADME studies.API 5000 LC/MS/MS System delivers the lowest limits of detection for the most demanding DMPK and ADME studies." . -SCR:018438 a owl:NamedIndividual ; +SCR:018438 a NLX:63400, + owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_3500xl", - "SCR_018447" ; + "SCR_018447", + "SCR_019574" ; rdfs:label "Applied Biosystems 3500xl Genetic Analyzer" ; - definition: "Genetic analyzer that utilizes capillary electrophoresis for genetic analysis. It has capillary lengths of 50 cm or 36 cm and can use 384 well plates or 96 well plates." . + definition: "Applied Biosystems 3500xL 24-capillary Genetic Analyzer is used for the Human Identification application.Genetic analyzer that utilizes capillary electrophoresis for genetic analysis. It has capillary lengths of 50 cm or 36 cm and can use 384 well plates or 96 well plates." . SCR:018439 a NLX:63400, owl:NamedIndividual ; @@ -133109,9 +133144,11 @@ SCR:018439 a NLX:63400, rdfs:label "Atago PAL-10S Pocket Refractometer" ; definition: "Digital hand held pocket refractometer that measures urine specific gravity. It has measurement temperature of 10 to 35 C and sample volume of 0.3ml." . -SCR:018440 a owl:NamedIndividual ; +SCR:018440 a NLX:63400, + owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_433A", - "SCR_018446" ; + "SCR_018446", + "SCR_019575" ; rdfs:label "Applied Biosystems 433A Peptide Sequencer" ; definition: "Automated peptide synthesizer for chain assembly steps in solid phase peptide synthesis or FastMoc chemistry. Data is based on conductance or ultraviolet UV absorbance of reagent, solutions, and solvents in the synthesis cycle." . @@ -133750,10 +133787,12 @@ SCR:018574 a NLX:63400, rdfs:label "Protein Interactions Calculator" ; definition: "Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex." . -SCR:018575 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_280A" ; +SCR:018575 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_280A", + "SCR_020143" ; rdfs:label "Fisher Scientific Isotemp 280A Vacuum Oven" ; - definition: "Vacuum oven and generates temperatures from ambient up to 200 degrees C. It has front mounted power indicator, dial thermometer, analog vacuum gauge, and hydraulic thermostat." . + definition: "Fisher Scientific Isotemp 280A is a Vacuum Oven offers a temperature range from ambient up to 200C with internal dimensions of 11.125\"D x 9.75\"W x 9.75\"H. Front-mounted power indicator and dial thermometer with top-mounted analog vacuum gauge. The 280A's hydraulic thermostat controls temperature. Large glass panel front door and stainless steel chamber." . SCR:018576 a NLX:63400, owl:NamedIndividual ; @@ -133767,40 +133806,59 @@ SCR:018577 a owl:NamedIndividual ; rdfs:label "GE Healthcare Biacore 3000 Real-time Biomolecular Interaction Analyzer" ; definition: "Label free real time biomolecular interaction analyzer that measures interaction characterization, rate constants, affinity, specificity, and concentration of components." . -SCR:018578 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_C1" ; +SCR:018578 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_C1", + "SCR_019930" ; rdfs:label "Fluidigm C1 Single-Cell Automated Preparation System" ; - definition: "Automated preparation system that isolates and prepares single cell templates for analysis. It can analyze mRNA and DNA sequencing, epigenetics or miRNA expression. It can extract, reverse transcribe, amplify, and analyze gene expression." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023.Automated preparation system that isolates and prepares single cell templates for analysis. It can analyze mRNA and DNA sequencing, epigenetics or miRNA expression. It can extract, reverse transcribe, amplify, and analyze gene expression." . -SCR:018579 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_GX_271" ; - rdfs:label "Gilson GX-271 HPLC Liquid Handler System" ; +SCR:018579 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_GX_271", + "SCR_019963" ; + rdfs:label "Gilson GX-271 HPLC System" ; definition: "HPLC liquid handler with midsize bed capacity and fraction collector. It has maximum flow rates up to 200 mL per min, injection loop volumes of 2 uL to 25 mL, and max sample mass of 15 grams per injection." . -SCR:018580 a owl:NamedIndividual ; +SCR:018580 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_cBot", + "SCR_020129" ; rdfs:label "Illumina cBot Genetic Amplifier" ; definition: "Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures." . -SCR:018581 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_FLA_1500" ; +SCR:018581 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_FLA_1500", + "SCR_019925" ; rdfs:label "Fujifilm Life Science FLA-5100 Scanner" ; - definition: "Imaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023. EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method." . -SCR:018582 a owl:NamedIndividual ; +SCR:018582 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_StarPlus", + "SCR_020003" ; rdfs:label "Hamilton StarPlus Automated Liquid Handler" ; + NIFRID:synonym "Hamilton STARplus" ; definition: "Liquid handling robot with 8 channel pipetting arm, dual HEPA filter top, and 96 channel pipeting head with 1ml capacity. It can have tube racks, microplate racks, and 50mL temperature controlled tube rack." . -SCR:018583 a owl:NamedIndividual ; +SCR:018583 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_NeoPrep", + "SCR_020139" ; rdfs:label "Illumina NeoPrep Library Preparation System" ; definition: "Library preparation system that produces 16 sequencing ready libraries per run. There are steps in NeoPrep workflow run preparation, library card loading, and library collection." . -SCR:018584 a owl:NamedIndividual ; +SCR:018584 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_EM" ; rdfs:label "Gemini EM Microplate Reader" ; - definition: "Microplate reader with dual monochromators for fluorescence intensity assays using multiple point well scanning. Temperature sensitive reactions are from ambient to 45 C." . + definition: "Microplate reader with top and bottom read capability with dual monochromators for fluorescence intensity assays using multiple point well scanning. Temperature sensitive reactions are from ambient to 45 C. Measures fluorescence on variety of sample formats from 6 to 384 well microplates in endpoint, kinetic, spectral scan, and well-scan modes." . -SCR:018585 a owl:NamedIndividual ; +SCR:018585 a NLX:63400, + owl:NamedIndividual ; rdfs:label "Kent Scientific Coda Blood Pressure System" ; - definition: "Mouse and rat tail cuff blood pressure system for blood pressure measurement using volume pressure recording sensor technology." . + definition: "CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. Using the included software allows you to continuously view data in real-time." . SCR:018586 a NLX:63400, owl:NamedIndividual ; @@ -133822,18 +133880,30 @@ SCR:018588 a NLX:63400, rdfs:label "Labnet C2400 Spectrafuge 24D Microcentrifuge" ; definition: "Microcentrifuge with brushless drive that accelerates rotor to maximum speed of 13,300 rpm and 16,000 x g. Features precise digital microprocessor control. Speed knob sets speed in either rpm or g-force. Timer knob sets time parameter." . -SCR:018589 a owl:NamedIndividual ; - rdfs:label "Luminex Amnis Image Stream Multispectral Imaging Flow Cytometer" ; - definition: "Benchtop multispectral imaging flow cytometer designed acquisition of up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry." . +SCR:018589 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_ImageStreamX_MkII", + "SCR_020142", + "SCR_020244" ; + rdfs:label "Luminex Amnis ImageStreamX Mk II System" ; + NIFRID:synonym "Luminex Amnis ImageStream MkII Multispectral Imaging Flow Cytometer", + "Luminex ImageStream MkII Flow Cytometer", + "Luminex ImageStream MkII Multispectral Imaging Flow Cytometer", + "MkII imaging flow cytometer" ; + definition: """Bench top multispectral imaging flow cytometer designed for the acquisition of +up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry.""" . -SCR:018590 a owl:NamedIndividual ; +SCR:018590 a NLX:63400, + owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_ITC 200" ; rdfs:label "Microcal ITC 200 Isothermal Titration Calorimeter" ; + NIFRID:synonym "MicroCal iTC200" ; definition: "Isothermal titration calorimeter for label free, in solution, study of biomolecular interactions. It delivers measurement of binding parameters with minimum of 10 ug sample." . -SCR:018591 a owl:NamedIndividual ; +SCR:018591 a NLX:63400, + owl:NamedIndividual ; rdfs:label "Life Technologies Countess Automated Cell Counter" ; - definition: "Automated cell counter that can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels." . + definition: "Invitrogen benchtop automated cell counter. Can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels." . SCR:018592 a NLX:63400, owl:NamedIndividual ; @@ -133842,10 +133912,13 @@ SCR:018592 a NLX:63400, rdfs:label "Mettler PB303-S Milligram Balance" ; definition: "Miligram balance that is used for weighing, tarring, percent weighing, and dynamic weighing for unstable samples. Has maximum capacity of 310 grams. Lab balance utilizes mono block weighing technology with permanent shock protection and built in overload protection as well as automatic calibration." . -SCR:018593 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_GX_II" ; - rdfs:label "Illumina Labchip GX II Protein Characterization System" ; - definition: "Protein characterization system that provides quantitation, molecular weight sizing and percent purity analysis of proteins. It uses microfluidic electrophoretic separation technology." . +SCR:018593 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_GX_II", + "SCR_020135" ; + rdfs:label "Illumina LabChip GXII Touch protein characterization system" ; + NIFRID:synonym "LabChip GXII Touch" ; + definition: "LabChip GXII Touch is a protein characterization system that provides reproducible quantitation, molecular weight sizing and percent purity analysis of protein samples. Leveraging microfluidic electrophoretic separation technology, the LabChip GXII Touch system enables rapid characterization with minimal sample preparation setup and sample input volume." . SCR:018594 a owl:NamedIndividual ; rdfs:label "Microcal VPViewerTM Differential Scanning Calorimeter VP--DSC" ; @@ -133889,10 +133962,13 @@ SCR:018600 a NLX:63400, rdfs:label "Nanodrop 8000 Spectrophotometer" ; definition: "Microvolume UV Vis spectrophotometer for nucleic acid and protein quantification that can measure multiple samples using 1 to 2 uL of samples. Can analyze spectrum of 220nm to 750nm and measure 96 samples in less than six minutes. Can measure multiple samples in one measurement cycle, up to eight samples at one time. Has single sample mode. Can analyze the full spectrum from 220 to 750nm and calculates sample purity ratios 260/280." . -SCR:018601 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_212" ; - rdfs:label "Molecular Devices CareStream 212 Pro Gel Imager" ; - definition: "Automated gel imaging system that is for imaging fluorescence or colorimetric data in sample formats such as gels, DNA, Coomassie, Silver stain, membranes, and 96 well plates. broadband UV excitation peaks at 306 nm." . +SCR:018601 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Carestream Gel Logic 212 PRO Imaging System" ; + NIFRID:synonym "Bruker BioSpin Gel Logic 212 PRO", + "Carestream Gel Pro 212 Imager", + "Gel Logic 212 PRO" ; + definition: "Automated gel imaging system for imaging fluorescence or colorimetric data in sample formats such as gels (DNA/Coomassie/Silver stain) membranes, and 96 well plates. Features include autofocusing and directed autoexposure." . SCR:018602 a NLX:63400, owl:NamedIndividual ; @@ -133919,17 +133995,22 @@ SCR:018604 a NLX:63400, SCR:018605 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_1500", - "SCR_020314" ; - rdfs:label "Nikon 1500 Fluorescence Dissection Microscope" ; + oboInOwl:hasDbXref "Model_Number_SMZ1500", + "SCR_020314", + "SCR_020327" ; + rdfs:label "Nikon SMZ1500 Zoom Stereoscope" ; + NIFRID:synonym "Nikon 1500 Fluorescence Dissection Microscope" ; definition: "SMZ1500 stereoscopic zoom microscope is system with apochromatic objectives, zoom ratio of 15 to 1, range of magnifications from 0.75x to 11.25x for total magnifying capability of 3.75x up to 540x, and is best for in depth imaging.Zoom knob allows to zoom from 1x to 11x at 1x-intervals without interrupting observations. Other facets include high eyepoint eyepieces with built-in diopter adjustments, wide field of view, and built-in aperture diaphragm for achieving optimal depth of focus and improved photomicrography.Provides options of either low eye-level viewing tube or tilting eyepiece tube, with or without eye-level risers. Three different diascopic stands with built-in power supplies may also be utilized with instrument, or standard stand that features low profile for increased clearance." . SCR:018606 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_E600", - "SCR_020322" ; - rdfs:label "Nikon E600 Fluorescence Microscope" ; - definition: "Fluorescence microscope that has detachable substage, 12 volt 100 watt tungsten halide lamp, filter magazine, and choice of sextuple nosepiece or sextuple DIC nosepiece.Has objectives for brightfield, darkfield, Nomarski DIC, epi fluorescence, or phase contrast techniques." . + "SCR_018858", + "SCR_020322", + "SCR_020330" ; + rdfs:label "Nikon Eclipse E600 Fluorescence Microscope" ; + NIFRID:synonym "Nikon Eclipse E600 Microscope" ; + definition: "Microscope equipped with CFI60 infinity optical system, providing images in all applications. Incorporates specifications adopted for CFI60 series objectives, including 60 millimeter parfocal distance, 25 millimeter thread size, and standard 22 millimeter field of view. Main components of CFI60 infinity optical system include objective, tube lens to converge light beam, and eyepiece lens to enlarge intermediate image. Fluorescence microscope that has detachable substage, 12 volt 100 watt tungsten halide lamp, filter magazine, and choice of sextuple nosepiece or sextuple DIC nosepiece.Has objectives for brightfield, darkfield, Nomarski DIC, epi fluorescence, or phase contrast techniques." . SCR:018607 a "Supercategory", owl:NamedIndividual ; @@ -133939,10 +134020,12 @@ SCR:018607 a "Supercategory", NIFRID:synonym "Olympus IV-100 Imaging System" ; definition: "Intravital laser scanning microscope for small animal imaging with up to four lasers 488nm, 561nm, 633nm, and 748nm. Able to image multiple fluorescence probes simultaneously. Scan head has tilting capability to image objective orientation in three dimensions.Three magnifications of MicroProbe lenses enable to capture either large field of view or high resolution images on living animal. Certain conventional microscope objectives can also be used on IV100 as well." . -SCR:018608 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_34700" ; - rdfs:label "Pelco 34700 Biowave Microwave Processor" ; - definition: "Laboratory microwave system that includes water recirculation system temperature restrictive temperature probe. It is also capable of variable wattage, programmable times, and four intermittent power settings." . +SCR:018608 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_34700", + "SCR_020392" ; + rdfs:label "PELCO BioWave 34700 laboratory microwave system" ; + definition: "Laboratory microwave system that includes True Variable Wattage, water recirculation system, temperature restrictive temperature probe, RS232 Port, Cable and Software, Programmable times, Four intermittent power settings, Magnetron prewarming, Air Bubbler, and Vacuum Cycling. System has precision temperature control and monitoring for microwave assisted processing of tissue. Can be used for formalin fixation, decalcification, special stains, immunocytochemistry and complete processing of tissue into paraffin." . SCR:018609 a NLX:63400, owl:NamedIndividual ; @@ -133971,15 +134054,21 @@ SCR:018612 a NLX:63400, rdfs:label "Olympus MVX10 Macroview Stereo Fluorescence Microscope" ; definition: "Microscope employs single zoom optical path with large diameter, which is optimized to collect light with efficiency and resolution at all magnifications. From fluorescent observation of whole organisms, such as zebrafish, at low magnification to detailed observation of gene expression at cellular level at high magnification, features pupil division mechanism in light path to mimic effect of stereo microscope." . -SCR:018613 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_2020" ; +SCR:018613 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_20/20", + "SCR_019972" ; rdfs:label "Promega GloMax 20/20 Luminometer" ; - definition: "Luminometer for bioluminescent assays, flash or glow type luminescence, and protocols. It can use 1.5ml microcentrifuge tubes." . + NIFRID:synonym "GloMax 20/20 Luminometer" ; + definition: "Luminometer combines instrumentation and software for uses includinh bioluminescent assays, protocols and support. You can measure flash or glow-type luminescence, have two fluorescent modules available, and it accommodates 1.5ml microcentrifuge tubes and 35mm petri dishes, with optional 12mm × 50mm test tube adapter. Measure light output from liquid and solid samples; no minimum volume requirements. The GloMax 20/20 blends user-friendly operation and a small footprint.This Instrument Was Retired September 1, 2023. Accessories and service available until September 1, 2028." . -SCR:018614 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_96" ; +SCR:018614 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_96", + "SCR_019964" ; rdfs:label "Promega GloMax 96 Microplate Luminometer" ; - definition: "Microplate luminometer that has injectors and reads both glow and flash luminescent reactions in 96 well plates. It can be used for luminescent assays, Promega bioluminescent reporter, cell based and biochemical assays." . + NIFRID:synonym "GloMax 96 Microplate Luminometer" ; + definition: "Microplate luminometer that features two optional injectors and reads both glow- and flash-luminescent reactions in 96-well plates. The sensitivity and range enable a wide range of luminescent assays, including Promega bioluminescent reporter, cell-based and biochemical assays." . SCR:018615 a owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_TBS_380" ; @@ -133991,16 +134080,22 @@ SCR:018616 a owl:NamedIndividual ; rdfs:label "Perkin Elmer Zephy G3 NGS liquid handler" ; definition: "Benchtop liquid handler designed to automate construction of 48 to 96 next generation sequencing libraries per day." . -SCR:018617 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_PSQ96" ; - rdfs:label "Qiagen PSQ96 Pyromark Q96 Pyrosequencer" ; - definition: "Sequencing and quantification pyrosequencer for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. It has a 96 well format." . +SCR:018617 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_Q96", + "SCR_020413" ; + rdfs:label "Qiagen PyroMark Q96 System" ; + definition: "Sequencing and quantification platform for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. With its 96-well format, automatic base-calling function, and dedicated software solutions for methylation analysis and assay design." . -SCR:018618 a owl:NamedIndividual ; - rdfs:label "Qiagen QIAcube DNA/RNA Protein Purification System" ; - definition: "Protein purification system that performs fully automated purification of nucleic acids and proteins in molecular biology applications." . +SCR:018618 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_QIACube", + "SCR_020414" ; + rdfs:label "Qiagen QIAcube Classic" ; + definition: "Purification system that performs fully automated purification of nucleic acids and proteins in molecular biology applications." . -SCR:018619 a owl:NamedIndividual ; +SCR:018619 a NLX:63400, + owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_XPR36" ; rdfs:label "Proteon XPR36 Protein Interaction Array System" ; definition: "Protein interaction array system for label free quantitative analysis of biomolecular interactions using surface plasmon resonance technology. Interactions are monitored by flowing analyte in microfluidic channel over ligand immobilized on sensor chip." . @@ -134012,13 +134107,20 @@ SCR:018620 a NLX:63400, rdfs:label "Qiagen Pyromark Q24 Sequencer" ; definition: "Sequencer that uses pyrosequencing technology for real time, sequence based detection, quantification of sequence variants, and epigenetic methylation. Used for analysis of CpG methylation, SNPs, insertion deletions, STRs, variable gene copy number, and for microbial identification and resistance typing." . -SCR:018621 a owl:NamedIndividual ; - rdfs:label "Perkin Elmer IVIS Spectrum In-Vivo Imaging System" ; - definition: "In vivo imaging system that combines two dimensional and three dimensional optical tomography. It can be used for non invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals." . +SCR:018621 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_IVIS", + "SCR_020397" ; + rdfs:label "Perkin Elmer IVIS Spectrum In Vivo Imaging System" ; + definition: "In vivo imaging system that combines two dimensional and three dimensional optical tomography in one platform.The system uses leading optical technology for preclinical imaging research and development best for non-invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals." . -SCR:018622 a owl:NamedIndividual ; - rdfs:label "Qiagen QIAgility PCR Setup Robot" ; - definition: "Benchtop PCR setup robot that sets up PCR experiments with automated software. Software automates worktable setup and automatic calculation of all mixes, eliminating programming pipetting steps." . +SCR:018622 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_QIAgility", + "SCR_020417" ; + rdfs:label "Qiagen QIAgility" ; + NIFRID:synonym "Qiagen QIAgility PCR Setup Robot" ; + definition: "PCR Setup Robot. Compact benchtop instrument for setup of PCR experiments with setup and automatic calculation of all mixes, eliminating the need to program pipetting steps." . SCR:018623 a NLX:63400, owl:NamedIndividual ; @@ -134038,29 +134140,38 @@ SCR:018624 a NLX:63400, "QIAxcel Advanced" ; definition: "Genetic analyzer that automates electrophoresis analysis of your DNA and RNA samples." . -SCR:018625 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Alchemist_II" ; +SCR:018625 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_Alchemist_II", + "SCR_019564" ; rdfs:label "Rigaku Alchemist II Liquid Handler" ; - definition: "Liquid handling system designed production of complex liquid formulations produced from individual solutions of various chemical and liquid properties." . + definition: "Liquid handling system for production of complex liquid formulations produced from individual stock solutions of various chemical and liquid properties. With a CV of less than 2%." . -SCR:018626 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_480" ; - rdfs:label "Roche Light Cycler 480 qPCR Real Time PCR System" ; - definition: "Real time PCR device that allows use of additional thermal block cycler units 96 well and 384 well format." . +SCR:018626 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_LightCycler_480", + "SCR_020502" ; + rdfs:label "Roche LightCycler 480 Real Time PCR System" ; + NIFRID:synonym "LightCycler 480 Real-Time PCR System" ; + definition: "LightCycler 480 Instrument is a real-time PCR device, allowing the use of additional thermal block cycler units (96-well and 384-well format) with the system. The LightCycler 480 Block Kit 384 Silver comprises a block cycler unit for 384-well PCR plates, a corresponding block lid for the 384-well PCR plates, and a storage box for both accessories." . SCR:018627 a owl:NamedIndividual ; rdfs:label "SCIEX QStar XL Mass Spectrometer" ; definition: "Hybrid quadrupole time of flight mass spectrometer with MS mass range 6,000 and 40,000 m z designed proteomics, drug discovery, metabolomics, and drug development. Instrument used with Analyst QS software." . -SCR:018628 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_3" ; +SCR:018628 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_Cytospin 3", + "SCR_020507" ; rdfs:label "Shandon Cytospin 3 Centrifuge" ; - definition: "Centrifuge that has speed range of between 200 and 2000 RPM, and has holding capacity of up to 24 samples in 12 chambers. It is used for hematology, cytology, histology, oncology, rheumatology, immunochemistry, microbiology, serology, and virology." . + definition: "Thermo Shandon Cytospin 3 is low speed centrifuge used to separate and deposit monolayer of cells on slides while maintaining cellular integrity.Centrifuge has speed range between 200 and 2000 RPM, and has holding capacity of up to 24 samples in 12 chambers." . -SCR:018629 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_400" ; +SCR:018629 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_Integra_400_Plus", + "SCR_020504" ; rdfs:label "Roche Cobas Integra 400 Plus Chemistry Analyzer" ; - definition: "Chemistry analyzer with test menu of assays and applications that consolidate clinical chemistry with specific proteins, therapeutic drug monitoring, and drug abuse testing." . + definition: "COBAS INTEGRA 400 plus analyzer is a chemistry analyzer with a broad test menu comprises over 120 assays and applications that consolidate clinical chemistry with specific proteins, therapeutic drug monitoring and drug abuse testing.The Cobas 400 analyzer is best for laboratories running up to 400 samples per day. This compact tabletop analyzer offers maximum versatility to improve efficiency and reduce costs. It uses the convenient cobas c pack reagent format, which standardizes patient results across integrated laboratory networks." . SCR:018630 a NLX:63400, owl:NamedIndividual ; @@ -134089,10 +134200,14 @@ SCR:018633 a owl:NamedIndividual ; rdfs:label "Rigaku X-Stream 2000 Cryo-Freezing System" ; definition: "Self contained cryo freezing system designed cooling crystals with range of negative 80C to 4C. It produces nitrogen, which is then cooled to negative 196C, and then rewarmed to desired temperature." . -SCR:018634 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_BNII" ; - rdfs:label "Siemens Dade Behring BNII Nephelometer" ; - definition: "Automated nephelometer for plasma protein determinations that tests cardiac risk assessment, kidney diseases and nutritional assessment. It supports markers such as Cystatin C and Carbohydrate Deficient Transferring." . +SCR:018634 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_BNII", + "SCR_019838" ; + rdfs:label "Siemens Dade Behring BNII Nephelometer System" ; + NIFRID:synonym "Dade Behring BN II Nephelometer", + "Siemens Dade Behring BNII Nephelometer" ; + definition: "Siemens Dade Behring BN II Nephelometer is leading fully automated system for plasma protein determinations. BN II systems offer advanced nephelometric technology that provides performance in plasma protein analysis. This instrument's menu covers assays, which support various clinical tests including cardiac risk assessment, kidney diseases and nutritional assessment. markers such as Cystatin C and Carbohydrate-Deficient Transferrin (CDT) are also supported. Other features of the Dade Behring BN II Nephelometer include rapid processing, easy operation and random-access mode. The nephelometer also permits users to put up to 100 samples on board, making it best for mid to high-volume processing." . SCR:018635 a owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_SH800Z" ; @@ -134106,9 +134221,12 @@ SCR:018636 a NLX:63400, rdfs:label "Sutter P-97/PC Pipette Puller" ; definition: "Pipette puller that fabricates pipettes for use in intracellular recording, patch clamping, transferring ICSI, ES Cells , microinjection, aspiration, and microperfusion. P-97 puller can indirectly sense viscosity of glass, giving the ability to pull pipettes from all glasses except quartz. Even difficult to pull formulations, such as aluminosilicate glasses, are handled with relative ease." . -SCR:018637 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_3200" ; - rdfs:label "TA Instruments Electroforce 3200 Series Mechanical Testing Apparatus" ; +SCR:018637 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_3200", + "SCR_019752" ; + rdfs:label "TA Instruments Electroforce 3200 Mechanical Testing Apparatus" ; + NIFRID:synonym "TA Instruments Electroforce 3200 Series Mechanical Testing Apparatus" ; definition: "Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications.." . SCR:018638 a owl:NamedIndividual ; @@ -134129,12 +134247,17 @@ SCR:018640 a NLX:63400, rdfs:label "Sutter P-2000 Laser Micropipette Puller" ; definition: "Microprocessor controlled, CO2 laser based micropipette puller.Default configuration allows fabrication of micropipettes for intracellular recording, patch clamping, microinjection and microperfusion.Can store up to 100 separate programs, each consisting of up to 8 command lines. The five parameters set in each command line allow exquisite control of the micropipette taper geometry. Allows the use of wide range of glass diameters from 0.125 to 1.2 mm." . -SCR:018641 a owl:NamedIndividual ; - rdfs:label "Thermo Fisher Arcturus XT Laser Capture Microdissection System" ; +SCR:018641 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_XT", + "SCR_019580" ; + rdfs:label "Arcturus Cellect Laser Capture Microdissection System" ; definition: "Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR." . -SCR:018642 a owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_815B" ; +SCR:018642 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_815B", + "SCR_019587" ; rdfs:label "Tousimis Autosamdri 815B Critical Point Dryer" ; definition: "Critical point dryer with wafer holders that allow automatic anti stiction processing up to 5 pieces of either 100mm, 75mm, 50mm wafers or 10mm square die per process run. All internal surfaces are inert to CO2 and ultra pure alcohols." . @@ -134207,9 +134330,11 @@ SCR:018654 a owl:NamedIndividual ; SCR:018655 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_LSRFortessa", + "SCR_019605" ; rdfs:label "BD LSRFortessa cell analyzer" ; NIFRID:synonym "BD LSRFortessa 4 SORP 4 Laser" ; - definition: "Flow cytometer for multicolor flow cytometry assays. BD flow cytometer to identify, count, and characterize cells to support cell analysis. Cell analyzer. BD LSRFortessa is configurable and upgradeable with up to 4 lasers to detect up to 18 colors simultaneously." . + definition: "BD LSRFortessa cell analyzer provides power, performance, and consistency and supports the expanding needs of multicolor flow cytometry assays." . SCR:018656 a NLX:63400, owl:NamedIndividual ; @@ -134293,7 +134418,7 @@ SCR:018668 a NLX:63400, "Stanford School of Medicine Protein and Nucleic Acid Facility", "Stanford University Protein and Nucleic Acid Facility (PAN)" ; NIFRID:abbrev "PAN" ; - definition: "Facility provides expertise in genomics and protein analytics. Services include Gene Expression Analysis, Microarrays,RT PCR, Pyrosequencing using PyroMark technology for methylation analysis and sequence variation analysis,Biomolecular Interaction Analysis (Surface Plasmon Resonance; Biacore),DNA Sequencing, Oligonucleotide Synthesis, Protein Sequencing, Peptide Synthesis, Protein Identification, Mass Spectrometry. Services include standard assays, as well as customized services." . + definition: "Offers instrumentation and technical capabilities and plays significant consultative role in application of these technologies to basic science projects.Genomic Services include Oligo Synthesis,Gene Expression,Real-Time PCR,PyroSequencing,Next-Generation Sequencing (NGS),DNA Sequencing (Sanger)/Fragment AnalysisSingle Cell Genomics,RNA-DNA QC - Bioanalyzer and Fragment Analyzer QC.Protein Services include Peptide Synthesis,Mass Spectrometry,Protein Analytics - Mass Mapping/Edman Sequencing,Surface Plasmon Resonance (Biacore)." . SCR:018669 a NLX:63400, owl:NamedIndividual ; @@ -134332,13 +134457,18 @@ SCR:018671 a NLX:63400, SCR:018672 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_390" ; - rdfs:label "Massachusetts University Medical School Mouse Phenotyping Center Core Facility" ; - NIFRID:synonym "Massachusetts University Medical School National Mouse Metabolic Phenotyping Center", - "National Mouse Metabolic Phenotyping Center" ; - NIFRID:abbrev "MMPC", + oboInOwl:hasDbXref "ABRF_390", + "SCR_015366" ; + rdfs:label "University of Massachusetts Medical School Metabolic Disease Research Center Core Facility" ; + NIFRID:synonym "Massachusetts University Medical School Mouse Phenotyping Center Core Facility", + "Massachusetts University Medical School National Mouse Metabolic Phenotyping Center", + "National Mouse Metabolic Phenotyping Center", + "UMass Medical School Metabolic Disease Research Center", + "University of Massachusetts Medical School Mouse Phenotyping Center Core Facility" ; + NIFRID:abbrev "MDRC", + "MMPC", "UMass MMPC" ; - definition: "Provides research tools for investigating mouse models of human diseases with particular focus on diabetes, obesity, and diabetic complications.Offers experimental testing services. Provided complementary phenotyping cores include Metabolism,Analytical,Islet,Cardiovascular,Microbiome,Humanized Mouse Cell Transplantation and Assessment core." . + definition: "UMass Metabolic Disease Research Center (MDRC), formerly the National Mouse Metabolic Phenotyping Center, is a core facility that performs standardized experiments using state-of-the-art equipment for the purpose of investigating transgenic mouse models of diabetes, obesity, and metabolic liver disease. Provides metabolic and functional characterization of mouse models of human diseases that are developed by academic and industry researchers in joint efforts to understand metabolic diseases and to identify new therapies." . SCR:018673 a NLX:63400, owl:NamedIndividual ; @@ -134445,7 +134575,8 @@ SCR:018688 a NLX:63400, SCR:018690 a NLX:63400, owl:NamedIndividual ; rdfs:label "CATlas" ; - NIFRID:synonym "Cis-element Atlas" ; + NIFRID:synonym "Cis-element Atlas", + "Ren lab web portal for chromatin accessibility data" ; definition: "Atlas of gene regulatory elements in adult mouse cerebrum. Atlas of CIS elements, providing information on accessible chromatin in individual cells from regions of adult mouse isocortex, olfactory bulb, hippocampus and cerebral nuclei. Uses resulting data to define candidate cis-regulatory DNA elements in distinct cell groups. Many are linked to putative target genes expressed in diverse cerebral cell types and uncover transcriptional regulators involved in broad spectrum of molecular and cellular pathways in different neuronal and glial cell populations. Used for analysis of gene regulatory programs of mammalian brain and interpretation of non-coding risk variants associated with various neurological disease and traits in humans." . SCR:018691 a owl:NamedIndividual ; @@ -134498,9 +134629,10 @@ SCR:018698 a NLX:63400, SCR:018699 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Shimadzu 8030 LC/MS mass spectrometer" ; + oboInOwl:hasDbXref "Model_Number_8030" ; + rdfs:label "Stanford Shimadzu 8030 LC/MS mass spectrometer" ; NIFRID:synonym "Shimadzu 8030 LC/MS" ; - definition: "Shimadzu 8030 triple quadrupole mass spectrometer used for targeted quantitation applications." . + definition: "Shimadzu 8030 triple quadrupole mass spectrometer used for targeted quantitation applications. Listed by Stanford University Mass Spectrometry Vincent Coates Foundation Instruments." . SCR:018700 a NLX:63400, owl:NamedIndividual ; @@ -134590,9 +134722,14 @@ SCR:018712 a NLX:63400, SCR:018713 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Leica_DMI6000B" ; + oboInOwl:hasDbXref "Model_Number_DMI6000_B", + "SCR_020216", + "SCR_020220", + "SCR_020228" ; rdfs:label " Leica DMI6000 B inverted microscope" ; - definition: "Inverted microscope for biomedical research. Offers Differential Interference Contrast for relief imaging of specimens with varying indices of refraction. Used for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. Features automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide convenience and reproducible results." . + NIFRID:synonym "Leica DMI6000 B", + "Leica DMI6000 B Fully Automated Inverted Research Microscope" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 16,2023. Inverted microscope for biomedical research. Offers Differential Interference Contrast for relief imaging of specimens with varying indices of refraction. Used for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. Features automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide convenience and reproducible results. Archived Product. Replaced by DMi8 S." . SCR:018714 a NLX:63400, owl:NamedIndividual ; @@ -135089,7 +135226,7 @@ SCR:018802 a NLX:63400, SCR:018803 a NLX:63400, owl:NamedIndividual ; - rdfs:label "iTasser" ; + rdfs:label "I-TASSER" ; NIFRID:synonym "Iterative Threading ASSEmbly Refinement" ; definition: "Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation." . @@ -135335,8 +135472,10 @@ SCR:018838 a NLX:63400, SCR:018840 a NLX:63400, owl:NamedIndividual ; - rdfs:label "PCU-2000 Dual Channel Pressure Control Unit" ; - NIFRID:synonym "PCU-2000 Pressure Control Unit" ; + oboInOwl:hasDbXref "SCR_018892" ; + rdfs:label "Millar PCU-2000 Pressure Control Unit with Patient Isolation" ; + NIFRID:synonym "PCU-2000 Dual Channel Pressure Control Unit", + "PCU-2000 Pressure Control Unit" ; definition: "Pressure Control Unit is two channel, patient isolated, line powered bridge amplifier for connecting one or two single sensor Millar Mikro-Tip catheters to clinical patient monitor or standalone data acquisition system. Provides built in ridge excitation eliminating need for separate bridge amplifier. Analog output signal level of 1V/100 mmHg is compatible with most pressure monitors and data acquisition systems. In line power supply adapts automatically to line voltages from 100 to 240 volts AC." . SCR:018841 a NLX:63400, @@ -135371,8 +135510,7 @@ SCR:018857 a NLX:63400, SCR:018858 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Nikon Eclipse E600 Microscope" ; - definition: "Microscope equipped with CFI60 infinity optical system, providing images in all applications. Incorporates specifications adopted for CFI60 series objectives, including 60 millimeter parfocal distance, 25 millimeter thread size, and standard 22 millimeter field of view. Main components of CFI60 infinity optical system include objective, tube lens to converge light beam, and eyepiece lens to enlarge intermediate image." . + definition: "Microscope equipped with CFI60 infinity optical system, providing images in all applications. Incorporates specifications adopted for CFI60 series objectives, including 60 millimeter parfocal distance, 25 millimeter thread size, and standard 22 millimeter field of view. Main components of CFI60 infinity optical system include objective, tube lens to converge light beam, and eyepiece lens to enlarge intermediate image. Fluorescence microscope that has detachable substage, 12 volt 100 watt tungsten halide lamp, filter magazine, and choice of sextuple nosepiece or sextuple DIC nosepiece.Has objectives for brightfield, darkfield, Nomarski DIC, epi fluorescence, or phase contrast techniques." . SCR:018860 a NLX:63400, owl:NamedIndividual ; @@ -135420,9 +135558,9 @@ SCR:018875 a NLX:63400, SCR:018876 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Zeiss Axio Imager 2 Microscope" ; + rdfs:label "Zeiss Axio Imager 2" ; NIFRID:synonym "Axio Imager 2" ; - definition: "Upright Research Microscope. Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software." . + definition: "Axio Imager 2 resolves samples from tissue sections in pathology to brain specimens in neuroscience to multi dyed FISH specimens. Works with ZEN imaging software." . SCR:018877 a NLX:63400, owl:NamedIndividual ; @@ -135534,7 +135672,8 @@ SCR:018891 a NLX:63400, SCR:018892 a NLX:63400, owl:NamedIndividual ; rdfs:label "Millar PCU-2000 Pressure Control Unit with Patient Isolation" ; - definition: "Two channel, patient isolated, line powered bridge amplifier for connecting catheters to clinical patient monitor or standalone data acquisition system. Each channel has electrically isolated input for patient safety." . + NIFRID:synonym "PCU-2000 Dual Channel Pressure Control Unit", + "PCU-2000 Pressure Control Unit" . SCR:018893 a NLX:63400, owl:NamedIndividual ; @@ -135555,7 +135694,9 @@ SCR:018895 a NLX:63400, SCR:018896 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Leica DM5500 B Microscope" ; + oboInOwl:hasDbXref "Model_Number_DM5500_B" ; + rdfs:label "Leica DM5500 B Automated Upright Microscope System" ; + NIFRID:synonym "Leica DM5500 B Microscope" ; definition: "Fluorescence microscope capable of contrast microscopy and has ability for fully automated Differential Interference Contrast techniques. This product has been archived and replaced with the Leica DM4 B and DM6 B microscopes." . SCR:018897 a NLX:63400, @@ -136236,7 +136377,9 @@ SCR:019004 a owl:NamedIndividual ; SCR:019005 a NLX:63400, owl:NamedIndividual ; - NIFRID:synonym "MBF Bioscience TissueMaker" ; + rdfs:label "TissueMaker" ; + NIFRID:synonym "MBF Bioscience TissueMaker", + "TissueMakerTM" ; definition: "Software tool to automatically align serial sections and visualize entire 3D organ. Generates full resolution 3D reconstructions from serial sections imaged with whole slide scanners and research microscopes. Used to assist with cell mapping, cytoarchitectonics, and other measures that require visualizing neuronal circuitry to create comprehensive anatomical reference." . SCR:019007 a NLX:63400, @@ -136397,9 +136540,11 @@ SCR:019032 a NLX:63400, SCR:019033 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Tecan Infinite M200 Pro" ; - NIFRID:synonym "Infinite 200 PRO" ; - definition: "ELISA multimode plate reader family that offers high performance detection solutions empowered by monochromator or filter based technologies." . + oboInOwl:hasDbXref "Model_Number_Infinite_M200_Pro" ; + rdfs:label "Tecan Infinite M200 Pro Multimode Microplate Reader" ; + NIFRID:synonym "Infinite M200 Pro", + "Tecan Infinite M200 Pro" ; + definition: "Tecan Infinite M200 Pro is multi-detection microplate reader used for biological applications including protein quantification, ELISA, binding studies, DNA quantification, gene expression, immunoassays, toxicity, cell viability, RNA quantification, cell-based and enzyme assays.This modular Tecan plate reader is monochromator based system, with no need for filters, giving range from 230-1000 nm Abs or 300-600nm FI in 1 nm steps. With spectrally enhanced, red-sensitive PMT, the FI range extends to 330-850nm for NIR readings. Modules featured can be Monochromator absorbance, fluorescence top, fluorescence bottom, Luminescence, Incubation, injection, and enhanced photomultiplier tube (PMT) for red sensitivity that brings the detection limit to 45 pM. Please see individual SKU numbers for a list of installed modules. Heating module that’s installed on the microplate reader, allows for the chamber to keep at 37°C for those temperature sensitive samples. Can read microplates from 6 up to 384 well plates, along with PCR plates. Tecan M200 Microplate Reader is driven by Magellan software, which allows you to easily navigate run from start to finish. The user can choose from predetermined assays or build their own from scratch." . SCR:019034 a NLX:63400, owl:NamedIndividual ; @@ -137176,10 +137321,11 @@ SCR:019164 a NLX:63400, SCR:019165 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_275" ; rdfs:label "Dartmouth Geisel School of Medicine Immunoassay and Flow Cytometry Core Facility" ; - NIFRID:synonym "DartLab Immune Monitoring and Flow Cytometry Shared Resource" ; - definition: "Offers services in customized end point assays using human WB/PBMCs for clinical trials, ELISPOT, multiplex cytokine analysis, cell energy analysis, blood processing and cryopreservation,up to 20 color flow cytometry phenotyping and up to 11color FACS cell subset sorting. Provides consultation, data analysis, and Flow Cytometry training course." . + NIFRID:synonym "DartLab Immune Monitoring and Flow Cytometry Shared Resource", + "Dartmouth College Geisel School of Medicine DartLab", + "Dartmouth DartLab", + "Geisel School of Medicine at Dartmouth DartLab Immune Monitoring and Flow Cytometry Shared Resource" . SCR:019166 a NLX:63400, owl:NamedIndividual ; @@ -137711,7 +137857,7 @@ SCR:019247 a NLX:63400, rdfs:label "MRI Compatible and Customizable Microdrive Design for Neuroscience Research" ; definition: "Open source designs for customizable, MRI compatible microdrive capable of positioning probes including stimulating electrodes, recording electrodes, drug cannulae, or optogenetic fibers within brain. Design integrates cranial implant, penetration grid for guiding probes, and microdrive body assembly with actuators. Used by neuroscience community related to electrical microstimulation, neuronal recording, and local drug delivery." . -SCR:019248 a NLX:152342, +SCR:019248 a NLX:152328, owl:NamedIndividual ; rdfs:label "Bio X Cell" ; definition: "A commercial supplier and developer of in vivo antibodies." . @@ -137890,12 +138036,10 @@ SCR:019283 a NLX:63400, SCR:019284 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_1119" ; - rdfs:label "University of Nottingham NASC Nottingham Arabidopsis Stock Centre Core Facility" ; - NIFRID:synonym "NASC-Nottingham Arabidopsis Stock Centre", - "University of Nottingham NASC-Nottingham Arabidopsis Stock Centre" ; - definition: """National and international arabidopsis germplasm resource.Stores over million genotypes in physical stocks servicing worldwide Arabidopsis community in more than 50 countries. -Stocks are provided under identical cost recovery conditions to academic and commercial researchers. Non-transgenic stocks are sent gratis to K-17 institutions and in special cases.""" . + oboInOwl:hasDbXref "ABRF_1119", + "nlx_56885", + "SCR_004576" ; + rdfs:label "University of Nottingham NASC Nottingham Arabidopsis Stock Centre Core Facility" . SCR:019285 a NLX:63400, owl:NamedIndividual ; @@ -138205,9 +138349,10 @@ SCR:019331 a NLX:63400, SCR:019332 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5800" ; - rdfs:label "AB Sciex 5800 MALDI TOF/TOF Mass Spectrometer" ; - definition: "Mass spectrometer for biomarker discovery, MALDI mass spectrometry imaging, and protein identification." . + oboInOwl:hasDbXref "Model_Number_5800", + "SCR_019336" ; + rdfs:label "ABI 5800 Mass Spectrometer" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8th, 2023. Mass spectrometer for biomarker discovery, MALDI mass spectrometry imaging, and protein identification." . SCR:019333 a NLX:63400, owl:NamedIndividual ; @@ -138217,9 +138362,7 @@ SCR:019333 a NLX:63400, SCR:019334 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_7500FAST" ; - rdfs:label "ABI 7500 Real Time PCR System 7500FAST" ; - definition: "This Real-Time PCR System offers you high performance, multicolor real-time PCR." . + rdfs:label "ABI 7500 Real Time PCR System 7500FAST" . SCR:019335 a NLX:63400, owl:NamedIndividual ; @@ -138227,11 +138370,9 @@ SCR:019335 a NLX:63400, rdfs:label "ABI 7300 Real-Time Instrument" ; definition: "Fast Real-Time PCR System uses fluorescent based PCR chemistries to provide quantitative detection of nucleic acid sequences using real-time analysis and qualitative detection of nucleic acid sequences using end-point and dissociation-curve analysis." . -SCR:019336 a NLX:63400, - owl:NamedIndividual ; +SCR:019336 a owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_5800" ; - rdfs:label "ABI 5800 Mass Spectrometer" ; - definition: "Mass spectrometer for biomarker discovery, MALDI mass spectrometry imaging, and protein identification." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8th, 2023. Mass spectrometer for biomarker discovery, MALDI mass spectrometry imaging, and protein identification." . SCR:019337 a NLX:63400, owl:NamedIndividual ; @@ -138517,9 +138658,7 @@ SCR:019383 a NLX:63400, SCR:019384 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_2565CA" ; - rdfs:label "Agilent 2565CA Microarray Scanner" ; - definition: "A Microarray Scanner is part of the microarray analysis solution from Agilent Technologies. The microarray scanner is a laser-induced fluorescence scanner designed to read microarrays printed on standard 1 in 3 in slides. The microarray scanner measures the fluorescence intensity of labeled sample nucleic acid (DNA and RNA) bound to microarrays." . + rdfs:label "Agilent 2565CA Microarray Scanner" . SCR:019385 a NLX:63400, owl:NamedIndividual ; @@ -138571,9 +138710,11 @@ SCR:019392 a NLX:63400, SCR:019393 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_4150" ; - rdfs:label "Agilent 4150 Tapestation Genetic Analyzer" ; - definition: "Agilent 4150 TapeStation system analyzes nucleic acids for up to 16 samples per run." . + oboInOwl:hasDbXref "Model_Number_4150", + "SCR_019394" ; + rdfs:label "Agilent 4150 TapeStation System" ; + NIFRID:synonym "Agilent 4150 Tapestation Genetic Analyzer" ; + definition: "System analyzes nucleic acids for up to 16 samples per run." . SCR:019394 a NLX:63400, owl:NamedIndividual ; @@ -138603,7 +138744,7 @@ SCR:019398 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_4200" ; rdfs:label "Agilent 4200 TapeStation System" ; - definition: "TapeStation System is used to analyze DNA and RNA samples for quality control." . + definition: "Benchtop genetic analyzer electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow." . SCR:019399 a NLX:63400, owl:NamedIndividual ; @@ -138649,8 +138790,10 @@ SCR:019405 a NLX:63400, SCR:019406 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5100" ; + oboInOwl:hasDbXref "Model_Number_5100", + "SCR_019408" ; rdfs:label "Agilent 5100 Inductively-Coupled Plasma-Optical Emission Spectrometer" ; + NIFRID:synonym "Agilent 5110 ICP-OES Instrument" ; definition: "Agilent 5110 ICP-OES Instrument enables synchronous radial and axial measurements and runs samples up to 55% faster using 50% less argon." . SCR:019407 a NLX:63400, @@ -138659,11 +138802,11 @@ SCR:019407 a NLX:63400, rdfs:label "Agilent 490-Mobile Micro GC System" ; definition: "490-Mobile Micro GC System allows analysis results to be viewed in full or reported in true/false." . -SCR:019408 a NLX:63400, - owl:NamedIndividual ; +SCR:019408 a owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_5110" ; - rdfs:label "Agilent 5110 ICP-OES Instrument" ; - definition: "ICP-OES Instrument enables synchronous radial and axial measurements and runs samples up to 55 percent faster using 50 percent less argon." . + rdfs:label "Agilent 5100 Inductively-Coupled Plasma-Optical Emission Spectrometer" ; + NIFRID:synonym "Agilent 5110 ICP-OES Instrument" ; + definition: "Agilent 5110 ICP-OES Instrument enables synchronous radial and axial measurements and runs samples up to 55% faster using 50% less argon." . SCR:019409 a NLX:63400, owl:NamedIndividual ; @@ -138704,9 +138847,10 @@ SCR:019414 a NLX:63400, SCR:019415 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5975C" ; + oboInOwl:hasDbXref "Model_Number_5975C", + "SCR_019419" ; rdfs:label "Agilent 5975C Gas Chromatography Mass Spectrometer" ; - definition: "Gas Chromatography Mass Spectrometer is used to meet challenges faced by today's polymer analyst." . + definition: "Agilent 5975C inert Mass Selective Detector delivers better MS resolution and the lowest mass deviation available and offers superior sensitivity and spectral integrity.The 5977 is the new Agilent GC/MSD platform and replaces the 5975C." . SCR:019416 a NLX:63400, owl:NamedIndividual ; @@ -138726,11 +138870,9 @@ SCR:019418 a NLX:63400, rdfs:label "Agilent 6230B Time of Flight (TOF) LC/MS" ; definition: "Time of Flight LC/MS gives you full spectrum data for screening, profiling and identification of small molecules, large biologic compounds, and everything in between." . -SCR:019419 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5975" ; - rdfs:label "Agilent 5975 Mass Spectrometer" ; - definition: "Agilent 5975C inert MSD delivers better MS resolution and the lowest mass deviation available and offers superior sensitivity and spectral integrity." . +SCR:019419 a owl:NamedIndividual ; + rdfs:label "Agilent 5975C Gas Chromatography Mass Spectrometer" ; + definition: "Agilent 5975C inert Mass Selective Detector delivers better MS resolution and the lowest mass deviation available and offers superior sensitivity and spectral integrity.The 5977 is the new Agilent GC/MSD platform and replaces the 5975C." . SCR:019420 a NLX:63400, owl:NamedIndividual ; @@ -138782,15 +138924,17 @@ SCR:019427 a NLX:63400, SCR:019428 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_6545" ; + oboInOwl:hasDbXref "Model_Number_6545", + "SCR_019429" ; rdfs:label "Agilent 6545 Liquid Chromatography" ; - definition: "Mid-range Quadrupole Time-of-Flight liquid chromatography mass spectrometer designed for untargeted sample analysis, it enables broad screening, comprehensive profiling, identification of unknowns, mass accuracy, and isotopic fidelity." . + NIFRID:synonym "Agilent 6545 LC/Q-TOF" ; + definition: "THIS RESOURCE IS NO LONGER AVAILABLE. Documented on August 4th, 2023. Mid-range Quadrupole Time-of-Flight liquid chromatography mass spectrometer designed for untargeted sample analysis, it enables broad screening, comprehensive profiling, identification of unknowns, mass accuracy, and isotopic fidelity." . SCR:019429 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_6545" ; - rdfs:label "Agilent 6545 LC/Q-TOF" ; - definition: "LF/Q-TOF is used for untargeted sample analysis and enables broad screening, comprehensive profiling, and identification of unknowns." . + NIFRID:synonym "Agilent 6545 LC/Q-TOF" ; + definition: "THIS RESOURCE IS NO LONGER AVAILABLE. Documented on August 4th, 2023.Mid-range Quadrupole Time-of-Flight liquid chromatography mass spectrometer designed for untargeted sample analysis, it enables broad screening, comprehensive profiling, identification of unknowns, mass accuracy, and isotopic fidelity." . SCR:019430 a NLX:63400, owl:NamedIndividual ; @@ -138800,9 +138944,11 @@ SCR:019430 a NLX:63400, SCR:019431 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_6560" ; + oboInOwl:hasDbXref "Model_Number_6560", + "SCR_019434" ; rdfs:label "Agilent 6560 Ion Mobility LC/Q-TOF" ; - definition: "Ion Mobility LC/Q-TOF delivers unrivaled separation and selectivity by combining chromatography, ion mobility, and mass spectrometry." . + NIFRID:synonym "Agilent 6560 Ion Mobility Quadrupole Time-of-Flight Liquid Chromatography Mass Spectrometer" ; + definition: "Ion Mobility LC/Q-TOF delivers unrivaled separation and selectivity by combining chromatography, ion mobility, and mass spectrometry.Quadrupole Time-of-Flight liquid chromatography mass spectrometer that combines chromatography, ion mobility, and mass spectrometry. The system has electrodynamic ion funnel technology and an attractive low field drift tube design." . SCR:019432 a NLX:63400, owl:NamedIndividual ; @@ -138819,8 +138965,9 @@ SCR:019433 a NLX:63400, SCR:019434 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_6560" ; - rdfs:label "Agilent 6560 Ion Mobility Quadrupole Time-of-Flight Liquid Chromatography Mass Spectrometer" ; - definition: "Quadrupole Time-of-Flight liquid chromatography mass spectrometer that combines chromatography, ion mobility, and mass spectrometry. The system has electrodynamic ion funnel technology and an attractive low field drift tube design." . + rdfs:label "Agilent 6560 Ion Mobility LC/Q-TOF" ; + NIFRID:synonym "Agilent 6560 Ion Mobility Quadrupole Time-of-Flight Liquid Chromatography Mass Spectrometer" ; + definition: "Ion Mobility LC/Q-TOF delivers unrivaled separation and selectivity by combining chromatography, ion mobility, and mass spectrometry.Quadrupole Time-of-Flight liquid chromatography mass spectrometer that combines chromatography, ion mobility, and mass spectrometry. The system has electrodynamic ion funnel technology and an attractive low field drift tube design." . SCR:019435 a NLX:63400, owl:NamedIndividual ; @@ -139204,7 +139351,7 @@ SCR:019498 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Femto Pulse" ; rdfs:label "Agilent Femto Pulse System" ; - definition: "Femto Pulse System separates large molecular weight DNA fragments and detects nucleic acids into femtogram range." . + definition: "Femto Pulse System separates large molecular weight DNA fragments and detects nucleic acids into femtogram range.Fragment analyzer that provides pulsed field power supply which allows large molecular weight DNA fragments to be separated and nucleic acids detected into femtogram range. Ability to separate high molecular weight DNA up to 165 kb and detect nucleic acids down to 50 fg per uL input concentration makes system ideal for long-read NGS QC, gDNA, small RNA, or cfDNA analysis from low concentration samples." . SCR:019499 a NLX:63400, owl:NamedIndividual ; @@ -139599,7 +139746,7 @@ SCR:019563 a NLX:63400, SCR:019564 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Alchemist II" ; - rdfs:label "Alchemist II Liquid Handler Alchemist II" ; + rdfs:label "Rigaku Alchemist II Liquid Handler" ; definition: "Liquid handling system for production of complex liquid formulations produced from individual stock solutions of various chemical and liquid properties. With a CV of less than 2%." . SCR:019565 a NLX:63400, @@ -139618,7 +139765,7 @@ SCR:019567 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_XL-A" ; rdfs:label "analytical ultracentrifuges (Beckman XL-I and XL-A) XL-A" ; - definition: "Centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures. It allows for In-solution testing in native conditions. It measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5th,2023. Centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures. It allows for In-solution testing in native conditions. It measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems." . SCR:019568 a NLX:63400, owl:NamedIndividual ; @@ -139636,7 +139783,7 @@ SCR:019570 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_860" ; rdfs:label "American Optical 860 Sliding Microtome" ; - definition: "Sliding microtome for accurately cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns using the automatic advance mechanism." . + definition: "THIS REOURCE IS NO LONGER IN SERVICE. Documented on September 29,2023. Sliding microtome for accurately cutting hard objects such as bone, wood, frozen celloidin, and paraffin preparations. Cutting thickness is adjustable from 1 to 40 microns using the automatic advance mechanism." . SCR:019571 a NLX:63400, owl:NamedIndividual ; @@ -139652,21 +139799,23 @@ SCR:019572 a NLX:63400, SCR:019573 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_4700" ; - rdfs:label "Applied Biosciences 4700 Proteomics Analyzer" ; + oboInOwl:hasDbXref "Model_Number_4700", + "SCR_020409" ; + rdfs:label "Applied Biosystems 4700 Proteomics Analyzer" ; + NIFRID:synonym "Applied Biosystems 4700 Mass Spectrometer" ; definition: "MALDI tandem time-of-flight mass spectrometer that provides a new level of productivity in high-resolution proteome analysis and complex systems biology. It can be used for carbohydrate, lipid, proteins, peptides, and other biological component analysis." . SCR:019574 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_3500xl" ; rdfs:label "Applied Biosystems 3500xl Genetic Analyzer" ; - definition: "Applied Biosystems 3500xL 24-capillary Genetic Analyzer is used for the Human Identification application." . + definition: "Applied Biosystems 3500xL 24-capillary Genetic Analyzer is used for the Human Identification application.Genetic analyzer that utilizes capillary electrophoresis for genetic analysis. It has capillary lengths of 50 cm or 36 cm and can use 384 well plates or 96 well plates." . SCR:019575 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_433A" ; rdfs:label "Applied Biosystems 433A Peptide Sequencer" ; - definition: "Fully automated, programmable peptide synthesizer that performs the chain assembly steps in solid-phase peptide synthesis. It can be usde in FastMoc chemistry. Feedback monitoring control is based on either the conductance or the ultraviolet (UV) absorbance of the reagent, solutions, and solvents used in a synthesis cycle." . + definition: "Automated peptide synthesizer for chain assembly steps in solid phase peptide synthesis or FastMoc chemistry. Data is based on conductance or ultraviolet UV absorbance of reagent, solutions, and solvents in the synthesis cycle." . SCR:019576 a NLX:63400, owl:NamedIndividual ; @@ -139677,8 +139826,8 @@ SCR:019576 a NLX:63400, SCR:019577 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_PCR 9700" ; - rdfs:label "Applied Biosystems PCR 9700 Matrix Assisted Laser Desorption Ionization Time of Flight Instrument" ; - definition: "GeneAmp PCR System 9700 is used for the amplification of nucleic acids using the Polymerase Chain Reaction (PCR) process." . + rdfs:label "Applied Biosystems GeneAmp 9700 PCR Thermocycler System" ; + definition: "Automated PCR instrument for automated amplification of nucleic acids with Polymerase Chain Reaction. It has reaction volumes of up to 50 uL and sample temperature range of 4 to 99.9 C." . SCR:019578 a NLX:63400, owl:NamedIndividual ; @@ -139695,14 +139844,15 @@ SCR:019579 a NLX:63400, SCR:019580 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_XT" ; - rdfs:label "ArcturusXT" ; - definition: "ArcturusXT offers infrared (IR) laser enabled laser capture microdissection (LCM) and ultraviolet (UV) laser cutting and provides a solution for microgenomics research." . + rdfs:label "Arcturus Cellect Laser Capture Microdissection System" ; + definition: "Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR." . SCR:019581 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_MFP_3D" ; - rdfs:label "Asylum MFP 3D Atomic Force Microscope" ; - definition: "MFP-3D Infinity is used for routine imaging tasks and can support your most ambitious projects." . + oboInOwl:hasDbXref "Model_Number_MFP_3D", + "SCR_020365" ; + rdfs:label "Asylum Research MFP 3D Atomic Force Microscopes" ; + definition: "Asylum Research MFP-3D family of AFM's extend beyond basic topography measurements with diverse set of available accessories designed to enhance capabilities of the AFM. These include accessories for making nano-electric measurements, for example conductivity and piezoelectric response, measurements under magnetic fields, measuring nanomechanical properties, and controlling the temperature and humidity." . SCR:019582 a NLX:63400, owl:NamedIndividual ; @@ -139737,8 +139887,8 @@ SCR:019586 a NLX:63400, SCR:019587 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Autosamdri 815B" ; - rdfs:label "Autosamdri 815B Critical Point Dryer" ; - definition: "Supercritical Autosamdri-815B´s is a Critical point dryer with wafer holders and inserts are provided that allow anti-stiction processing up to 5 pieces of either 4\" (100mm), 3\" (75mm), 2\" (50mm) wafers or 10mm square die per process run! Microprocessor controller allows for complete automatic processing. All internal surfaces are inert to CO2 and ultra pure alcohols. Repeatable operating parameters insuring reproducibility of results. Integrated temperature controls. Internal rupture disc built in for safety. Processes up to 5 x 4\" (100mm) diam. wafers per run; comes with additional HF compatible wafer holders to process 5 x 3\" (75mm), 5 x 2\" (50mm) diameter wafers or 5 x 10mm square die (Tousimis HF compatible Wafer Holders* can be used to transport and process your wafers and die from HF)." . + rdfs:label "Tousimis Autosamdri 815B Critical Point Dryer" ; + definition: "Critical point dryer with wafer holders that allow automatic anti stiction processing up to 5 pieces of either 100mm, 75mm, 50mm wafers or 10mm square die per process run. All internal surfaces are inert to CO2 and ultra pure alcohols." . SCR:019588 a NLX:63400, owl:NamedIndividual ; @@ -139766,9 +139916,10 @@ SCR:019591 a NLX:63400, SCR:019592 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Aria_IIu" ; + oboInOwl:hasDbXref "Model_Number_Aria_IIu", + "SCR_019598" ; rdfs:label "BD Biosciences FACSAria IIu High Speed Cell Sorter" ; - definition: "The High Speed Cell Sorter's primary function is to examine complex populations of cells and yield pure populations of cells." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5,2023. High Speed Cell Sorter's primary function is to examine complex populations of cells and yield pure populations of cells." . SCR:019593 a NLX:63400, owl:NamedIndividual ; @@ -139802,31 +139953,35 @@ SCR:019597 a NLX:63400, SCR:019598 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Aria IIu" ; - rdfs:label "BD FACSAria IIu High Speed Cell Sorter" ; - definition: "Aria has four lasers, 405, 488, 561 and 633 nm, and can detect light in sixteen photomultiplier tubes. Its primary function is to examine complex populations of cells and yield pure populations of cells. The Aria can sort lymphocytes at a rate of approximately 15,000 events per second. For larger cells, the rate is much slower in order to optimize the passage of cells through the instrument. Cells from single populations can be sorted into 96-well plates. Alternatively, the Aria can sort into two 15-ml tubes or four 5-ml tubes. The Aria can purify samples that are simply positive and negative for a single fluorophore or as complex as nine-color samples with intricate gating schemes. The BD FACSAria IIu cell sorter is a high speed benchtop digital flow cytometer equipped with a sensitive, fixed-alignment cuvette flow cell. It has three spatially separated lasers - 405 nm, 488 nm and 633 nm. Its primary function is to analyze complex populations of cells and yield pure populations of cells meeting defined criteria. The sorter can purify samples that are simply positive and negative for a single fluorophore or as complex as multi-color samples with complex gating strategies. Sorting can be performed into two or four tubes with speeds up to 25,000 events/second. The system sorts by incorporating cells from the sample tube into a stream of sterile PBS. The stream is interrogated by the lasers at the flow cell and the system electronics keeps track of each cell as they pass through the laser and determines specific cells that meet the sort criteria. A transducer vibrates the stream and induces droplet formation, with cells in the stream being incorporated into the droplets. If a cell meets the sorting criteria and is in the last drop before the break off, the instrument will charge that drop. The charged droplet is then deflected into the proper collection tube by the charge plates. Different cell types can be sorted with the use of 70 �m, 85 �m and 100 �m nozzles. If you need a yellow-green (561 nm) laser, check the BD FACSAria III instead." . + rdfs:label "BD Biosciences FACSAria IIu High Speed Cell Sorter" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5,2023. High Speed Cell Sorter's primary function is to examine complex populations of cells and yield pure populations of cells." . SCR:019599 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_FACS Jazz" ; - rdfs:label "BD FACSJazz JazzFlow" ; - definition: "BD FACSJazz cell sorter incorporates design features that simplify operation of stream-in-air cell sorters, to increase the operational efficiency of labs with high workloads, making the most commonly used sorting applications accessible to researchers with limited flow cytometry experience. The key features include factory-optimized settings, alignment, real-time video monitoring, and BD FACS Accudrop technology. Requiring less than 2 x 2 ft (20 x 20 in, 51 x 51 cm) of bench space, the BD FACSJazz is an easy fit in a core facility or an individual lab. The power supply, electronics, and fluid tanks are placed below the lab bench to allow the instrument to occupy a reduced footprint or be installed easily in a biological safety cabinet (BSC). The BD FACSJazz can be configured with up to three lasers and eight parameters to support application requirements for individuals and core labs. In a core lab, the BD FACSJazz can offload sorting demand and free high-end sorters by handling routine applications such as cloning. The system has also been designed to meet the needs of individuals for applications such as single-cell analysis, which are driving the accelerated pace of genomics and nextgeneration sequencing." . + oboInOwl:hasDbXref "Model_Number_FACSJazz", + "SCR_019875" ; + rdfs:label "BD FACS Jazz Cell Sorter" ; + definition: "Cell sorter that uses principles of flow cytometry to collect only cells of interest from heterogenous suspension. Can be configured with up to three lasers and eight parameters." . SCR:019600 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Fortessa X-20" ; - rdfs:label "BD LSRFortessa X-20 Fortessa Flow Cytometer" ; + oboInOwl:hasDbXref "Model_Number_LSRFortessa", + "SCR_019601", + "SCR_019602" ; + rdfs:label "BD LSRFortessa Flow Cytometer" ; + NIFRID:synonym "BD LSRFortessa Cell Analyzer" ; definition: "BD LSRFortessa cell analyzer offers the ultimate in choice for flow cytometry, providing power, performance, and consistency. Designed to be and expandable, the BD LSRFortessa has the flexibility to support the expanding needs of multicolor flow cytometry assays. The BD LSRFortessa system can be configured with up to 7 lasers*,blue, red, violet, UV and yellow-green. The instrument can accommodate the detection of up to 18 colors simultaneously with a defined set of optical filters that meet or exceed the majority of today's assay requirements. BD FACSDiva software controls the efficient setup, acquisition, and analysis of flow cytometry data from the BD LSRFortessa workstation. The software is common across BD FACS instrument families, including the BD FACSCanto cell analyzer and BD FACSAria cell sorter systems." . SCR:019601 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Fortessa" ; - rdfs:label "BD LSRFortessa Fortessa Flow Cytometer" ; + oboInOwl:hasDbXref "Model_Number_LSRFortessa" ; + rdfs:label "BD LSRFortessa Flow Cytometer" ; definition: "BD LSRFortessa cell analyzer offers the ultimate in choice for flow cytometry, providing power, performance, and consistency. Designed to be and expandable, the BD LSRFortessa has the flexibility to support the expanding needs of multicolor flow cytometry assays. The BD LSRFortessa system can be configured with up to 7 lasers*,blue, red, violet, UV and yellow-green. The instrument can accommodate the detection of up to 18 colors simultaneously with a defined set of optical filters that meet or exceed the majority of today's assay requirements. BD FACSDiva software controls the efficient setup, acquisition, and analysis of flow cytometry data from the BD LSRFortessa workstation. The software is common across BD FACS instrument families, including the BD FACSCanto cell analyzer and BD FACSAria cell sorter systems." . SCR:019602 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Fortessa X-50" ; - rdfs:label "BD LSRFortessa X-50 Fortessa Flow Cytometer" ; + oboInOwl:hasDbXref "Model_Number_LSRFortessa" ; + rdfs:label "BD LSRFortessa Flow Cytometer" ; definition: "BD LSRFortessa cell analyzer offers the ultimate in choice for flow cytometry, providing power, performance, and consistency. Designed to be and expandable, the BD LSRFortessa has the flexibility to support the expanding needs of multicolor flow cytometry assays. The BD LSRFortessa system can be configured with up to 7 lasers*,blue, red, violet, UV and yellow-green. The instrument can accommodate the detection of up to 18 colors simultaneously with a defined set of optical filters that meet or exceed the majority of today's assay requirements. BD FACSDiva software controls the efficient setup, acquisition, and analysis of flow cytometry data from the BD LSRFortessa workstation. The software is common across BD FACS instrument families, including the BD FACSCanto cell analyzer and BD FACSAria cell sorter systems." . SCR:019603 a NLX:63400, @@ -139843,8 +139998,8 @@ SCR:019604 a NLX:63400, SCR:019605 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_X50" ; - rdfs:label "BD LSRFortessa X-50 X50" ; + oboInOwl:hasDbXref "Model_Number_LSRFortressa" ; + rdfs:label "BD LSRFortessa cell analyzer" ; definition: "BD LSRFortessa cell analyzer provides power, performance, and consistency and supports the expanding needs of multicolor flow cytometry assays." . SCR:019606 a NLX:63400, @@ -139963,9 +140118,10 @@ SCR:019624 a NLX:63400, SCR:019625 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Biomek FX" ; - rdfs:label "Beckman Coulter Biomek FX Liquid Handler" ; - definition: "Beckman Coulter Biomek NXp Robotic Liquid Handler is and uatomated liquid handler designed to handle every aspect of liquid handling, pipetting, dilution, dispensing and integration in to one compact unit that will let you add laboratory automation where you need it. This efficient robotic liquid handler is set with a Span-8 pipette model, 4 fixed tip heads and 4 disposables, with rotating gripper and 8 channel liquid level sensing for an efficient and hands-free workflow. This automated workstation has up to 12 deck positions, automated labware positioners, and labware stacking for on deck storage. The open-ended flexibility of this robotic handler helps keep your lab agile and adaptable to your needs. The Beckman Coulter Biomek NXp Automated Workstation has a dispensing volume of between 0.5 �L - 5,000 �L and supports labware from tubes to 1,536-well microplates with accurate intra-well pipetting. The Biomek NXP can integrate with third party devices, and is configurable to meet specific applications needs. This automated workstation is computer controlled through the Biomek software, a robust suite that compliments this efficient instrument with methods and capabilities for genomic, drug discovery & basic research workflows. The Biomek software guides users through set up and protocols, quickly and easily through an icon based interface, with data tracking and LIMS connectivity." . + oboInOwl:hasDbXref "Model_Number_Biomek_NXp", + "SCR_019720" ; + rdfs:label "Beckman Coulter Biomek NXp Robotic Liquid Handler" ; + definition: "Beckman Coulter Biomek NXp Robotic Liquid Handler is and automated liquid handler designed to handle every aspect of liquid handling, pipetting, dilution, dispensing and integration in to one compact unit that will let you add laboratory automation where you need it. This efficient robotic liquid handler is set with a Span-8 pipette model, 4 fixed tip heads and 4 disposables, with rotating gripper and 8 channel liquid level sensing for an efficient and hands-free workflow. This automated workstation has up to 12 deck positions, automated labware positioners, and labware stacking for on deck storage. The open-ended flexibility of this robotic handler helps keep your lab agile and adaptable to your needs." . SCR:019626 a NLX:63400, owl:NamedIndividual ; @@ -140071,9 +140227,10 @@ SCR:019642 a NLX:63400, SCR:019643 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Dxl_800" ; - rdfs:label "Beckman Coulter Dxl 800 Immunoassay Analyzer" ; - definition: "Immunoassay Analyzer can run up to 400 tests per hour and handle workloads with ease." . + oboInOwl:hasDbXref "Model_Number_Dxl_800", + "SCR_019668" ; + rdfs:label "Beckman Coulter UniCel DxI 800 Access Immunoassay System" ; + definition: "Immunoassay analyzer that can run up to 400 tests per hour and has a broad assay test menu." . SCR:019644 a NLX:63400, owl:NamedIndividual ; @@ -140126,9 +140283,11 @@ SCR:019651 a NLX:63400, SCR:019652 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_L_90K" ; + oboInOwl:hasDbXref "Model_Number_L-90K", + "SCR_019673" ; rdfs:label "Beckman Coulter Optima L-90K Ultracentrifuge" ; - definition: "Centrifuge that has a performance capability of 694,000 x g at up to 90,000 rpm. The floor model is compatible with range of rotors including zonal and continuous flow for large-volume separations." . + NIFRID:synonym "Beckman L-90K Ultracentrifuge" ; + definition: "Beckman Optima L-90K Ultracentrifuge has a performance capability of 694,000 x g at up to 90,000 rpm. This versatile floor model is compatible with a wide range of superior rotors including zonal and continuous flow for large-volume separations. The Optima L-90 K is for applications such as subcellular particles and virus isolations, and high-purity plasmid DNA. Featuring an imbalance-tolerant drive, the L-90 K provides unmatched reliability with its highly efficient vacuum-encased induction drive which allows smooth and quiet performance. Plus, this ultracentrifuge model is sized for efficient operation within laminar flow hoods. Equipped with easy-to-use, environment-friendly and microprocessor based control cooling systems, the Beckman L-90 K eliminated the use of CFCs and other dangerous liquid refrigerants. This Beckman centrifuge also has an overspeed system to ensure that rotors do not exceed maximum speed." . SCR:019653 a NLX:63400, owl:NamedIndividual ; @@ -140146,7 +140305,8 @@ SCR:019655 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_XL-I" ; rdfs:label "Beckman Coulter ProteomeLab XL-I AUC XL-I" ; - definition: "ProteomeLab XL-A/XL-I is a centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures delivers accurate results you can rely on time and again. In-solution characterization allows for testing in native conditions, meaning you determine the sample testing environment that best suits your needs. The column-free separating technique of the ProteomeLab XL-A/XL-I measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems. And, because the measurements are based on the first principles of thermodynamics and hydrodynamics, no standards or calibrations are required. As a result, you spend less time on setup and more time on discovery. Our analytical ultracentrifuge platform offers a variety of customizable options, to meet your needs. Sensitive absorbance optics enable analysis of most samples, and interference optics can be used for low concentrations. Both systems can be implemented simultaneously, to maximize data acquisition in a single run. Additionally, we offer two different rotor configurations, and a variety of cell types, to enable multiple experimental designs. The wide range of rotational velocities also allow investigators to probe protein size, dimerization, and binding constants." . + definition: """THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 5th,2023. +ProteomeLab XL-A/XL-I is a centrifuge with in-solution characterization of proteins, oligomers, aggregates, particles, colloids, and small structures delivers accurate results you can rely on time and again. In-solution characterization allows for testing in native conditions, meaning you determine the sample testing environment that best suits your needs. The column-free separating technique of the ProteomeLab XL-A/XL-I measures the relative change in the distribution of molecular weights, providing an efficient way to measure heterogeneity, stoichiometry and self-associating systems. And, because the measurements are based on the first principles of thermodynamics and hydrodynamics, no standards or calibrations are required. As a result, you spend less time on setup and more time on discovery. Our analytical ultracentrifuge platform offers a variety of customizable options, to meet your needs. Sensitive absorbance optics enable analysis of most samples, and interference optics can be used for low concentrations. Both systems can be implemented simultaneously, to maximize data acquisition in a single run. Additionally, we offer two different rotor configurations, and a variety of cell types, to enable multiple experimental designs. The wide range of rotational velocities also allow investigators to probe protein size, dimerization, and binding constants.""" . SCR:019656 a NLX:63400, owl:NamedIndividual ; @@ -140198,8 +140358,9 @@ SCR:019663 a NLX:63400, SCR:019664 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Vicell XR" ; - rdfs:label "Beckman Coulter Vi-Cell XR cell counter (ISO 6 clean room) Vicell" ; + oboInOwl:hasDbXref "Model_Number_Vicell XR", + "SCR_019672" ; + rdfs:label "Beckman Coulter Vi-CELL XR Cell Viability Analyzer" ; definition: "Cell counter that provides an automatic means to perform the Trypan Blue Dye Exclusion method, allowing users to load up to 9 samples at once for easy and automated cell analysis, and offers pre-programmed and customizable analysis options for consistent and accurate analysis." . SCR:019665 a NLX:63400, @@ -140246,14 +140407,15 @@ SCR:019671 a NLX:63400, SCR:019672 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Vicell" ; - rdfs:label "Beckman-Coulter ViCell Vicell" ; + oboInOwl:hasDbXref "Model_Number_Vicell XR" ; + rdfs:label "Beckman Coulter Vi-CELL XR Cell Viability Analyzer" ; definition: "Cell counter that provides an automatic means to perform the Trypan Blue Dye Exclusion method, allowing users to load up to 9 samples at once for easy and automated cell analysis, and offers pre-programmed and customizable analysis options for consistent and accurate analysis." . SCR:019673 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_L-90K" ; - rdfs:label "Beckman L-90K Ultracentrifuge" ; + rdfs:label "Beckman Coulter Optima L-90K Ultracentrifuge" ; + NIFRID:synonym "Beckman L-90K Ultracentrifuge" ; definition: "Beckman Optima L-90K Ultracentrifuge has a performance capability of 694,000 x g at up to 90,000 rpm. This versatile floor model is compatible with a wide range of superior rotors including zonal and continuous flow for large-volume separations. The Optima L-90 K is for applications such as subcellular particles and virus isolations, and high-purity plasmid DNA. Featuring an imbalance-tolerant drive, the L-90 K provides unmatched reliability with its highly efficient vacuum-encased induction drive which allows smooth and quiet performance. Plus, this ultracentrifuge model is sized for efficient operation within laminar flow hoods. Equipped with easy-to-use, environment-friendly and microprocessor based control cooling systems, the Beckman L-90 K eliminated the use of CFCs and other dangerous liquid refrigerants. This Beckman centrifuge also has an overspeed system to ensure that rotors do not exceed maximum speed." . SCR:019674 a NLX:63400, @@ -140272,6 +140434,8 @@ SCR:019676 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_3000" ; rdfs:label "Biacore 3000 Real Time Biomolecular Interaction Analyzer" ; + NIFRID:synonym "BIACORE 3000 GOLDSEAL", + "BiaCore 3000 Surface Plasmon Resonance" ; definition: "Biacore 3000 processing unit is an established, label-free system for detailed studies of biomolecular interactions. The system delivers comprehensive characterization of the interaction, answers questions about the rate constants, affinity, specificity, and determines the active concentration of components. The ability to recover and transfer interaction partners directly to MALDI targets for identification and further characterization makes the system highly applicable to fast identification of unknown interactants." . SCR:019677 a NLX:63400, @@ -140300,15 +140464,18 @@ SCR:019680 a NLX:63400, SCR:019681 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Biologic" ; + oboInOwl:hasDbXref "Model_Number_Biologic_LP", + "SCR_019682" ; rdfs:label "Bio-Rad Biologic Protein Purification System" ; + NIFRID:synonym "Bio-Rad BioLogic LP System" ; definition: "Low-pressure chromatography system that is used for biomolecule purification with nucleic acid and protein detection. It has 254 and 280 nm filters, conductive cell, and a peristaltic pump with flow rate range of 0.05 to 40 ml per min." . SCR:019682 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_LP" ; - rdfs:label "Bio-Rad BioLogic LP System" ; - definition: "Low-pressure chromatography system that is used for biomolecule purification. Its compact design minimizes workspace required in coldroom or on laboratory bench." . + oboInOwl:hasDbXref "Model_Number_Biologic_LP" ; + rdfs:label "Bio-Rad Biologic Protein Purification System" ; + NIFRID:synonym "Bio-Rad BioLogic LP System" ; + definition: "Low-pressure chromatography system that is used for biomolecule purification with nucleic acid and protein detection. It has 254 and 280 nm filters, conductive cell, and a peristaltic pump with flow rate range of 0.05 to 40 ml per min." . SCR:019683 a NLX:63400, owl:NamedIndividual ; @@ -140348,9 +140515,10 @@ SCR:019688 a NLX:63400, SCR:019689 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_ELx_808" ; - rdfs:label "Bio-Rad ELx808 Microplate Reader" ; - definition: "Microplate reader that has four-zone temperature control for temperature sensitive assays. It can be used for Kinetic ELISA, Protein quantification, ELISA, Endotoxin analysis, and Microbial growth assays. It is used with Gen5 software." . + oboInOwl:hasDbXref "Model_Number_ELx_808", + "SCR_019739" ; + rdfs:label "Biotek ELx808 Microplate Reader" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 31,2023. Microplate reader that offers performance for many applications, from endpoint to fast kinetic protocols. Offers 4 Zone temperature control, which optimizes conditions for temperature sensitive assays.Can be used for Kinetic ELISA, Protein quantification, ELISA, Endotoxin analysis, and Microbial growth assays. It is used with Gen5 software." . SCR:019690 a NLX:63400, owl:NamedIndividual ; @@ -140398,7 +140566,7 @@ SCR:019697 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Quest_100" ; rdfs:label "Bio-Rad NGC Quest 100 Chromatography System" ; - definition: "Chromatography system that is used for the all-purpose purification of biomolecules from samples in the mg to g range with accurate buffer gradients and high-resolution separations." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 31,2023. Chromatography system that is used for the all-purpose purification of biomolecules from samples in the mg to g range with accurate buffer gradients and high-resolution separations." . SCR:019698 a NLX:63400, owl:NamedIndividual ; @@ -140486,14 +140654,20 @@ SCR:019711 a NLX:63400, SCR:019712 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_ZE5" ; + oboInOwl:hasDbXref "Model_Number_ZE5", + "SCR_019713", + "SCR_019717" ; rdfs:label "Bio-Rad ZE5 Cell Analyzer" ; - definition: "Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals." . + NIFRID:synonym "Bio-Rad ZE5 Cell Analyzer Flow Cytometer", + "Bio-Rad ZE5/Yeti Cell Analyzer Flow Cytometer", + "BioRad ZE5" ; + definition: "BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals." . SCR:019713 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_ZE5" ; - rdfs:label "Bio-Rad ZE5 Cell Analyzer Flow Cytometer" ; + rdfs:label "Bio-Rad ZE5 Cell Analyzer" ; + NIFRID:synonym "Bio-Rad ZE5 Cell Analyzer Flow Cytometer" ; definition: "Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals." . SCR:019714 a NLX:63400, @@ -140516,9 +140690,12 @@ SCR:019716 a NLX:63400, SCR:019717 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_ZE5/Yeti" ; - rdfs:label "Bio-Rad ZE5/Yeti Cell Analyzer Flow Cytometer" ; - definition: "Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals." . + oboInOwl:hasDbXref "Model_Number_ZE5" ; + rdfs:label "Bio-Rad ZE5 Cell Analyzer" ; + NIFRID:synonym "Bio-Rad ZE5 Cell Analyzer Flow Cytometer", + "Bio-Rad ZE5/Yeti Cell Analyzer Flow Cytometer", + "BioRad ZE5" ; + definition: "BioRad ZE5 was formerly known as the Propel Labs YETI Cytometer with configurations to meet broad range of experimental complexities and throughput needs. Accessible for novice flow cytometry users yet flexible enough for most experienced flow cytometry professionals." . SCR:019718 a NLX:63400, owl:NamedIndividual ; @@ -140534,9 +140711,9 @@ SCR:019719 a NLX:63400, SCR:019720 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_NXp" ; - rdfs:label "BioMek NXp NXp" ; - definition: "Beckman Coulter Biomek NXp Robotic Liquid Handler is designed to handle every aspect of liquid handling, pipetting, dilution, dispensing and integration in to one compact unit that will let you add laboratory automation where you need it. This efficient robotic liquid handler is set with a Span-8 pipette model, 4 fixed tip heads and 4 disposables, with rotating gripper and 8 channel liquid level sensing for an efficient and hands-free workflow. This automated workstation has up to 12 deck positions, automated labware positioners, and labware stacking for on deck storage. The open-ended flexibility of this robotic handler helps keep your lab agile and adaptable to your needs. The Beckman Coulter Biomek NXp Automated Workstation has a dispensing volume of between 0.5 �L - 5,000 �L and supports labware from tubes to 1,536-well microplates with accurate intra-well pipetting. The Biomek NXP can integrate with third party devices, and is configurable to meet specific applications needs. This automated workstation is computer controlled through the Biomek software, a robust suite that compliments this efficient instrument with methods and capabilities for genomic, drug discovery & basic research workflows. The Biomek software guides users through set up and protocols, quickly and easily through an icon based interface, with data tracking and LIMS connectivity." . + oboInOwl:hasDbXref "Model_Number_Biomek_NXp" ; + rdfs:label "Beckman Coulter Biomek NXp Robotic Liquid Handler" ; + definition: "Beckman Coulter Biomek NXp Robotic Liquid Handler is and automated liquid handler designed to handle every aspect of liquid handling, pipetting, dilution, dispensing and integration in to one compact unit that will let you add laboratory automation where you need it. This efficient robotic liquid handler is set with a Span-8 pipette model, 4 fixed tip heads and 4 disposables, with rotating gripper and 8 channel liquid level sensing for an efficient and hands-free workflow. This automated workstation has up to 12 deck positions, automated labware positioners, and labware stacking for on deck storage. The open-ended flexibility of this robotic handler helps keep your lab agile and adaptable to your needs." . SCR:019721 a NLX:63400, owl:NamedIndividual ; @@ -140624,8 +140801,10 @@ SCR:019734 a NLX:63400, SCR:019735 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_EL406" ; + oboInOwl:hasDbXref "Model_Number_EL406", + "SCR_019747" ; rdfs:label "BioTek EL406 Washer Dispenser" ; + NIFRID:synonym "BioTek EL406 Microtiter Plate Washer" ; definition: "Microplate washer that is equipped for full plate washing along with three reagent dispensers in one and includes washing and dispensing for standard assays, biomagnetic separation and vacuum filtration protocols." . SCR:019736 a NLX:63400, @@ -140648,9 +140827,10 @@ SCR:019738 a NLX:63400, SCR:019739 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_ELx808" ; - rdfs:label "BioTek ELx808 Absorbance Reader" ; - definition: "Microplate reader that offers performance for many applications, from endpoint to fast kinetic protocols. Offers 4 Zone temperature control, which optimizes conditions for temperature sensitive assays." . + oboInOwl:hasDbXref "Model_Number_ELx_808" ; + rdfs:label "Biotek ELx808 Microplate Reader" ; + NIFRID:synonym "BioTek ELx808 Absorbance Reader" ; + definition: "Microplate reader that offers performance for many applications, from endpoint to fast kinetic protocols. Offers 4 Zone temperature control, which optimizes conditions for temperature sensitive assays.Can be used for Kinetic ELISA, Protein quantification, ELISA, Endotoxin analysis, and Microbial growth assays. It is used with Gen5 software." . SCR:019740 a NLX:63400, owl:NamedIndividual ; @@ -140697,7 +140877,8 @@ SCR:019746 a NLX:63400, SCR:019747 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_EL406" ; - rdfs:label "Biotek EL406 Microtiter Plate Washer" ; + rdfs:label "BioTek EL406 Washer Dispenser" ; + NIFRID:synonym "BioTek EL406 Microtiter Plate Washer" ; definition: "Microplate washer that is equipped for full plate washing along with three reagent dispensers in one and includes washing and dispensing for standard assays, biomagnetic separation and vacuum filtration protocols." . SCR:019748 a NLX:63400, @@ -140727,25 +140908,29 @@ SCR:019751 a NLX:63400, SCR:019752 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_3200" ; - rdfs:label "Bose 3200 Mechanical Testing Apparatus" ; - definition: "Mechanical testing apparatus that features a 225 N (450 N optional) maximum force and is adaptable to a variety of biomedical research and engineered materials test applications, including torsion testing, creep under dynamic loading and special environments (hot/cold chambers)." . + rdfs:label "TA Instruments Electroforce 3200 Mechanical Testing Apparatus" ; + definition: "Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications." . SCR:019753 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_OpenArray NT Cycler" ; - rdfs:label "BioTrove OpenArray NT Thermal Cycler" ; + oboInOwl:hasDbXref "Model_Number_OpenArray NT Cycler", + "SCR_020349" ; + rdfs:label "BioTrove OpenArray NT Cycler System" ; definition: "Optical thermal cycler that is capable of cycling and imaging up to three OpenArray plates simultaneously. System includes: NT Cycler, computer, flat-panel monitor, OpenArray AutoLoader, and Case Sealing Station. Requires analysis software kit for operation." . SCR:019754 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_BI-200SM" ; - rdfs:label "Brookhaven Instruments BI-200SM Goniometer" ; - definition: "Bl-200SM Research Goniometer System is a precision instrument designed for exacting scattering measurements. It provides access to automatic, modular, and versatile system applications. Based on a special turntable with precision ball bearings and stepping motor, the Bl-200SM's modern design and quality construction guarantee precise measurements due to the wobble-free movement of the detector. It is field in hundreds of laboratories. It is best for macro-molecular studies and submicron particle sizing. By taking advantage of the multiple inputs available on the TurboCorr correlator a new capability of the BI-200SM system is created. By adding an optical signal splitter to the beam of scattered light and a second detector it is possible to eliminate the effects of very high speed interference from the detector(s). This Cross Correlation System provides remarkably clean information as seen in the article we have presented. The BI-200SM's modularity simplifies system expansion. Featuring a standard optical rail, the BI-200SM can be used with neutral density filters, a polarizer, an analyzer, and a reference detector. Special sample requirements can often be met by changing the cell holder design or size." . + oboInOwl:hasDbXref "Model_Number_BI-200SM", + "SCR_019755" ; + rdfs:label "Brookhaven Instruments BI-200SM Research Goniometer" ; + NIFRID:synonym "Brookhaven Instruments BI-200SM Goniometer" ; + definition: "Goniometer that is used for macro molecular studies and submicron particle sizing with static and dynamic light scattering. It can be used with neutral density filters, polarizer, analyzer, and reference detector." . SCR:019755 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_BI200SM" ; + oboInOwl:hasDbXref "Model_Number_BI-200SM" ; rdfs:label "Brookhaven Instruments BI-200SM Research Goniometer" ; + NIFRID:synonym "Brookhaven Instruments BI-200SM Goniometer" ; definition: "Goniometer that is used for macro molecular studies and submicron particle sizing with static and dynamic light scattering. It can be used with neutral density filters, polarizer, analyzer, and reference detector." . SCR:019756 a NLX:63400, @@ -140897,8 +141082,10 @@ SCR:019780 a NLX:63400, SCR:019781 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_microTof" ; - rdfs:label "Bruker micrOTOF-Q II LC/MS" ; + oboInOwl:hasDbXref "Model_Number_micrOTOF-Q II", + "SCR_019784" ; + rdfs:label "Bruker micrOTOF-Q II Liquid Chromatography Mass Spectrometer" ; + NIFRID:synonym "Bruker micrOTOF-Q II LC/MS" ; definition: "Benchtop Q-Tof, applied to a variety of applications such as small molecule accurate mass determination (HRMS), intact protein analysis including antibodies, peptide mapping, and other custom projects. This system is operated with an Agilent 1260 UPLC and includes an inline diode array detector and ESI source." . SCR:019782 a NLX:63400, @@ -140915,8 +141102,9 @@ SCR:019783 a NLX:63400, SCR:019784 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_microTof-Q II" ; + oboInOwl:hasDbXref "Model_Number_micrOTOF-Q II" ; rdfs:label "Bruker micrOTOF-Q II Liquid Chromatography Mass Spectrometer" ; + NIFRID:synonym "Bruker micrOTOF-Q II LC/MS" ; definition: "Benchtop Q-Tof mass spectrometer for small molecule accurate mass determination (HRMS), intact protein analysis, and peptide mapping. This system is operated with Agilent 1260 UPLC." . SCR:019785 a NLX:63400, @@ -141011,9 +141199,10 @@ SCR:019799 a NLX:63400, SCR:019800 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_In_Vitro" ; - rdfs:label "Bruker Ultima In Vitro Multiphoton Microscope" ; - definition: "Multiphoton microscope that provides simultaneous imaging and electrophysiology, plus uncaging and photostimulation for complete stimulus and recording environment required for research for neuroscientists." . + oboInOwl:hasDbXref "Model_Number_Ultima_In_Vitro" ; + rdfs:label "Bruker Ultima In Vitro Multiphoton Microscope System" ; + NIFRID:synonym "Bruker Ultima In Vitro Multiphoton Microscope" ; + definition: "Fluorescence microscopy system by Bruker. Multiphoton imaging system for intravital imaging applications in neuroscience, oncology and immunology using Bruker Prairie View software to provide turnkey operation for imaging as well as synchronizing Ultima system with external stimulus and experimental control devices." . SCR:019801 a NLX:63400, owl:NamedIndividual ; @@ -141197,7 +141386,8 @@ SCR:019830 a NLX:63400, SCR:019831 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_R730" ; + oboInOwl:hasDbXref "Model_Number_R730", + "SCR_019843" ; rdfs:label "Dell PowerEdge R730 Rack Server" ; definition: "Server delivers outstanding functionality in just 2U of rack space. With the combination of processors, large memory, fast storage options and GPU accelerator support, the R730 performs exceptionally well in a number of demanding environments." . @@ -141240,8 +141430,10 @@ SCR:019837 a NLX:63400, SCR:019838 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_BNII" ; - rdfs:label "Dade Behring BNII Nephelometer" ; - definition: "Siemens Dade Behring BN II Nephelometer is leading fully automated system for plasma protein determinations. This third generation nephelometer combines reliability with a highly cost-effective performance. BN II systems offer advanced nephelometric technology that provides an performance in plasma protein analysis. This instrument's menu covers assays, which support various clinical tests including cardiac risk assessment, kidney diseases and nutritional assessment. markers such as Cystatin C and Carbohydrate-Deficient Transferrin (CDT) are also supported. Other features of the Dade Behring BN II Nephelometer include rapid processing, easy operation and random-access mode. The nephelometer also permits users to put up to 100 samples on board, making it best for mid to high-volume processing." . + rdfs:label "Siemens Dade Behring BNII Nephelometer System" ; + NIFRID:synonym "Dade Behring BN II Nephelometer", + "Siemens Dade Behring BNII Nephelometer" ; + definition: "Siemens Dade Behring BN II Nephelometer is leading fully automated system for plasma protein determinations. BN II systems offer advanced nephelometric technology that provides performance in plasma protein analysis. This instrument's menu covers assays, which support various clinical tests including cardiac risk assessment, kidney diseases and nutritional assessment. markers such as Cystatin C and Carbohydrate-Deficient Transferrin (CDT) are also supported. Other features of the Dade Behring BN II Nephelometer include rapid processing, easy operation and random-access mode. The nephelometer also permits users to put up to 100 samples on board, making it best for mid to high-volume processing." . SCR:019839 a NLX:63400, owl:NamedIndividual ; @@ -141270,8 +141462,8 @@ SCR:019842 a NLX:63400, SCR:019843 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_R730" ; - rdfs:label "Dell R730" ; - definition: "With the Intel Xeon processor E5-2600 v4 product family and up to 24 DIMMs of DDR4 RAM, the R730 has the processing cycles and threads and large memory footprint necessary to deliver more, larger and higher-performing virtual machines for data centers and cloud platforms. Highly scalable storage, with up to 16 x 12Gb SAS drives and the high-performance 12Gb PowerEdge RAID Controller (PERC9), can greatly accelerate data access for your virtualized environment. In addition, the R730 can take advantage of optional SanDisk DAS Cache application acceleration technology for even faster data access." . + rdfs:label "Dell PowerEdge R730 Rack Server" ; + definition: "Server delivers outstanding functionality in just 2U of rack space. With the combination of processors, large memory, fast storage options and GPU accelerator support, the R730 performs exceptionally well in a number of demanding environments." . SCR:019844 a NLX:63400, owl:NamedIndividual ; @@ -141371,21 +141563,22 @@ SCR:019859 a NLX:63400, SCR:019860 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5804_5804R" ; - rdfs:label "Eppendorf Centrifuge 5804/5804R Centrifuge" ; + oboInOwl:hasDbXref "Model_Number_5804R" ; + rdfs:label "Eppendorf 5804R Centrifuge" ; definition: "Centrifuge for medium capacity needs that allows for molecular applications in tubes up to 250 mL and offers additional swing bucket and fixed angle rotors as well as deepwell plate capacity for versatility. It has a centrifugation speed of up to14,000 rpm." . SCR:019861 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5810_5810R" ; - rdfs:label "Eppendorf Centrifuge 5810/ 5810 R Centrifuge" ; + oboInOwl:hasDbXref "Model_Number_5810" ; + rdfs:label "Eppendorf 5810 Centrifuge" ; definition: "Centrifuge that is used for medium to high throughput laboratories and combines versatility and capacity for both tubes and plates with compact footprint." . SCR:019862 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5073m" ; - rdfs:label "Eppendorf epMotion 5073m Liquid Handler" ; - definition: "Automated liquid handling system that is tailored for nucleic acid purification, but is flexible for other liquid handling tasks. Integrated magnetic finger and ThermoMixer module is used for magnetic bead based purifications." . + oboInOwl:hasDbXref "Model_Number_5073m", + "SCR_019871" ; + rdfs:label "Eppendorf epMotion 5073m Automated Pipetting system" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 3, 2023. Automated pipetting workstation that is tailored for nucleic acid purification, but can be used for other liquid handling tasks. Integrated magnetic finger and ThermoMixer module is used for magnetic bead based purifications." . SCR:019863 a NLX:63400, owl:NamedIndividual ; @@ -141433,13 +141626,13 @@ SCR:019870 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_4i" ; rdfs:label "Eppendorf FemtoJet 4i" ; - definition: "Eppendorf's electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the \"heavy duty\" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only." . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023. Eppendorf's electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the \"heavy duty\" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only." . SCR:019871 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_epMotion_5073m" ; - rdfs:label "Eppendorf epMotion 5073m Automated Pipetting" ; - definition: "Automated pipetting workstation that is tailored for nucleic acid purification, but can be used for other liquid handling tasks. Integrated magnetic finger and ThermoMixer module is used for magnetic bead based purifications." . + rdfs:label "Eppendorf epMotion 5073m Automated Pipetting system" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 3, 2023. Automated pipetting workstation that is tailored for nucleic acid purification, but can be used for other liquid handling tasks. Integrated magnetic finger and ThermoMixer module is used for magnetic bead based purifications." . SCR:019872 a NLX:63400, owl:NamedIndividual ; @@ -141462,8 +141655,8 @@ SCR:019874 a NLX:63400, SCR:019875 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_FACSJazz" ; - rdfs:label "FACS Jazz Cell Sorter" ; - definition: "BD FACSJazz cell sorter incorporates design features that simplify operation of stream-in-air cell sorters, to increase the operational efficiency of labs with high workloads, making the most commonly used sorting applications accessible to researchers with limited flow cytometry experience. The key features include factory-optimized settings, alignment, real-time video monitoring, and BD FACS Accudrop technology. Requiring less than 2 x 2 ft (20 x 20 in, 51 x 51 cm) of bench space, the BD FACSJazz is an easy fit in a core facility or an individual lab. The power supply, electronics, and fluid tanks are placed below the lab bench to allow the instrument to occupy a reduced footprint or be installed easily in a biological safety cabinet (BSC). The BD FACSJazz can be configured with up to three lasers and eight parameters to support application requirements for individuals and core labs. In a core lab, the BD FACSJazz can offload sorting demand and free high-end sorters by handling routine applications such as cloning. The system has also been designed to meet the needs of individuals for applications such as single-cell analysis, which are driving the accelerated pace of genomics and nextgeneration sequencing." . + rdfs:label "BD FACS Jazz Cell Sorter" ; + definition: "Cell sorter that uses principles of flow cytometry to collect only cells of interest from heterogenous suspension. Can be configured with up to three lasers and eight parameters." . SCR:019876 a NLX:63400, owl:NamedIndividual ; @@ -141702,8 +141895,8 @@ SCR:019914 a NLX:63400, SCR:019915 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_4x" ; - rdfs:label "FemtoJet 4x electronic microinjector" ; - definition: "Eppendorf electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the \"heavy duty\" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only." . + rdfs:label "Eppendorf FemtoJet 4x electronic microinjector" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14, 2023. Eppendorf electronic microinjectors FemtoJet 4i and FemtoJet 4x with their operation menu and a range of functionalities are perfectly suited for injecting small to intermediate volumes. With a built-in compressor, the FemtoJet 4i is the tool of choice for injecting aqueous solutions into adherent cells and suspension cells. If your research demands injecting volumes greater than 100 pL and/or longer series at higher pressures, FemtoJet 4x with its external pressure supply (not included) delivers the precise and continuous pressure required. Featuring the same quality design and compatibility features as the FemtoJet 4i, the FemtoJet 4x is the \"heavy duty\" device for those more demanding applications. Both the FemtoJet 4i and FemtoJet 4x, form the system with Eppendorf micromanipulators, yet they integrate just as easily with non-Eppendorf micromanipulation systems. The electronic connection between FemtoJet 4i or 4x and TransferMan 4r or InjectMan 4 guarantees simple, rapid and reproducible microinjections into cells, simplifying your daily work and speeding up your workflow. The FemtoJet 4i/ 4x injectors are for research use only." . SCR:019916 a NLX:63400, owl:NamedIndividual ; @@ -141761,9 +141954,9 @@ SCR:019924 a NLX:63400, SCR:019925 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_FLA-1500" ; - rdfs:label "FujiFilm FLA-5100 Imager" ; - definition: "Fujifilm Life Science FLA-5100 imaging system allows imaging of fluorescent and radioisotopic samples as large as 40 x 46cm at a pixel size as low as 10 microns. This system is especially suitable for protein electrophoresis in the proteomics field and general array analysis for genomics. Fuji s FLA-5100 includes four imaging solutions in a single system. While optimized for fluorescence, the system also excels at radioisotope (RI) detection using the Imaging Plate method. Additional imaging methodologies include digitization using fluorescence board and chemiluminescence detection by the direct detection method." . + oboInOwl:hasDbXref "Model_Number_FLA_1500" ; + rdfs:label "Fujifilm Life Science FLA-5100 Scanner" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14, 2023. Imaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method." . SCR:019926 a NLX:63400, owl:NamedIndividual ; @@ -141792,8 +141985,8 @@ SCR:019929 a NLX:63400, SCR:019930 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_C1" ; - rdfs:label "Fluidigm C1 C1" ; - definition: "Automated system that carefully isolates single cells into individual reaction chambers in the exclusive Fluidigm integrated fluidic circuit (IFC). C1 lets you prepare single-cell templates for mRNA sequencing, DNA sequencing, epigenetics or miRNA expression. You can extract, reverse transcribe, amplify, and ultimately detect and analyze gene expression using just one technology, eliminating the added variability introduced by human error and multi-platform approaches. With an optimized protocol, pre-formulated reagent kits, and disposable IFCs, users can achieve single-cell accuracy and a cDNA product that is ready for use with the Epigenetics Core's Biomark HD high throughput PCR system." . + rdfs:label "Fluidigm C1 Single-Cell Automated Preparation System" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 14,2023.Automated preparation system that isolates and prepares single cell templates for analysis. It can analyze mRNA and DNA sequencing, epigenetics or miRNA expression. It can extract, reverse transcribe, amplify, and analyze gene expression." . SCR:019931 a NLX:63400, owl:NamedIndividual ; @@ -141942,8 +142135,9 @@ SCR:019954 a NLX:63400, SCR:019955 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_4000B" ; - rdfs:label "GenePix 4000B Rotating hyb ovens for spotted arrays (or Combimatrix arrays). 4000B" ; - definition: "GenePix 4000B Microarray Scanner is a benchmark for quality, reliability and ease-of-use in microarray scanning technology. Coupled with GenePix ProMicroarray Image Analysis Software and Acuity Microarray Informatics Software, the GenePix System sets the highest standards in the acquisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells. GenePix Microarray Scanner flexibility allows you to configure scanning and analysis of one slide or many, whether they are all alike or each is different. The slide loader accommodates low- and high-density; opaque, mirrored, or translucent; plastic or glass; commercial or homebrew slides." . + rdfs:label "Molecular Devices GenePix 4000B Microarray Scanner" ; + NIFRID:synonym "GenePix 4000B Scanner" ; + definition: "Microarray scanner that performs genetic and compound analysis. Coupled with GenePix ProMicroarray Image Analysis Software and Acuity Microarray Informatics Software for acquisition and analysis of data from all types of arrays, including nucleic acids, proteins, tissues, and cells. Scanner flexibility allows to configure scanning and analysis of one slide or many, whether they are all alike or each is different. Slide loader accommodates low- and high-density, opaque, mirrored, or translucent, plastic or glass, commercial or homebrew slides." . SCR:019956 a NLX:63400, owl:NamedIndividual ; @@ -141971,9 +142165,9 @@ SCR:019959 a NLX:63400, SCR:019960 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_EM XPS" ; - rdfs:label "Gemini EM Fluorimeter" ; - definition: "Microplate reader with dual monochromators that can determine the optimal excitation and emission settings for fluorescence intensity assays. Multiple-point well scanning optimizes cell-based assay sensitivity. Comparison of relative fluorescence units (RFUs) between samples is allowed by a calibration against an internal standard. Temperature-sensitive reactions are monitored with consistent temperature regulation from ambient to 45C." . + oboInOwl:hasDbXref "Model_Number_XPS" ; + rdfs:label "Gemini XPS Microplate Reader" ; + definition: "Reader with top-read capability measures fluorescence on variety of sample formats from 6- to 384-well microplates in endpoint, kinetic, spectral scan, and well-scan modes." . SCR:019961 a NLX:63400, owl:NamedIndividual ; @@ -141989,14 +142183,15 @@ SCR:019962 a NLX:63400, SCR:019963 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_GX-271" ; + oboInOwl:hasDbXref "Model_Number_GX_271" ; rdfs:label "Gilson GX-271 HPLC System" ; - definition: "Liquid handler/fraction collector with separate fluid pathways that reduce cross-contamination of samples and fractions. The system accommodates injection loop volumes of 2 �L to 25 mL and sample mass of up to 15 grams per injection. The system can accommodate flow rates up to 200 mL/min." . + definition: "HPLC liquid handler with midsize bed capacity and fraction collector. It has maximum flow rates up to 200 mL per min, injection loop volumes of 2 uL to 25 mL, and max sample mass of 15 grams per injection." . SCR:019964 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_96" ; - rdfs:label "GloMax 96 Microplate Luminometer" ; + rdfs:label "Promega GloMax 96 Microplate Luminometer" ; + NIFRID:synonym "GloMax 96 Microplate Luminometer" ; definition: "Microplate luminometer that features two optional injectors and reads both glow- and flash-luminescent reactions in 96-well plates. The sensitivity and range enable a wide range of luminescent assays, including Promega bioluminescent reporter, cell-based and biochemical assays." . SCR:019965 a NLX:63400, @@ -142037,15 +142232,17 @@ SCR:019970 a NLX:63400, SCR:019971 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_BiOS L" ; - rdfs:label "Hamilton BiOS L Automated Sample Management Platform" ; - definition: "Automated large capacity storage system that is designed for high density, high capacity storage in a compact footprint." . + oboInOwl:hasDbXref "Model_Number_BiOS", + "SCR_019974" ; + rdfs:label "Hamilton BiOS Automated Ultra Low Temperature Freezer system" ; + definition: "BiOS is automated bio freezer storage system specifically designed to store sensitive biological samples. This ultra low temperature freezer is capable of reaching temperatures as low as minus 80°C, ensuring biological specimen integrity. BiOS can be scaled to fit your laboratory needs as a premier option for storing biological samples.Automated sample storage platforms run on INSTINCT S software." . SCR:019972 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_20/20" ; - rdfs:label "GloMax 20/20 Luminometer" ; - definition: "GloMax 20/20 Luminometer combines instrumentation and software for uses includinh bioluminescent assays, protocols and support. You can measure flash or glow-type luminescence, have two fluorescent modules available, and it accommodates 1.5ml microcentrifuge tubes and 35mm petri dishes, with optional 12mm × 50mm test tube adapter. Measure light output from liquid and solid samples; no minimum volume requirements. The GloMax 20/20 blends user-friendly operation and a small footprint." . + rdfs:label "Promega GloMax 20/20 Luminometer" ; + NIFRID:synonym "GloMax 20/20 Luminometer" ; + definition: "Luminometer combines instrumentation and software for uses includinh bioluminescent assays, protocols and support. You can measure flash or glow-type luminescence, have two fluorescent modules available, and it accommodates 1.5ml microcentrifuge tubes and 35mm petri dishes, with optional 12mm × 50mm test tube adapter. Measure light output from liquid and solid samples; no minimum volume requirements. The GloMax 20/20 blends user-friendly operation and a small footprint.This Instrument Was Retired September 1, 2023. Accessories and service available until September 1, 2028." . SCR:019973 a NLX:63400, owl:NamedIndividual ; @@ -142055,9 +142252,9 @@ SCR:019973 a NLX:63400, SCR:019974 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_BiOS XL" ; - rdfs:label "Hamilton BiOS XL Automated Sample Management Platform" ; - definition: "Automated large capacity storage system that is designed for the largest studies to store millions of sensitive biological samples, with the greatest number of safeguards in place" . + oboInOwl:hasDbXref "Model_Number_BiOS" ; + rdfs:label "Hamilton BiOS Automated Ultra Low Temperature Freezer system" ; + definition: "BiOS is automated bio freezer storage system specifically designed to store sensitive biological samples. This ultra low temperature freezer is capable of reaching temperatures as low as minus 80°C, ensuring biological specimen integrity. BiOS can be scaled to fit your laboratory needs as a premier option for storing biological samples.Automated sample storage platforms run on INSTINCT S software." . SCR:019975 a NLX:63400, owl:NamedIndividual ; @@ -142231,7 +142428,8 @@ SCR:020003 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_StarPlus" ; rdfs:label "Hamilton StarPlus Automated Liquid Handler" ; - definition: "Hamilton STARplus liquid handling robotinstrument includes an 8 channel pipetting arm with independent Y axis, and CORE Technology for tip mounting, a 96 channel pipeting head with 1ml capacity, dual HEPA filter top with dial control, barcode scanner, and an iSwap 5 axis gripper with paddle grippers are optional. The unit may include deck hardware: pipette tip racks, temperature controlled plate racks, tube racks, microplate racks, and 50mL temperature controlled tube rack. An extruded aluminum table with locking wheels is available with this unit. All instruments are fully refurbished in excellent condition and come with a minimum 90 day warranty. Application training is not available for Hamilton instruments." . + NIFRID:synonym "Hamilton STARplus" ; + definition: "Liquid handling robot with 8 channel pipetting arm, dual HEPA filter top, and 96 channel pipeting head with 1ml capacity. It can have tube racks, microplate racks, and 50mL temperature controlled tube rack." . SCR:020004 a NLX:63400, owl:NamedIndividual ; @@ -142247,9 +142445,11 @@ SCR:020005 a NLX:63400, SCR:020006 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Verso S1 SE" ; - rdfs:label "Hamilton Verso S1 SE Automated Sample Management Platform" ; - definition: "Verso is used for compound and sample management applications at temperatures from ambient to -20�C." . + oboInOwl:hasDbXref "Model_Number_Verso", + "SCR_020011" ; + rdfs:label "Hamilton Verso Automated Freezer Sample Storage System" ; + NIFRID:synonym "Hamilton Verso" ; + definition: "Hamilton Verso is modular compound management system for automated storage at temperatures from ambient to minus 20°C for high-throughput applications. This compound storage system can easily be configured to meet your needs." . SCR:020007 a NLX:63400, owl:NamedIndividual ; @@ -142278,8 +142478,9 @@ SCR:020010 a NLX:63400, SCR:020011 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Verso" ; - rdfs:label "Hamilton Verso Automated Sample Management Platform" ; - definition: "Verso is used for compound and sample management applications at temperatures from ambient to -20�C." . + rdfs:label "Hamilton Verso Automated Freezer Sample Storage System" ; + NIFRID:synonym "Hamilton Verso" ; + definition: "Hamilton Verso is modular compound management system for automated storage at temperatures from ambient to minus 20°C for high-throughput applications. This compound storage system can easily be configured to meet your needs." . SCR:020012 a NLX:63400, owl:NamedIndividual ; @@ -142951,7 +143152,7 @@ SCR:020123 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_HiSeq 2500" ; rdfs:label "Illumina HiSeq 2500 System" ; - definition: "High throughput sequencing system High quality data using Illumina SBS chemistry," . + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. High-throughput sequencing system. High-quality data using proven Illumina SBS chemistry has made it the instrument of choice for major genome centers and research institutions throughout the world.HiSeq 2500 System has been discontinued. Illumina will support the instrument and intends to supply the reagents through February 28, 2023." . SCR:020124 a NLX:63400, owl:NamedIndividual ; @@ -142963,7 +143164,7 @@ SCR:020125 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_iSeq 100" ; rdfs:label "Illumina iSeq 100 Sequencing System" ; - definition: "Makes next generation sequencing easier. Designed for simplicity, it allows labs of all sizes to sequence DNA and RNA at push of button." . + definition: "Benchtop next-generation sequencer to sequence DNA and RNA." . SCR:020126 a NLX:63400, owl:NamedIndividual ; @@ -142974,8 +143175,8 @@ SCR:020126 a NLX:63400, SCR:020127 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_HiSeq 3000/4000" ; - rdfs:label "Illumina HiSeq 3000/HiSeq 4000 Systems" ; - definition: "Leverage patterned flow cell technology to provide rapid, high performance sequencing Perform production scale, high throughput exome or transcriptome sequencing projects quickly and economically." . + rdfs:label "Illumina HiSeq 3000/HiSeq 4000 Sequencing System" ; + definition: "Sequencer that uses patterned flow cell technology to provide high-performance sequencing. Perform production-scale, high-throughput exome or transcriptome sequencing projects quickly and economically." . SCR:020128 a NLX:63400, owl:NamedIndividual ; @@ -142987,67 +143188,68 @@ SCR:020129 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_cBot" ; rdfs:label "Illumina cBot Genetic Amplifier" ; - definition: "cBot is a Genetic Amplifier that uses amplification to create hundreds of millions of single-molecule DNA templates simultaneously. The cBot software dispenses reagents and controls reaction times, flow rates, and temperatures. Setup and operation are performed on-instrument from the cBot software interface using the touch screen monitor. An on-instrument barcode reader records the reagents and flow cell used for each experiment." . + definition: "Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures." . SCR:020130 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_HiSeq 2000" ; - rdfs:label "Illumina HiSeq 200 HiSeq 200" ; - definition: "HiSeq 2000 sequencing system (Figure 1) offers unprecedented output and a breakthrough user experience. Leveraging Illumina's and widely-adopted, reversible terminator-based sequencing by synthesis chemistry in combination with engineering, HiSeq 2000 delivers the industry's highest sequencing output and fastest data generation rate. Human interaction design features and the easiest sequencing workflow set a new standard for simplicity and user experience. With unmatched cost-effectiveness, HiSeq 2000 is the first commercially available sequencer to enable researchers to obtain ~30× coverage of two human genomes in a single run for under $10,000 (USD)* per sample." . + oboInOwl:hasDbXref "Model_Number_HiSeq2000", + "SCR_020132" ; + rdfs:label "Illumina HiSeq2000 Sequencing System" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15, 2023. HiSeq 2000 sequencing system for sequencing and fastest data generation rate." . SCR:020131 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_HiSeq X" ; - rdfs:label "Illumina HiSeq X Five and Ten Systems" ; - definition: "Discontinued Breaks 1000 dollars genome barrier for human whole genome sequencing." . + rdfs:label "Illumina HiSeq X" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15,2023. Sequencer for whole-genome sequencing. System consists of HiSeq X ultra-high-throughput instruments that deliver over 18,000 human genomes per year." . SCR:020132 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_HiSeq2000" ; - rdfs:label "Illumina HiSeq2000 High Throughput Genetic Sequencer" ; - definition: "HiSeq 2000 sequencing system (Figure 1) offers unprecedented output and a breakthrough user experience. Leveraging Illumina's and widely-adopted, reversible terminator-based sequencing by synthesis chemistry in combination with engineering, HiSeq 2000 delivers the industry's highest sequencing output and fastest data generation rate. Human interaction design features and the easiest sequencing workflow set a new standard for simplicity and user experience. With unmatched cost-effectiveness, HiSeq 2000 is the first commercially available sequencer to enable researchers to obtain ~30× coverage of two human genomes in a single run for under $10,000 (USD)* per sample." . + rdfs:label "Illumina HiSeq2000 Sequencing System" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 15, 2023. HiSeq 2000 sequencing system for sequencing and fastest data generation rate." . SCR:020133 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_MiSeq FGx" ; rdfs:label "Illumina MiSeq FGx System" ; - definition: "Next generation sequencing NGS solution designed for forensic science Dedicated library kits and analytical software take you from DNA to answer with streamlined efficiency." . + definition: "MiSeq FGx Forensic Genomics System is the first fully validated, next-generation sequencing (NGS) solution designed for forensic science. Dedicated library kits and analytical software take you from DNA-to-answer with streamlined efficiency." . SCR:020134 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_MiSeq" ; rdfs:label "Illumina MiSeq System" ; - definition: "Access focused applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more. MiSeq reagents enable up to 15 Gb of output with 25 million sequencing reads and 2 × 300 bp read lengths." . + definition: "MiSeq System offers wide range of sequencing applications. Capable of automated paired end reads and up to 15 Gb per run, delivering over 600 bases of sequence data per read. The library prep kits are optimized for variety of applications, including targeted gene, small genome, and amplicon sequencing, 16S metagenomics." . SCR:020135 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_GX II" ; - rdfs:label "Illumina Labchip GX II" ; + oboInOwl:hasDbXref "Model_Number_GX_II" ; + rdfs:label "Illumina LabChip GXII Touch protein characterization system" ; definition: "LabChip GXII Touch is a protein characterization system that provides reproducible quantitation, molecular weight sizing and percent purity analysis of protein samples. Leveraging microfluidic electrophoretic separation technology, the LabChip GXII Touch system enables rapid characterization with minimal sample preparation setup and sample input volume." . SCR:020136 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_MiniSeq" ; - rdfs:label "Illumina MiniSeq Next Generation Sequencer" ; - definition: "Illumina NGS technology performs broad range of targeted DNA and RNA applications." . + rdfs:label "Illumina MiniSeq System" ; + definition: "MiniSeq System to perform range of targeted DNA and RNA applications for low numbers of samples." . SCR:020137 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_MiSeqDx" ; rdfs:label "Illumina MiSeqDx System" ; - definition: "FDA regulated, CE IVD marked, NGS platform for in vitro diagnostic IVD testing." . + definition: "MiSeqDx System is FDA-regulated, CE-IVD-marked, NGS platform for in vitro diagnostic (IVD) testing. System offers both diagnostic and research modes." . SCR:020138 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_NextSeq 550Dx" ; rdfs:label "Illumina NextSeq 550Dx System" ; - definition: "FDA regulated and CE in vitro diagnostic IVD marked, enabling clinical laboratories to develop and perform wide range of applications, from NGS IVD assays using targeted panels, to clinical research applications that include methods from targeted panels to whole genomes." . + definition: "Sequencer that is CE-in vitro diagnostic (IVD) marked, enabling clinical laboratories to develop and perform a wide range of applications, from NGS IVD assays using targeted panels, to clinical research applications that include methods from targeted panels to whole genomes." . SCR:020139 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_NeoPrep" ; rdfs:label "Illumina NeoPrep Library Preparation System" ; - definition: "NeoPrep Library Prep System is a fully integrated library preparation solution with a workflow that produces 16 quantified and normalized sequencing-ready libraries per run. This seamless solution delivers high quality and reproducible results, even with low input amounts of DNA or RNA. There are 3 steps in the NeoPrep workflow: run preparation, library card loading, and library collection. The same workflow prepares any type of library, including libraries that require complex workflows when prepared manually, and needs just 30 minutes of hands-on time." . + definition: "Library preparation system that produces 16 sequencing ready libraries per run. There are steps in NeoPrep workflow run preparation, library card loading, and library collection." . SCR:020140 a NLX:63400, owl:NamedIndividual ; @@ -143063,17 +143265,18 @@ SCR:020141 a NLX:63400, SCR:020142 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_ImageStreamX" ; - rdfs:label "Amnis ImageStreamX Mk II Imaging Flow Cytometer" ; - NIFRID:synonym "Image Analyzer (4 lasers/10 colors) Multiple", - "ImageStream-X", - "ImageStreamX Mk II System" ; - definition: "Benchtop, multispectral, imaging flow cytometer designed for acquisition of up to 12 channels of cellular imagery. By collecting large numbers of digital images per sample and providing a numerical representation of image-based features, the ImageStreamX Mk II combines the per cell information content provided by standard microscopy with the statistical significance afforded by large sample sizes common to standard flow cytometry. With the ImageStreamX Mk II System, fluorescence intensity measurements are acquired as with a conventional flow cytometer; however, the best applications for the ImageStreamX Mk II take advantage of the system's imaging abilities to locate and quantitate the distribution of signals on in or between cells." . + oboInOwl:hasDbXref "Model_Number_MkII" ; + rdfs:label "Luminex Amnis ImageStream MkII Multispectral Imaging Flow Cytometer" ; + NIFRID:synonym "Luminex ImageStream MkII Flow Cytometer", + "Luminex ImageStream MkII Multispectral Imaging Flow Cytometer", + "MkII imaging flow cytometer" ; + definition: """Bench top multispectral imaging flow cytometer designed for the acquisition of +up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry.""" . SCR:020143 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_280A" ; - rdfs:label "Isotemp 280A Vacuum Oven" ; + rdfs:label "Fisher Scientific Isotemp 280A Vacuum Oven" ; definition: "Fisher Scientific Isotemp 280A is a Vacuum Oven offers a temperature range from ambient up to 200C with internal dimensions of 11.125\"D x 9.75\"W x 9.75\"H. Front-mounted power indicator and dial thermometer with top-mounted analog vacuum gauge. The 280A's hydraulic thermostat controls temperature. Large glass panel front door and stainless steel chamber." . SCR:020144 a NLX:63400, @@ -143090,9 +143293,10 @@ SCR:020145 a NLX:63400, SCR:020146 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_100CX" ; - rdfs:label "JEOL 100C/CX Transmission Electron Microscope" ; - definition: "JEOL JEM-100CX II transmission electron microscope is an electron microscope with imaging capabilities at low to high magnifications (90X to 800, 000X). A 10M-pixel HAMAMASTU C4742-95 digital camera is integrated to the system for high-resolution image acquisition." . + oboInOwl:hasDbXref "Model_Number_100CX II", + "SCR_020153" ; + rdfs:label "JEOL JEM-100CX II Transmission Electron Microscope" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2023.JEOL JEM-100CX II transmission electron microscope is an electron microscope with imaging capabilities at low to high magnifications (90X to 800, 000X). A 10M-pixel HAMAMASTU C4742-95 digital camera is integrated to the system for high- image acquisition." . SCR:020147 a NLX:63400, owl:NamedIndividual ; @@ -143132,9 +143336,9 @@ SCR:020152 a NLX:63400, SCR:020153 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_100C" ; - rdfs:label "JEOL 100C Transmission Electron Microscope" ; - definition: "JEOL JEM-100CX II transmission electron microscope is an electron microscope with imaging capabilities at low to high magnifications (90X to 800, 000X). A 10M-pixel HAMAMASTU C4742-95 digital camera is integrated to the system for high-resolution image acquisition." . + oboInOwl:hasDbXref "Model_Number_100CX II" ; + rdfs:label "JEOL JEM-100CX II Transmission Electron Microscope" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 5,2023. JEOL JEM-100CX II transmission electron microscope is an electron microscope with imaging capabilities at low to high magnifications (90X to 800, 000X). A 10M-pixel HAMAMASTU C4742-95 digital camera is integrated to the system for high-resolution image acquisition." . SCR:020154 a NLX:63400, owl:NamedIndividual ; @@ -143447,7 +143651,7 @@ SCR:020205 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_6" ; rdfs:label "Kent Scientific 6 Blood Pressure System" ; - definition: "CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. The included software allows you to continuously view data in real-time." . + definition: "CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. The included software allows you to continuously view data in real-time.CODA High Throughput System with 6 Activated Channels." . SCR:020206 a NLX:63400, owl:NamedIndividual ; @@ -143511,9 +143715,11 @@ SCR:020215 a NLX:63400, SCR:020216 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_DMI6000B" ; - rdfs:label "Leica 6000B 6000B" ; - definition: "Leica DMI6000 B inverted microscope for biomedical research offers Differential Interference Contrast (DIC) for relief imaging of specimens with varying indices of refraction. The , automated Leica DMI6000 B is best for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. The system features an automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide and reproducible results. For special diagnostics requirements, the microscope is certified for in-vitro-diagnostics (IVD) like in-vitro-fertilization (IVF)." . + oboInOwl:hasDbXref "Model_Number_DMI6000_B" ; + rdfs:label "Leica DMI6000 B inverted microscope" ; + NIFRID:synonym "Leica DMI6000 B", + "Leica DMI6000 B Fully Automated Inverted Research Microscope" ; + definition: "Inverted microscope for biomedical research. Offers Differential Interference Contrast for relief imaging of specimens with varying indices of refraction. Used for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. Features automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide convenience and reproducible results." . SCR:020217 a NLX:63400, owl:NamedIndividual ; @@ -143529,15 +143735,18 @@ SCR:020218 a NLX:63400, SCR:020219 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_5500B" ; - rdfs:label "Leica DM 5500B Automated Upright Microscope System" ; - definition: "With motorized z-focus, coded 7x nosepiece, fully automated transmitted light axis, and fully automated 5x or 8x fluorescence axis, the automated Leica DM5500 B research microscope provides all transmitted and fluorescence light contrast methods including the world's first fully automated Differential Interference Contrast (DIC).The Z drive is motorized, which offers the of automatic parfocality adjustment, saved focus levels, and automated positioning of various Z levels." . + oboInOwl:hasDbXref "Model_Number_DM5500_B" ; + rdfs:label "Leica DM5500 B Automated Upright Microscope System" ; + NIFRID:synonym "Leica DM5500 B Microscope" ; + definition: "Fluorescence microscope capable of contrast microscopy and has ability for fully automated Differential Interference Contrast techniques. This product has been archived and replaced with the Leica DM4 B and DM6 B microscopes." . SCR:020220 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_6000B" ; - rdfs:label "Leica DMI 6000B Fully Automated Inverted Research Microscope" ; - definition: "Leica DMI6000 B is an inverted microscope for biomedical research, is best for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. The system features an automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide and reproducible results." . + oboInOwl:hasDbXref "Model_Number_DM6000_B" ; + rdfs:label "Leica DMI6000 B inverted microscope" ; + NIFRID:synonym "Leica DMI6000 B", + "Leica DMI6000 B Fully Automated Inverted Research Microscope" ; + definition: "Inverted microscope for biomedical research. Offers Differential Interference Contrast for relief imaging of specimens with varying indices of refraction. Used for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. Features automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide convenience and reproducible results." . SCR:020221 a NLX:63400, owl:NamedIndividual ; @@ -143547,9 +143756,11 @@ SCR:020221 a NLX:63400, SCR:020222 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_EM AFS2" ; - rdfs:label "Leica EM AFS2 EM AFS2" ; - definition: "Leica EM AFS2 performs freeze substitution and progressive lowering of temperature (PLT) techniques and allows low temperature embedding and polymerization of resins. The Leica EM FSP (freeze substitution processor), an automatic reagent handling system combined with the Leica EM AFS2, dispenses reagents for both freeze substitution and PLT applications. The LED illumination from within the chamber and the attached stereomicroscope for viewing and positioning of samples ensures ease of use." . + oboInOwl:hasDbXref "Model_Number_EM_AFS2", + "SCR_020230" ; + rdfs:label "Leica EM AFS2 Freeze Substitution and Low Temperature Embedding System" ; + NIFRID:synonym "Leica EM AFS2" ; + definition: "System for Light and Electron Microscopy. Performs freeze substitution and progressive lowering of temperature techniques and allows low temperature embedding and polymerization of resins. Leica EM FSP (freeze substitution processor), automatic reagent handling system combined with Leica EM AFS2, dispenses reagents for both freeze substitution and PLT applications. The LED illumination from within the chamber and the attached stereomicroscope for viewing and positioning of samples ensures ease of use." . SCR:020223 a NLX:63400, owl:NamedIndividual ; @@ -143583,9 +143794,9 @@ SCR:020227 a NLX:63400, SCR:020228 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_6000" ; - rdfs:label "Leica DMi6000 Spinning Disk Microscope" ; - definition: "Leica DMI6000 B inverted microscope for biomedical research is best for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. The system features an automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide and reproducible results. For special diagnostics requirements, the microscope is certified for in-vitro-diagnostics (IVD) like in-vitro-fertilization (IVF)." . + oboInOwl:hasDbXref "Model_Number_DMI6000_B" ; + rdfs:label "Leica DMI6000 B inverted microscope" ; + definition: "Inverted microscope for biomedical research. Offers Differential Interference Contrast for relief imaging of specimens with varying indices of refraction. Used for fluorescence, live cell, time-lapse imaging, high-speed multi-fluorescence optical sectioning, and micromanipulation. Features automated contrast and illumination manager, motorized Z focus, parfocality function, automatic brightness and diaphragm adjustment, and many other automated functions that provide convenience and reproducible results.Archived Product. Replaced by DMi8 S." . SCR:020229 a NLX:63400, owl:NamedIndividual ; @@ -143595,9 +143806,9 @@ SCR:020229 a NLX:63400, SCR:020230 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_AFS2" ; - rdfs:label "Leica EM AFS2 Freeze Substitution Device" ; - definition: "Leica EM AFS2 is a freeze substitution platform that performs freeze substitution and progressive lowering of temperature (PLT) techniques and allows low temperature embedding and polymerization of resins. The Leica EM FSP (freeze substitution processor), an automatic reagent handling system combined with the Leica EM AFS2, dispenses reagents for both freeze substitution and PLT applications. The LED illumination from within the chamber and the attached stereomicroscope for viewing and positioning of samples ensures ease of use." . + oboInOwl:hasDbXref "Model_Number_EM_AFS2" ; + rdfs:label "Leica EM AFS2 Freeze Substitution and Low Temperature Embedding System" ; + definition: "System for Light and Electron Microscopy. Performs freeze substitution and progressive lowering of temperature techniques and allows low temperature embedding and polymerization of resins. Leica EM FSP (freeze substitution processor), automatic reagent handling system combined with Leica EM AFS2, dispenses reagents for both freeze substitution and PLT applications. The LED illumination from within the chamber and the attached stereomicroscope for viewing and positioning of samples ensures ease of use." . SCR:020231 a NLX:63400, owl:NamedIndividual ; @@ -143631,9 +143842,8 @@ SCR:020235 a NLX:63400, SCR:020236 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Countess FL" ; rdfs:label "Life Technologies Countess Automated Cell Counter" ; - definition: "Countess Automated Cell Counter from Invitrogen is a benchtop automated cell counter. It can perform cell counts as well as viability and cell calculations. The Countess has a touch screen display and allows data to be transferred via USB drive to a computer for data access and storage.Automated cell counter with the option for a reusable hemocytometer and fluorescence capabilities. With the option for a reusable slide and fluorescence capabilities brightfield and two user-changeable fluorescence channels the Invitrogen Countess II FL Automated Cell Counter can count cells, monitor fluorescent protein expression, and measure cell viability in as little as 10 seconds." . + definition: "Invitrogen benchtop automated cell counter. Can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels." . SCR:020237 a NLX:63400, owl:NamedIndividual ; @@ -143661,9 +143871,10 @@ SCR:020240 a NLX:63400, SCR:020241 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Ultracut E" ; - rdfs:label "Leica Ultracut E Ultramicrotome" ; - definition: "Ultracut E microtome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5,�m and has adjustable cutting speeds of 0.1 to 50 mm/sec. Comes with a control box with power cord, a microtome sectioning unit, and a microscope assembly with AO Stereostar 570 zoom body (0.7X - 4.2X) with attached 10X eyepieces. It has a 6V, 10W halogen illumination system." . + oboInOwl:hasDbXref "Model_Number_Ultracut E", + "SCR_020426" ; + rdfs:label "Leica Reichert-Jung Ultracut E Microtome" ; + definition: "Ultracut E microtome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5,m and has adjustable cutting speeds of 0.1 to 50 mm/sec. Comes with a control box with power cord, a microtome sectioning unit, and a microscope assembly with AO Stereostar 570 zoom body (0.7X - 4.2X) with attached 10X eyepieces. It has a 6V, 10W halogen illumination system." . SCR:020242 a NLX:63400, owl:NamedIndividual ; @@ -143675,13 +143886,15 @@ SCR:020243 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_VT1200S" ; rdfs:label "Leica VT1200S vibrating microtome" ; - definition: "Fully automated Leica VT1200 S vibrating blade microtome is designed to meet the highest sectioning demands for cutting fresh and fixed tissue in Neuroscience. To achieve sections of the highest quality that retain viable cells on the section surface, the vertical deflection of the blade can be measured by Leica's Vibrocheck measurement device and minimised with the blade holder. The instrument was designed in collaboration with Prof. Dr. Peter Jonas and his group at the Physiology Department, Freiburg Germany." . + definition: "Vibrating blade microtome for sectioning by Leica Biosystems used in neurophysiology, neuropathology, experimental pathology, botany. Fully automated Leica VT1200 S vibrating blade microtome for cutting fresh and fixed tissue in Neuroscience. To achieve sections of the highest quality that retain viable cells on the section surface, the vertical deflection of the blade can be measured by Leica's Vibrocheck measurement device and minimised with the blade holder. The instrument was designed in collaboration with Prof. Dr. Peter Jonas and his group at the Physiology Department, Freiburg Germany." . SCR:020244 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_ImageStream" ; - rdfs:label "Luminex Amnis Image Stream Flow Cytometer" ; - definition: "ImageStreamX Mk II System is a benchtop, multispectral, imaging flow cytometer designed for the acquisition of up to 12 channels of cellular imagery. By collecting large numbers of digital images per sample and providing a numerical representation of image-based features, the ImageStreamX Mk II combines the per cell information content provided by standard microscopy with the statistical significance afforded by large sample sizes common to standard flow cytometry. With the ImageStreamX Mk II System, fluorescence intensity measurements are acquired as with a conventional flow cytometer; however, the best applications for the ImageStreamX Mk II take advantage of the system's imaging abilities to locate and quantitate the distribution of signals on in or between cells." . + oboInOwl:hasDbXref "Model_Number_ImageStreamX_MkII" ; + rdfs:label "Luminex Amnis ImageStreamX Mk II System" ; + NIFRID:synonym "ImageStreamX Mk II System" ; + definition: """Bench top multispectral imaging flow cytometer designed for the acquisition of +up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry.""" . SCR:020245 a NLX:63400, owl:NamedIndividual ; @@ -143766,7 +143979,8 @@ SCR:020260 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_ITC 200" ; rdfs:label "Microcal ITC 200 Isothermal Titration Calorimeter" ; - definition: "Highly sensitive, low volume isothermal titration calorimeter for the label-free in solution study of biomolecular interactions. It delivers direct measurement of all binding parameters in a single experiment and can analyze weak to high affinity binders, using as little as 10 �g sample. Semi-automated maintenance minimizes operator intervention and the system is upgradable to the fully automated MicroCal Auto-iTC200, making it best for laboratories where speed, sensitivity and the ability to accommodate higher workloads in the future are paramount." . + NIFRID:synonym "MicroCal iTC200" ; + definition: "Isothermal titration calorimeter for label free, in solution, study of biomolecular interactions. It delivers measurement of binding parameters with minimum of 10 ug sample." . SCR:020261 a NLX:63400, owl:NamedIndividual ; @@ -143794,9 +144008,10 @@ SCR:020264 a NLX:63400, SCR:020265 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_007 HF" ; - rdfs:label "Micromax 007 HF Generator" ; - definition: "Generator used as home lab X-ray source for protein crystallography.Popular source for small molecule crystallographers who need the additional flux of a rotating anode generator. The original MicroMax 007 introduced the world to the concept of a sub-100 micron focal spot size along the increased brilliance that can be more effectively used to illuminate small crystals. The current HF version increases the power loading by 50% over the original model providing an X-ray source that rivals second generation synchrotron sources - but with better beam stability and, of course, easy access." . + oboInOwl:hasDbXref "Model_Number_MicroMax 007HF", + "SCR_020445" ; + rdfs:label "Rigaku MicroMax-007 HF generator" ; + definition: "Microfocus rotating anode X ray generator.Used for Protein crystallography, small molecule crystallography, SAXS, micro diffraction, phase contrast imaging. Home lab X-ray source for protein crystallography and a popular source for small molecule crystallographers who need the additional flux of a rotating anode generator. The original MicroMax 007 introduced the world to the concept of a sub-100 micron focal spot size along the increased brilliance that can be more effectively used to illuminate small crystals. The current HF version increases the power loading by 50% over the original model providing an X-ray source that rivals second generation synchrotron sources - but with better beam stability and, of course, easy access." . SCR:020266 a NLX:63400, owl:NamedIndividual ; @@ -144114,7 +144329,7 @@ SCR:020317 a NLX:63400, SCR:020318 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_A1" ; - rdfs:label "Nikon A1 Confocal Laser Microscope" ; + rdfs:label "Nikon A1 Confocal Laser Scanning Microscope" ; definition: "Fully automated A1 offers standard paired galvanometers with high resolution scanning at up to 4096 x 4096 pixels. The A1R model incorporates a hybrid scanner system utilizing a high speed resonant galvanometer capable of acquisitions up to 240 frames per second. Both scanners can be used simultaneously for experiments requiring acquisition and photoactivation by concurrently scanning the specimen. This supports advanced research methods using photoactivation fluorescence proteins and facilitates high-speed, live-cell work with a huge array of new imaging strategies. A spectral imaging detector further enables the A1 and A1R models to obtain up to 32 discreet spectral bandwidths of data in one acquisition, with spectral unmixing capabilities. The total system is controlled through NIS-Elements C applications software, which also enables full control of the Nikon Ti-E research inverted microscope equipped with Nikon's Focus System (PFS), widefield CCD cameras and an array of hardware devices." . SCR:020319 a NLX:63400, @@ -144162,14 +144377,14 @@ SCR:020325 a NLX:63400, SCR:020326 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_E800" ; - rdfs:label "Nikon E800 E800" ; + rdfs:label "Nikon E800" ; definition: "Building upon the success of the popular CFI60 optical system (60-millimeter parfocal distance and 25-millimeter objective thread size) first installed on the Eclipse E600, Nikon has moved a step further by introducing ultra-low magnification objectives and has increased the standard field of view to 25 millimeters. Introduced with the Eclipse E800 was a plan 0.5x magnification objective, which accommodates a 50-millimeter field of view at the unprecedented magnification of 0.5x. When coupled with a 2x projection lens, the 0.5x objective permits macrophotography at 1:1 magnification (in effect, actual size documentation). The new macro objective lens is particularly useful for investigating large specimens such as brain slices, developing embryos, and extensive tissue sections. This objective is easily accommodated into the microscope without major re-configuration, and is interchangeable with other objectives on a standard rotating nosepiece." . SCR:020327 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_SMZ1500" ; rdfs:label "Nikon SMZ1500 Zoom Stereoscope" ; - definition: "First manufactured in 2000, the Nikon SMZ1500 features new apochromatic objectives that improve resolving power and achieve higher numerical apertures than previous models. A zoom ratio of 15 to 1 provides the SMZ1500 with a range of magnifications from 0.75x to 11.25x for a total magnifying capability of 3.75x up to 540x, depending on the oculars and objectives selected. Click stops on the instrument's zoom knob allow the microscopist to zoom from 1x to 11x at 1x-intervals without interrupting observations. Other facets of the SMZ1500 optical system include high-eyepoint eyepieces with built-in diopter adjustments, a wide field of view, and a built-in aperture diaphragm for achieving optimal depth of focus and improved photomicrography." . + definition: "SMZ1500 stereoscopic zoom microscope is system with apochromatic objectives, zoom ratio of 15 to 1, range of magnifications from 0.75x to 11.25x for total magnifying capability of 3.75x up to 540x, and is best for in depth imaging.Zoom knob allows to zoom from 1x to 11x at 1x-intervals without interrupting observations. Other facets include high eyepoint eyepieces with built-in diopter adjustments, wide field of view, and built-in aperture diaphragm for achieving optimal depth of focus and improved photomicrography.Provides options of either low eye-level viewing tube or tilting eyepiece tube, with or without eye-level risers. Three different diascopic stands with built-in power supplies may also be utilized with instrument, or standard stand that features low profile for increased clearance." . SCR:020328 a NLX:63400, owl:NamedIndividual ; @@ -144185,9 +144400,9 @@ SCR:020329 a NLX:63400, SCR:020330 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Qi Click" ; - rdfs:label "Nikon E600 microscope with a Qimaging QI Click camera E600" ; - definition: "E600 Fluorescence Microscope is equipped with a detachable substage, a 12-volt 100-watt tungsten-halide lamp, filter magazine, and a choice of sextuple nosepiece or sextuple DIC nosepiece. The microscope features a longer focal length tube lens, a characteristic feature of the new CFI60 infinity optical system, and a new multiple point rigid design for attaching accessories. Advanced universal objectives allow for multiple observation techniques -- such as brightfield, darkfield, Nomarski DIC, epi-fluorescence or phase contrast -- eliminating the need to change objectives while maintaining the same optical quality as dedicated lenses." . + oboInOwl:hasDbXref "Model_Number_E600" ; + rdfs:label "Nikon Eclipse E600 Fluorescence Microscope" ; + definition: "Microscope equipped with CFI60 infinity optical system, providing images in all applications. Incorporates specifications adopted for CFI60 series objectives, including 60 millimeter parfocal distance, 25 millimeter thread size, and standard 22 millimeter field of view. Main components of CFI60 infinity optical system include objective, tube lens to converge light beam, and eyepiece lens to enlarge intermediate image. Fluorescence microscope that has detachable substage, 12 volt 100 watt tungsten halide lamp, filter magazine, and choice of sextuple nosepiece or sextuple DIC nosepiece.Has objectives for brightfield, darkfield, Nomarski DIC, epi fluorescence, or phase contrast techniques." . SCR:020331 a NLX:63400, owl:NamedIndividual ; @@ -144239,7 +144454,8 @@ SCR:020338 a NLX:63400, SCR:020339 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_300" ; + oboInOwl:hasDbXref "Model_Number_FV300", + "SCR_020345" ; rdfs:label "Olympus FluoView 300 Confocal Microscope" ; definition: "Confocal microscopy can improve conventional fluorescence images by recording fluorescence generated from the focal plane within the sample, while rejecting all other light coming from above or below the focal plane. The efficient point-scan/pinhole-detection confocal optics of the FluoView systems virtually eliminate out of focus light to produce high-contrast images with superb resolution. The FluoView systems are fully integrated workstations that incorporate user-friendly image acquisition and image analysis software with high-resolution confocal optics that require no user alignment. An , Windows-based graphic user interface allows new users to quickly generate images in various scan modes, such as XY, XZ, XT, XYZ, XYT, and XYZT. Standard image formats, including TIFF and AVI, permit easy, direct export of FluoView images to off-line analysis packages. XY scanning is performed with a pair of galvanometric mirrors, yielding a wide scanning range to cover up to a field number of 20. The optical zoom (up to 10x magnification) can be performed by narrowing the scanning range while maintaining the maximum pixel resolution of up to 2048 x 2048 pixels." . @@ -144300,8 +144516,8 @@ SCR:020348 a NLX:63400, SCR:020349 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_NTCycler" ; - rdfs:label "OpenArray NTCycler (Life Technologies)" ; + oboInOwl:hasDbXref "Model_Number_OpenArray NT Cycler" ; + rdfs:label "BioTrove OpenArray NT Cycler System" ; definition: "Optical thermal cycler capable of cycling and imaging up to three OpenArray plates simultaneously. System includes: NT Cycler, computer, flat-panel monitor, OpenArray AutoLoader, and Case Sealing Station. Requires analysis software kit for operation." . SCR:020350 a NLX:63400, @@ -144396,9 +144612,9 @@ SCR:020364 a NLX:63400, SCR:020365 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Infinity" ; - rdfs:label "Oxford MFP-3D Infinity AFM" ; - definition: "MFP 3D Infinity makes routine imaging tasks easier and faster to complete while also supporting projects." . + oboInOwl:hasDbXref "Model_Number_MFP_3D" ; + rdfs:label "Asylum Research MFP 3D Atomic Force Microscopes" ; + definition: "Asylum Research MFP-3D family of AFM's extend beyond basic topography measurements with diverse set of available accessories designed to enhance capabilities of the AFM. These include accessories for making nano-electric measurements, for example conductivity and piezoelectric response, measurements under magnetic fields, measuring nanomechanical properties, and controlling the temperature and humidity." . SCR:020366 a NLX:63400, owl:NamedIndividual ; @@ -144559,9 +144775,9 @@ SCR:020391 a NLX:63400, SCR:020392 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_3441" ; - rdfs:label "Pelco 34700 Biowave Microwave Processor" ; - definition: "Laboratory microwave system has a combination of features not found with any other microwave system. These include: True Variable Wattage, water recirculation system, temperature restrictive temperature probe, RS232 Port, Cable and Software, Programmable times, Four intermittent power settings, Magnetron prewarming, Air Bubbler, and Vacuum Cycling." . + oboInOwl:hasDbXref "Model_Number_34700" ; + rdfs:label "PELCO BioWave 34700 laboratory microwave system" ; + definition: "Laboratory microwave system that includes True Variable Wattage, water recirculation system, temperature restrictive temperature probe, RS232 Port, Cable and Software, Programmable times, Four intermittent power settings, Magnetron prewarming, Air Bubbler, and Vacuum Cycling. System has precision temperature control and monitoring for microwave assisted processing of tissue. Can be used for formalin fixation, decalcification, special stains, immunocytochemistry and complete processing of tissue into paraffin." . SCR:020393 a NLX:63400, owl:NamedIndividual ; @@ -144590,8 +144806,8 @@ SCR:020396 a NLX:63400, SCR:020397 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_IVIS" ; - rdfs:label "Perkin Elmer IVIS Spectrum In-Vivo Imaging System" ; - definition: "In vivo imaging system combines 2D optical and 3D optical tomography in one platform. The system uses leading optical technology for preclinical imaging research and development best for non-invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals." . + rdfs:label "Perkin Elmer IVIS Spectrum In Vivo Imaging System" ; + definition: "In vivo imaging system that combines two dimensional and three dimensional optical tomography in one platform.The system uses leading optical technology for preclinical imaging research and development best for non-invasive longitudinal monitoring of disease progression, cell trafficking and gene expression patterns in living animals." . SCR:020398 a NLX:63400, owl:NamedIndividual ; @@ -144649,8 +144865,8 @@ SCR:020406 a NLX:63400, SCR:020407 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_XPR36" ; - rdfs:label "Proteon XPR36 Surface Plasmon Resonance System" ; - definition: "Protein interaction array system that enables label-free quantitative analysis of biomolecular interactions in real time using surface plasmon resonance (SPR) technology. The interactions are monitored over time by flowing an analyte in a microfluidic channel over a ligand immobilized on a sensor chip and detecting the binding of the analyte to the ligand by measuring changes in the propagation of electromagnetic waves at the sensor surface. In this section, you will learn more about SPR technology, the heart of the ProteOn XPR36 system, and the types of biological research that can benefit from using the ProteOn system." . + rdfs:label "Proteon XPR36 Protein Interaction Array System" ; + definition: "Protein interaction array system for label free quantitative analysis of biomolecular interactions using surface plasmon resonance technology. Interactions are monitored by flowing analyte in microfluidic channel over ligand immobilized on sensor chip." . SCR:020408 a NLX:63400, owl:NamedIndividual ; @@ -144661,8 +144877,9 @@ SCR:020408 a NLX:63400, SCR:020409 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_4700" ; - rdfs:label "Proteomics 4700 Mass Spectrometer" ; - definition: "Applied Biosystems 4700 Proteomics Analyzer with TOF/TOF optics is a MALDI tandem time-of-flight mass spectrometer that provides a new level of productivity in high-resolution proteome analysis and complex systems biology. Fast and flexible mass spectrometry and automated results dependent analysis using RDA Software maximizes experimental efficiency. High-sensitivity instrument performance with wide dynamic range allows you to target low-abundance constituents of complex protein mixtures. Superior peak detection, reproducible spectral quality and accurate mass provide protein identification and enhanced characterization. Information-rich fragmentation patterns unavailable on other instrument platforms for carbohydrate, lipid, and other biological component analysis. Ultra-Wide Mass Range of TOF/TOF optics enables you to analyze large proteins and peptides." . + rdfs:label "Applied Biosystems 4700 Proteomics Analyzer" ; + NIFRID:synonym "Applied Biosystems 4700 Mass Spectrometer" ; + definition: "MALDI tandem time-of-flight mass spectrometer that provides a new level of productivity in high-resolution proteome analysis and complex systems biology. It can be used for carbohydrate, lipid, proteins, peptides, and other biological component analysis." . SCR:020410 a NLX:63400, owl:NamedIndividual ; @@ -144686,14 +144903,15 @@ SCR:020412 a NLX:63400, SCR:020413 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Q96" ; - rdfs:label "Qiagen PyroMark Q96 ID System" ; - definition: "Sequencing and quantification platform for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. With its 96-well format, automatic base-calling function, and dedicated software solutions for methylation analysis and assay design." . + rdfs:label "Qiagen PyroMark Q96 System" ; + NIFRID:synonym "PyroMark Q96" ; + definition: "THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2023. Sequencing and quantification pyrosequencer for epigenetics, mutation gene expression analysis, and microbial identification and resistance typing. It has 96 well format." . SCR:020414 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_QIACube" ; - rdfs:label "Qiagen QIAcube" ; - definition: "DNA/RNA Protein Purification System for automated purification of nucleic acids and proteins in molecular biology applications." . + rdfs:label "Qiagen QIAcube Classic" ; + definition: "Purification system that performs fully automated purification of nucleic acids and proteins in molecular biology applications." . SCR:020415 a NLX:63400, owl:NamedIndividual ; @@ -144767,9 +144985,9 @@ SCR:020425 a NLX:63400, SCR:020426 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_ultracut E" ; - rdfs:label "Reichert-Jung Ultracut E Microtome" ; - definition: "Ultracut E microtome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5,�m and has adjustable cutting speeds of 0.1 to 50 mm/sec. Comes with a control box with power cord, a microtome sectioning unit, and a microscope assembly with AO Stereostar 570 zoom body (0.7X - 4.2X) with attached 10X eyepieces. It has a 6V, 10W halogen illumination system." . + oboInOwl:hasDbXref "Model_Number_Ultracut E" ; + rdfs:label "Leica Reichert-Jung Ultracut E Microtome" ; + definition: "Ultracut E microtome is designed for extremely precise cutting, and achieves consistent high quality ultra thin sections for electron microscopy, or semi-thin sections for light microscopy. It features a continuous feed range from 0 to 2.5,m and has adjustable cutting speeds of 0.1 to 50 mm/sec. Comes with a control box with power cord, a microtome sectioning unit, and a microscope assembly with AO Stereostar 570 zoom body (0.7X - 4.2X) with attached 10X eyepieces. It has a 6V, 10W halogen illumination system." . SCR:020427 a NLX:63400, owl:NamedIndividual ; @@ -144881,7 +145099,7 @@ SCR:020444 a NLX:63400, SCR:020445 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Micromax 007HF" ; + oboInOwl:hasDbXref "Model_Number_MicroMax 007HF" ; rdfs:label "Rigaku MicroMax-007 HF generator" ; definition: "Microfocus rotating anode X ray generator.Used for Protein crystallography, small molecule crystallography, SAXS, micro diffraction, phase contrast imaging. Home lab X-ray source for protein crystallography and a popular source for small molecule crystallographers who need the additional flux of a rotating anode generator. The original MicroMax 007 introduced the world to the concept of a sub-100 micron focal spot size along the increased brilliance that can be more effectively used to illuminate small crystals. The current HF version increases the power loading by 50% over the original model providing an X-ray source that rivals second generation synchrotron sources - but with better beam stability and, of course, easy access." . @@ -145223,8 +145441,8 @@ SCR:020501 a NLX:63400, SCR:020502 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_LC480" ; - rdfs:label "Roche Light Cycler 480 Instrument" ; + oboInOwl:hasDbXref "Model_Number_LightCycler_480" ; + rdfs:label "Roche LightCycler 480 Real Time PCR System" ; definition: "LightCycler 480 Instrument is a real-time PCR device, allowing the use of additional thermal block cycler units (96-well and 384-well format) with the system. The LightCycler 480 Block Kit 384 Silver comprises a block cycler unit for 384-well PCR plates, a corresponding block lid for the 384-well PCR plates, and a storage box for both accessories." . SCR:020503 a NLX:63400, @@ -145235,8 +145453,8 @@ SCR:020503 a NLX:63400, SCR:020504 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_Integra 400" ; - rdfs:label "Roche Cobas Integra 400 Chemistry Analyzer" ; + oboInOwl:hasDbXref "Model_Number_Integra_400_Plus" ; + rdfs:label "Roche Cobas Integra 400 Plus Chemistry Analyzer" ; definition: "COBAS INTEGRA 400 plus analyzer is a chemistry analyzer with a broad test menu comprises over 120 assays and applications that consolidate clinical chemistry with specific proteins, therapeutic drug monitoring and drug abuse testing.The Cobas 400 analyzer is best for laboratories running up to 400 samples per day. This compact tabletop analyzer offers maximum versatility to improve efficiency and reduce costs. It uses the convenient cobas c pack reagent format, which standardizes patient results across integrated laboratory networks." . SCR:020505 a NLX:63400, @@ -145255,7 +145473,7 @@ SCR:020507 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Cytospin 3" ; rdfs:label "Shandon Cytospin 3 Centrifuge" ; - definition: "Thermo Shandon Cytospin 3 is a low speed centrifuge used to separate and deposit a monolayer of cells on slides while maintaining cellular integrity." . + definition: "Thermo Shandon Cytospin 3 is low speed centrifuge used to separate and deposit monolayer of cells on slides while maintaining cellular integrity.Centrifuge has speed range between 200 and 2000 RPM, and has holding capacity of up to 24 samples in 12 chambers." . SCR:020508 a NLX:63400, owl:NamedIndividual ; @@ -145469,9 +145687,12 @@ SCR:020542 a NLX:63400, SCR:020543 a NLX:63400, owl:NamedIndividual ; - oboInOwl:hasDbXref "Model_Number_M200" ; - rdfs:label "Tecan M200 Multi-mode Microplate Reader" ; - definition: "Infinite 200 PRO is an multimode plate reader family that offers high performance detection solutions. Based on this customer experience and feedback, the Infinite 200 PRO microplate plate reader has been continuously engineered for excellence. This platform has now evolved into a budget-friendly reader family consisting of six application-focused configurations, delivering performance and value to every lab, every day, for every assay." . + oboInOwl:hasDbXref "Model_Number_Infinite_200_Pro" ; + rdfs:label "Tecan Infinite 200 PRO Multimode Microplate Reader" ; + NIFRID:synonym "Infinite 200 PRO", + "Tecan Infinite 200 PRO", + "Tecan Infinite 200 Pro" ; + definition: "Infinite 200 PRO is multimode plate reader family that offers affordable high performance detection solutions empowered by monochromator or filter based technologies. The six new tailored configurations provide excellence in ELISA assays, nucleic acid quantifications, reporter assay technologies, and drug discovery assays including HTRF and fluorescence polarization. This fully upgradeable reader family is designed to simplify your target applications." . SCR:020544 a NLX:63400, owl:NamedIndividual ; @@ -147830,7 +148051,7 @@ SCR:020927 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "Model_Number_Axioscan" ; rdfs:label "ZEISS Axio Scan.Z1 Slide Scanner" ; - definition: "Digitize your specimens with the Axio Scan.Z1 slide scanner and create high-quality virtual slides. Axio Scan.Z1 tackles the most demanding virtual microscopy research tasks as easily as it handles your routine work. The software module ZEN slidescan is designed specifically for the workflow of capturing virtual slides, while ZEN image analysis tools prepare your data accurately. Organize your virtual slides with ZEN browser, the web-based database, then view your data from any location using any operating system , or share virtual microscopy images online with colleagues and organize your projects, even when you are on the go." . + definition: "Used to digitize specimens with the Axio Scan.Z1 slide scanner to create high-quality virtual slides. Axio Scan.Z1 tackles the most demanding virtual microscopy research tasks as easily as it handles your routine work. The software module ZEN slidescan is designed specifically for the workflow of capturing virtual slides, while ZEN image analysis tools prepare your data accurately. Organize your virtual slides with ZEN browser, the web-based database, then view your data from any location using any operating system , or share virtual microscopy images online with colleagues and organize your projects, even when you are on the go." . SCR:020928 a NLX:63400, owl:NamedIndividual ; @@ -148694,7 +148915,7 @@ SCR:021069 a NLX:63400, SCR:021070 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_1148" ; - rdfs:label "University of Wisconsin Madison Genome Editing and Animal Models Core Facility" ; + rdfs:label "University of Wisconsin Madison Genome Editing Core Facility" ; NIFRID:synonym "Genome Editing and Animal Models Core", "Transgenic Animal Facility", "University of Wisconsin Madison UW-Genome Editing & Animal Models", @@ -149839,6 +150060,7 @@ SCR:021245 a NLX:63400, SCR:021246 a NLX:63400, owl:NamedIndividual ; rdfs:label "Prodigal" ; + NIFRID:synonym "Prokaryotic Dynamic Programming Genefinding Algorithm" ; definition: "Software tool for protein coding gene prediction for prokaryotic genomes." . SCR:021247 a NLX:63400, @@ -150079,10 +150301,10 @@ SCR:021292 a NLX:63400, SCR:021293 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_995" ; - rdfs:label "Dartmouth Geisel School of Medicine Molecular Biology Resource Core Facility" ; + rdfs:label "Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR)" ; NIFRID:synonym "Molecular Biology Resource", "Molecular Biology Shared Resource" ; - definition: "Provides molecular biology products, services, and support to help investigators solve their basic, translational, and clinical research problems.Services include DNA fragment analysis, qPCR, Sanger sequencing and NanoString Technology." . + definition: "Genomics Section provides services and instrumentation that enable DNA/RNA extraction and quality control, next-generation Illumina and Nanopore sequencing, epigenetic profiling, and microarray analysis on a whole-genome scale, from the level organisms to single cells. Molecular Biology Section provides DNA fragment analysis qPCR, Sanger sequencing and NanoString Technology." . SCR:021294 a NLX:63400, owl:NamedIndividual ; @@ -151349,9 +151571,11 @@ SCR:021504 a NLX:63400, SCR:021505 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Live Mouse Tracker" ; - NIFRID:abbrev "LMT" ; - definition: "Software tool for Live Mouse Tracker analysis." . + rdfs:label "Live Mouse Tracker analysis" ; + NIFRID:synonym "live mouse tracker analysis", + "LMT analysis", + "lmt-analysis" ; + definition: "Software package for Live Mouse Tracker analysis. lmt-analysis provides all analysis tools needed to extract information from tracking performed by live mouse tracker." . SCR:021506 a NLX:63400, owl:NamedIndividual ; @@ -152072,7 +152296,7 @@ SCR:021633 a NLX:63400, SCR:021634 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Structure" ; + rdfs:label "STRUCTURE" ; definition: "Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms." . SCR:021635 a NLX:63400, @@ -152158,7 +152382,7 @@ SCR:021648 a NLX:63400, rdfs:label "Terra" ; NIFRID:synonym "BCDC cloud computing environment", "Terra Cloud Native Platform" ; - definition: "Open source platform for biomedical researchers to access data, run analysis tools, and collaborate. Terra powers important scientific projects including AnVIL, BioData Catalyst, Human Cell Atlas, BICCN, and many others. Easily access both open and access-controlled datasets hosted in cloud repositories. Explore, analyze, and visualize data using Jupyter Notebooks, RStudio, RShinyApps, and Galaxy." . + definition: "Open ecosystem of data repositories hosted by various partner organizations, who work together to ensure that their data can be federated across participating platforms. Open source platform for biomedical researchers to access data, run analysis tools, and collaborate. Terra powers important scientific projects including AnVIL, BioData Catalyst, Human Cell Atlas, BICCN, and many others. Easily access both open and access-controlled datasets hosted in cloud repositories. Explore, analyze, and visualize data using Jupyter Notebooks, RStudio, RShinyApps, and Galaxy." . SCR:021649 a NLX:63400, owl:NamedIndividual ; @@ -156383,9 +156607,9 @@ SCR:022376 a NLX:63400, oboInOwl:hasDbXref "ARBF_1389" ; rdfs:label "University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory Core Facility" ; NIFRID:synonym "Cytomics and Cell Sorting Resource Laboratory", + "Penn Cytomics", "University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory" ; - NIFRID:abbrev "FCCSRL" ; - definition: "Provides flow cytometric services and scientific expertise. Offers training for investigator performed analysis on all bench top analyzers, and cell sorter training is also available upon staff approval. Single cell genomic pipeline allows users to perform RNAseq library preparation immediately after sorting. Offers consultation on implementing advanced data analysis methods for large scale or high dimensional experiments and access commercial data analysis software." . + definition: "Flow cytometry shared resource laboratory at the University of Pennsylvania. Facility has instruments, which include analyzers, cell sorters, small particle detectors, dual fluorescence cell counter/viability instrument, tissue dissociator for cell preparation. Provides on-site and off-site support to instrument users, including analyzer and cell sorter training. Core's Research and Development team collaborates/consults with principal investigators in developing high-dimensional panels, as well as staining, acquisition, and analysis." . SCR:022377 a NLX:63400, owl:NamedIndividual ; @@ -160061,7 +160285,7 @@ SCR:022966 a NLX:63400, owl:NamedIndividual ; rdfs:label "Collaborative Brain Wave Analysis Pipeline" ; NIFRID:abbrev "Cobrawap" ; - definition: "Software Python tool to adapt to heterogenous neural activity input data including ECoG, calcium imaging, or simulation. Analysis pipeline for analysis of cortical wave activity." . + definition: "Software adaptable and reusable analysis pipeline for multi scale, multi methodology analysis of cortical wave activity. Pipeline ingests data from multiple measurements types of spatially organized neuronal activity, such as ECoG or calcium imaging recordings. Pipeline returns statistical measures to quantify dynamic wave like activity patterns found in data." . SCR:022967 a NLX:63400, owl:NamedIndividual ; @@ -160184,6 +160408,7 @@ SCR:022985 a NLX:63400, SCR:022986 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2461" ; rdfs:label "Stanford University Community of Shared Advanced Research Platforms" ; NIFRID:synonym "Community of Shared Advanced Research Platforms" ; NIFRID:abbrev "C-ShARP" ; @@ -160260,7 +160485,9 @@ SCR:022999 a NLX:63400, definition: "Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity." . SCR:023000 a NLX:63400, - owl:NamedIndividual . + owl:NamedIndividual ; + rdfs:label "BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain" ; + definition: "Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex." . SCR:023001 a NLX:63400, owl:NamedIndividual ; @@ -160843,8 +161070,10 @@ SCR:023110 a NLX:63400, SCR:023111 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "10.57761" ; rdfs:label "Redivis" ; - definition: "Commercial collaborative research platform for hosting and analyzing datasets." . + NIFRID:synonym "Red Vis" ; + definition: "Commercial collaborative research platform for hosting and analyzing datasets.Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data." . SCR:023112 a NLX:63400, owl:NamedIndividual ; @@ -161204,13 +161433,15 @@ SCR:023172 a NLX:63400, rdfs:label "GenomeThreader" ; definition: "Software tool to compute gene structure predictions.Gene structure predictions are calculated using similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments." . -SCR:023173 a owl:NamedIndividual ; - rdfs:label "openMINDS" ; +SCR:023173 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Open Metadata Initiative (2020) openMINDS metadata framework" ; NIFRID:synonym "open Metadata Initiative for Neuroscience Data Structures", - "openminds" ; - definition: """A metadata framework that develops and maintains a set of metadata models, libraries of controlled terminologies, brain atlases, and common coordinate spaces, as well as supportive tooling for neuroscience graph database systems. - -Note that openMINDS is developed as an open-source project on distributed GitHub repositories with one main GitHub repository for central access and maintenance. A full technical and usage documentation can be found on the openMINDS Collab. For browsing through schemas and lists of all controlled terminologies, brain atlases, and common coordinate spaces please navigate to the openMINDS HTML documentation.""" . + "openminds", + "openMINDS framework", + "openMINDS metadata framework" ; + NIFRID:abbrev "openMINDS" ; + definition: "Metadata framework for linked data comprises: schema specifications for multiple, interlocked metadata models, instance libraries for serviceable, well defined terms and constructs, as well as supportive tooling. openMINDS is developed as open source project by Open Metadata Initiative on GitHub. Framework is distributed over multiple, interlinked GitHub projects with one main GitHub repository for central access and maintenance." . SCR:023174 a NLX:63400, owl:NamedIndividual ; @@ -161557,6 +161788,7 @@ SCR:023227 a NLX:63400, SCR:023228 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2462" ; rdfs:label "Stanford Graduate School of Business Library" ; NIFRID:synonym "Stanford Business Library", "Stanford GSB Library" ; @@ -161565,6 +161797,7 @@ SCR:023228 a NLX:63400, SCR:023229 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2465" ; rdfs:label "Stanford System Prototyping Core Facility" ; NIFRID:synonym "System Prototyping Facility" ; NIFRID:abbrev "SNF-SPF", @@ -161573,6 +161806,7 @@ SCR:023229 a NLX:63400, SCR:023230 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2466" ; rdfs:label "Stanford Nano Shared Core Facility" ; NIFRID:synonym "Stanford Nano Shared Facilities" ; NIFRID:abbrev "SNSF" ; @@ -161580,6 +161814,7 @@ SCR:023230 a NLX:63400, SCR:023231 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2463" ; rdfs:label "Stanford Graduate School of Business Behavioral Lab Core Facility" ; NIFRID:synonym "Behavioral Lab", "GSB Behavioral Lab", @@ -161589,6 +161824,7 @@ SCR:023231 a NLX:63400, SCR:023232 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2468" ; rdfs:label "Stanford Sarafan Medicinal Chemistry Knowledge Center Core Facility" ; NIFRID:synonym "ChEM-H Knowledge Centers Medicinal Chemistry", "Medicinal Chemistry Knowledge Center (MCKC)" ; @@ -161597,6 +161833,7 @@ SCR:023232 a NLX:63400, SCR:023233 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2471" ; rdfs:label "Stanford Sarafan Macromolecular Structure Knowledge Center Core Facility" ; NIFRID:synonym "Macromolecular Structure Knowledge Center" ; NIFRID:abbrev "MSKC" ; @@ -161604,6 +161841,7 @@ SCR:023233 a NLX:63400, SCR:023234 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2464" ; rdfs:label "Stanford Nanofabrication Core Facility" ; NIFRID:synonym "Stanford Nanofabrication Facility" ; NIFRID:abbrev "SNF" ; @@ -161611,6 +161849,7 @@ SCR:023234 a NLX:63400, SCR:023235 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2460" ; rdfs:label "Stanford Sarafan High Throughput Screening Knowledge Center Core Facility" ; NIFRID:synonym "High Throughput Screening Knowledge Center" ; NIFRID:abbrev "HTSKC" ; @@ -161618,6 +161857,7 @@ SCR:023235 a NLX:63400, SCR:023236 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2473" ; rdfs:label "Stanford Sarafan Metabolomics Knowledge Center Core Facility" ; NIFRID:synonym "Metabolomics Knowledge Center" ; NIFRID:abbrev "MKC" ; @@ -161625,6 +161865,7 @@ SCR:023236 a NLX:63400, SCR:023237 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2474" ; rdfs:label "Stanford Sarafan Protein Engineering Knowledge Center Core Facility" ; NIFRID:synonym "Protein Engineering Knowledge Center" ; NIFRID:abbrev "PEKC" ; @@ -161703,6 +161944,7 @@ SCR:023247 a NLX:63400, SCR:023248 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2475" ; rdfs:label "Stanford Vincent V.C. Woo Sandbox Laboratory Core Facility" ; NIFRID:synonym "Stanford Vincent V.C. Woo Sandbox Laboratory (SBCL)", "Vincent V.C. Woo Sandbox Laboratory (SBCL)" ; @@ -161711,6 +161953,7 @@ SCR:023248 a NLX:63400, SCR:023249 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2476" ; rdfs:label "Stanford Behavioral and Functional Neuroscience Laboratory Core Facility" ; NIFRID:synonym "Behavioral and Functional Neuroscience Laboratory (BFNL)", "Stanford Behavioral and Functional Neuroscience Laboratory (BFNL)" ; @@ -161719,6 +161962,7 @@ SCR:023249 a NLX:63400, SCR:023250 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2477" ; rdfs:label "Stanford Neuroscience Gene Vector and Virus Core Facility" ; NIFRID:synonym "Neuroscience Gene Vector and Virus Core (GVVC)", "Stanford Neuroscience Gene Vector and Virus Core" ; @@ -161727,6 +161971,7 @@ SCR:023250 a NLX:63400, SCR:023251 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2479" ; rdfs:label "Stanford Visualization Laboratory Core Facility" ; NIFRID:synonym "Stanford Visualization Laboratory", "Visualization Laboratory" ; @@ -161735,6 +161980,7 @@ SCR:023251 a NLX:63400, SCR:023252 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2480" ; rdfs:label "Stanford Geochronology Cluster Core Facility" ; NIFRID:synonym "Geochronology Cluster", "Stanford Geochronology Cluster" ; @@ -161743,6 +161989,7 @@ SCR:023252 a NLX:63400, SCR:023253 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2481" ; rdfs:label "Stanford Stable Isotope Biogeochemistry Laboratory Core Facility" ; NIFRID:synonym "Stable Isotope Biogeochemistry Laboratory", "Stanford Stable Isotope Biogeochemistry Laboratory" ; @@ -161751,6 +161998,7 @@ SCR:023253 a NLX:63400, SCR:023254 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2478" ; rdfs:label "Stanford Neuroscience Preclinical Imaging Laboratory Core Facility" ; NIFRID:synonym "Neuroscience Preclinical Imaging Laboratory", "Stanford Neuroscience Preclinical Imaging Laboratory" ; @@ -161759,6 +162007,7 @@ SCR:023254 a NLX:63400, SCR:023255 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2484" ; rdfs:label "Stanford Environmental Measurements Core Facility" ; NIFRID:synonym "Environmental Measurements Facility", "Stanford Environmental Measurements Facility" ; @@ -161767,6 +162016,7 @@ SCR:023255 a NLX:63400, SCR:023256 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2482" ; rdfs:label "Stanford Microchemical Analysis Core Facility" ; NIFRID:synonym "Microchemical Analysis Facility", "Stanford Microchemical Analysis Facility" ; @@ -161775,6 +162025,7 @@ SCR:023256 a NLX:63400, SCR:023257 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_520" ; rdfs:label "Stanford Neuroscience Microscopy Service Core Facility" ; NIFRID:synonym "Neuroscience Microscopy Service", "Stanford Neuroscience Microscopy Service" ; @@ -161783,6 +162034,7 @@ SCR:023257 a NLX:63400, SCR:023258 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2485" ; rdfs:label "Stanford Doerr School of Sustainability Sample Preparation Laboratory Core Facility" ; NIFRID:synonym "Sample Preparation Laboratory", "SDSS Sample Preparation Laboratory", @@ -161792,6 +162044,7 @@ SCR:023258 a NLX:63400, SCR:023259 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2483" ; rdfs:label "Stanford SIGMA Core Facility" ; NIFRID:synonym "SIGMA Facility", "Stanford SIGMA Facility" ; @@ -161905,8 +162158,9 @@ SCR:023276 a NLX:63400, SCR:023277 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Julich Brain Atlas" ; - definition: "3D probabilistic atlas of human brain’s cytoarchitecture. Atlas containing cytoarchitectonic maps of cortical areas and subcortical nuclei. Interoperable, enabling connection to other atlases and resources." . + NIFRID:synonym "Julich-Brain Atlas" ; + NIFRID:abbrev "JBA" ; + definition: "Atlas presents cytoarchitectonic maps in several coordinate spaces, such as MNI colin27, MNI152, and freesurfer. These maps originate from peer-reviewed probability maps that define both cortical and subcortical brain regions and account for the brain's inter-individual variability by analyzing data from multiple post-mortem samples. For a whole-brain parcellation, the available probability maps are combined into a maximum probability map by considering for each voxel the probability of all cytoarchitectonic brain regions, and determining the most probable assignment. Atlas stands as reference atlas for the Human Brain Project and is embedded within the European research infrastructure platform, EBRAINS." . SCR:023278 a NLX:63400, owl:NamedIndividual ; @@ -162134,7 +162388,8 @@ SCR:023320 a NLX:63400, SCR:023321 a NLX:63400, owl:NamedIndividual ; rdfs:label "Brain Cell Data Viewer" ; - definition: "Web application that allows users to view and explore brain cell data. Composed of three, interlinked tabs. GeneExp allows users to plot expression of one or two genes in Slide-seq atlas. SingleCell allows users to plot gene expression in snRNA-seq atlas. CellSpatial shows spatial localization of snRNA-seq cell types in Slide-seq dataset." . + NIFRID:synonym "Masoko lab Brain Cell Data Viewer" ; + definition: "Web application that allows users to view and explore brain cell data. Composed of three, interlinked tabs. GeneExp allows users to plot expression of one or two genes in Slide-seq atlas. SingleCell allows users to plot gene expression in snRNA-seq atlas. CellSpatial shows spatial localization of snRNA-seq cell types in Slide-seq dataset. Used to visualize, interact with, and download data." . SCR:023322 a NLX:63400, owl:NamedIndividual ; @@ -162158,6 +162413,7 @@ SCR:023324 a NLX:63400, SCR:023325 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2486" ; rdfs:label "Stanford University Chemistry Department NMR Facility" ; NIFRID:synonym "Stanford University Chemistry Department NMR Laboratory" ; NIFRID:abbrev "NMR" ; @@ -162165,8 +162421,10 @@ SCR:023325 a NLX:63400, SCR:023326 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Stanford Protein and Nucleic Acid Biotechnology Core Facility" ; - NIFRID:synonym "Stanford Protein and Nucleic Acid Biotechnology Facility" ; + oboInOwl:hasDbXref "ABRF_226" ; + rdfs:label "Stanford University School of Medicine Protein and Nucleic Acid Core Facility" ; + NIFRID:synonym "Stanford Protein and Nucleic Acid Biotechnology Core Facility", + "Stanford Protein and Nucleic Acid Biotechnology Facility" ; NIFRID:abbrev "PAN" ; definition: "Offers instrumentation and technical capabilities and plays significant consultative role in application of these technologies to basic science projects.Genomic Services include Oligo Synthesis,Gene Expression,Real-Time PCR,PyroSequencing,Next-Generation Sequencing (NGS),DNA Sequencing (Sanger)/Fragment AnalysisSingle Cell Genomics,RNA-DNA QC - Bioanalyzer and Fragment Analyzer QC.Protein Services include Peptide Synthesis,Mass Spectrometry,Protein Analytics - Mass Mapping/Edman Sequencing,Surface Plasmon Resonance (Biacore)." . @@ -162179,6 +162437,7 @@ SCR:023327 a NLX:63400, SCR:023328 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_776" ; rdfs:label "Stanford School of Medicine Translational Applications Service Center Core Facility" ; NIFRID:synonym "Translational Applications Service Center" ; NIFRID:abbrev "TASC" ; @@ -162244,6 +162503,7 @@ SCR:023339 a NLX:63400, SCR:023340 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2488" ; rdfs:label "Stanford University School of Medicine Genetics Bioinformatics Service Center Core Facility" ; NIFRID:synonym "Stanford Genetics Bioinformatics Service Center" ; NIFRID:abbrev "GBSC" ; @@ -162257,6 +162517,7 @@ SCR:023341 a NLX:63400, SCR:023342 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2489" ; rdfs:label "Stanford University School of Medicine In Vitro Biosafety Level3 Service Center Core Facility" ; NIFRID:synonym "In Vitro Biosafety Level-3 Service Center" ; NIFRID:abbrev "BSL3" ; @@ -162264,6 +162525,7 @@ SCR:023342 a NLX:63400, SCR:023343 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2490" ; rdfs:label "Stanford University School of Medicine PET/MRI Metabolic Service Center Core Facility" ; NIFRID:synonym "PET/MRI Metabolic Service Center" ; NIFRID:abbrev "PMMSC" ; @@ -162271,12 +162533,14 @@ SCR:023343 a NLX:63400, SCR:023344 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2491" ; rdfs:label "Stanford University School of Medicine Richard M. Lucas Center for Imaging Core Facility" ; NIFRID:synonym "Stanford Lucas MRI Service Center Richard M. Lucas Center for Imaging" ; definition: "Houses four whole-body MRI systems (three 3.0T, one 7.0T). 3T2 and 3T3 are part of the Lucas Service Center. Individual researchers are trained in magnet safety and scanner operations by the magnet manager or MR research technologists." . SCR:023345 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2493" ; rdfs:label "Stanford University School of Medicine Center for Innovation in In vivo Imaging Core Facility" ; NIFRID:synonym "Stanford Center for Innovation in In vivo Imaging (SCi3)" ; NIFRID:abbrev "SCi3" ; @@ -162284,6 +162548,7 @@ SCR:023345 a NLX:63400, SCR:023346 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2492" ; rdfs:label "Stanford University School of Medicine Biobank Core Facility" ; NIFRID:synonym "Stanford Biobank" ; definition: "Provides infrastructure for self service sample management tools, centralized broad consent, standardized laboratory services, and long term sample storage solutions.Tracks biological samples collected in every study at Stanford and linking each with associated electronic health records (i.e., EPIC), REDCap, and molecular data." . @@ -162516,6 +162781,7 @@ refrigerator, and microfuges and lab support areas for cell culture and sample p SCR:023381 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2494" ; rdfs:label "Stanford Canary Center Preclinical Imaging Core Facility" ; NIFRID:synonym "Preclinical Imaging Core Facility" ; NIFRID:abbrev "SCi3-P" ; @@ -162523,6 +162789,7 @@ SCR:023381 a NLX:63400, SCR:023382 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2495" ; rdfs:label "Stanford University School of Medicine Transgenic, Knockout and Tumor model Center Core Facility" ; NIFRID:synonym "Knockout and Tumor model", "Stanford School of Medicine Transgenic" ; @@ -162538,6 +162805,7 @@ SCR:023383 a NLX:63400, SCR:023384 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2497" ; rdfs:label "Stanford University School of Medicine Animal Diagnostic Laboratory Core Facility" ; NIFRID:synonym "Animal Diagnostic Laboratory", "Stanford School of Medicine Animal Diagnostic Laboratory" ; @@ -162551,6 +162819,7 @@ SCR:023385 a NLX:63400, SCR:023386 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2500" ; rdfs:label "Stanford University School of Medicine Clinical and Translational Research Unit Core Facility" ; NIFRID:synonym "Clinical and Translational Research Unit (CTRU)", "Stanford University School of Medicine Clinical and Translational Research Unit (CTRU)" ; @@ -162559,12 +162828,14 @@ SCR:023386 a NLX:63400, SCR:023387 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2499" ; rdfs:label "Stanford University School of Medicine Cancer Institute Tissue Procurement Shared Resource Core Facility" ; NIFRID:synonym "Stanford Cancer Institute Tissue Procurement Shared Resource" ; definition: "Procures and provides needed tissue specimens to Stanford Cancer Institute investigators to support cancer related research. Services include collecting and banking freshly frozen tumor and normal tissue from surgical material and autopsy specimens;Providing fresh tumor tissue for viable cell studies;Processing and banking blood from cancer patients;Maintaining tissue database with links to clinicopathological data;Providing histological staining and pathological review;Coordinating patient consent and assuring regulatory compliance.Provides portal to virtual bank which links inventories of specialized satellite repositories, including collections of hematological and neurosurgical specimens." . SCR:023388 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2496" ; rdfs:label "Stanford University School of Medicine Veterinary Service Center Core Facility" ; NIFRID:synonym "Stanford School of Medicine Veterinary Service Center" ; definition: "Provides medical care, in vivo research support, and disease surveillance to laboratory animals at Stanford University . Our board certified and board eligible veterinarians offer consultation in appropriate animal modeling, animal care techniques, experimental methodology, anesthetic techniques, surgical techniques, pain management, humane euthanasia techniques, and animal use (APLAC) protocol consultation. AALAS certified veterinary technicians are available to provide technical support including dosing, biosampling, conducting anesthesia and post-operative care, for example." . @@ -162648,6 +162919,7 @@ SCR:023402 a NLX:63400, SCR:023403 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2501" ; rdfs:label "Stanford University School of Medicine Laboratory for Cell and Gene Medicine Core Facility" ; NIFRID:synonym "Laboratory for Cell and Gene Medicine (LCGM)", "Stanford Laboratory for Cell and Gene Medicine", @@ -162657,6 +162929,7 @@ SCR:023403 a NLX:63400, SCR:023404 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_374" ; rdfs:label "Stanford University School of Medicine Computational Services and Bioinformatics Core Facility" ; NIFRID:synonym "Computational Services and Bioinformatics Facility", "Stanford Computational Services and Bioinformatics Facility" ; @@ -162665,12 +162938,14 @@ SCR:023404 a NLX:63400, SCR:023405 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2503" ; rdfs:label "Stanford University Chemistry Department Optics Core Facility" ; NIFRID:synonym "Stanford University Chemistry Department Optics Facility" ; definition: "Houses optical spectroscopy instruments including Fluorolog 3 Fluorimeter,Vertex 70 FTIR with RAM II Raman accessory, Cary 6000i UV/Vis/NIR Spectrometer." . SCR:023406 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2504" ; rdfs:label "Stanford University Biomaterials and Advanced Drug Delivery Laboratory Core Facility" ; NIFRID:synonym "Biomaterials and Advanced Drug Delivery (BioADD) Laboratory" ; NIFRID:abbrev "BioADD" ; @@ -162678,6 +162953,7 @@ SCR:023406 a NLX:63400, SCR:023407 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2505" ; rdfs:label "Stanford University Cyclotron and Radiochemistry Core Facility" ; NIFRID:synonym "Cyclotron and Radiochemistry Facility" ; NIFRID:abbrev "CRF" ; @@ -162685,6 +162961,7 @@ SCR:023407 a NLX:63400, SCR:023408 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2502" ; rdfs:label "Stanford University Instrumentation Shop Core Facility" ; NIFRID:synonym "MCP / NIS Engineering Shop", "Stanford University instrumentation shop" ; @@ -162706,6 +162983,7 @@ SCR:023410 a NLX:63400, SCR:023411 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2506" ; rdfs:label "Stanford University High Performance Computing Center Core Facility" ; NIFRID:synonym "Stanford High Performance Computing Center", "Stanford University High Performance Computing Center" ; @@ -162713,6 +162991,7 @@ SCR:023411 a NLX:63400, SCR:023412 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2507" ; rdfs:label "Stanford University Physics Machine Shop Core Facility" ; NIFRID:synonym "Physics Machine Shop", "Physics Varian Machine Shop", @@ -162722,6 +163001,7 @@ SCR:023412 a NLX:63400, SCR:023413 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2508" ; rdfs:label "Stanford University Research Computing Center Core Facility" ; NIFRID:synonym "Stanford Research Computing Center", "Stanford Research Computing Facility (SRCF)", @@ -163270,11 +163550,12 @@ SCR:023497 a NLX:63400, NIFRID:abbrev "VVC" ; definition: "Core uses technologies to create and produce variety of high quality viral vectors.Provides investigators with the most suitable and efficient gene transfer vectors.Vectors produced include AD, AAV, and Lenti/retro. VVC staff can assist investigators with selection of gene transfer vector, its design and potential applications. Services include AdV vector creation and production, AAV vector production, Lentiviral vector production,AAV neutralizing antibody screening and titration." . -SCR:023498 a owl:NamedIndividual ; - rdfs:label "OpenMINDS Spatial Anchoring of Neuroscience Data Structures" ; - NIFRID:abbrev "OpenMIND SANDS", - "OpenMIND_SANDS" ; - definition: "Repository provides metadata schemas for Spatial Anchoring of Neuroscience Data Structures, including brain atlas definitions. Covers brain atlases, as well as anatomical locations and relations of non-atlas data." . +SCR:023498 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "openMINDS SANDS metadata model" ; + NIFRID:abbrev "openMINDS SANDS", + "openMINDS_SANDS" ; + definition: "One of metadata models of openMINDS metadata framework. Defines modular metadata schemas for spatial anchoring of neuroscience data structures. Includes in depth descriptions of brain atlases, common coordinate spaces, relations between atlases, and anatomical locations for non atlas data." . SCR:023499 a NLX:63400, owl:NamedIndividual ; @@ -163435,10 +163716,13 @@ SCR:023526 a NLX:63400, SCR:023527 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_1744" ; - rdfs:label "Emory University Emory Integrated Metabolomics and Lipodomics Core Facility" ; - NIFRID:synonym "Emory Integrated Metabolomics & Lipodomics Core", - "Emory University Emory Integrated Metabolomics and Lipodomics Core" ; - definition: "Provides quantitative lipidomics analyses on lipid samples from biological matrices included blood, serum, plasma, solid tissues, cell extracts to support both clinical and basic research efforts on campus. These analyses will provide insight on lipids and lipid precursors whose abundance can be monitored as biomarkers to predict and follow progression of a wide range of diseases, such as metabolic disorders (e.g.. obesity, Type II diabetes, and NAFLD), neurodegenerative diseases (e.g. Alzheimers Disease and Parkinsons Disease), and cancer (e.g. prostate cancer and breast cancer)." . + rdfs:label "Emory University Emory Integrated Metabolomics and Lipidomics Core Facility" ; + NIFRID:synonym "Emory Integrated Lipidomics Core", + "Emory Integrated Metabolomics & Lipidomics Core", + "Emory University Emory Integrated Metabolomics and Lipidomics Core" ; + NIFRID:abbrev "EILC", + "EILMC" ; + definition: "Provides quantitative analysis of lipids and soluble metabolites using cutting-edge mass spectrometry methods as a service to both clinical and basic biomedical research efforts. We deliver quantitative lipidomics and metabolomics analyses on samples from a wide variety of biological matrices, e.g. blood, serum, plasma, solid tissues, fecal/urine samples, cell extracts, etc., to support both clinical and basic research efforts." . SCR:023528 a NLX:63400, owl:NamedIndividual ; @@ -164137,8 +164421,9 @@ SCR:023644 a NLX:63400, SCR:023645 a NLX:63400, owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_1779" ; - rdfs:label "Pennsylvania State University Huck Institutes of the Life Sciencies Genomics Core Facility" ; + rdfs:label "Pennsylvania State University Huck Institutes of the Life Sciences Genomics Core Facility" ; NIFRID:synonym "HUC-Genomics", + "Huck Institutes Genomics Core Facility", "Huck Institutes of the Life Sciencies Genomics Core Facility", "PennState Huck Institutes of the Life Sciencies Genomics Core Facility", "PennState UHC Genomics", @@ -164237,15 +164522,10 @@ SCR:023663 a NLX:63400, NIFRID:abbrev "rsHRF" ; definition: "Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images." . -SCR:023664 a NLX:63400, - owl:NamedIndividual ; - oboInOwl:hasDbXref "ABRF_1783" ; - rdfs:label """ -Catholic University of Louvain Institute of Experimental and Clinical Research Flow Cytomerty Platform Core Facility""" ; +SCR:023664 a owl:NamedIndividual ; NIFRID:synonym "Catholic University of Louvain Institute of Experimental and Clinical Research Flow Cytomerty Platform", "CytoFlux", - "Flow Cytomerty Platform" ; - definition: "Offers tissues dissociation and single cell preparation, analysis and cell sorting under supervision of research logistician.Provides instruments BD FACSCantoII for analysis and BD FACSAriaIII for cell separation and services including Samples preparations and multiparametric panels consultancy, Acquisition and analysis of multiparametric samples, Cell Sorting, Data Analysis." . + "Flow Cytomerty Platform" . SCR:023665 a NLX:63400, owl:NamedIndividual ; @@ -164316,8 +164596,9 @@ SCR:023675 a NLX:63400, SCR:023676 a NLX:63400, owl:NamedIndividual ; rdfs:label "OmicsBox" ; - NIFRID:synonym "BioBam OmicsBox" ; - definition: "Software aplication for NGS data analysis of genomes, transcriptomes, and metagenomes. Allows researchers to easily process large and complex data sets, and streamline their analysis process." . + NIFRID:synonym "BioBam OmicsBox", + "OmicsBox v.3.0.29" ; + definition: "Software aplication for NGS data analysis of genomes, transcriptomes, and metagenomes. Allows researchers to easily process large and complex data sets, and streamline their analysis process. Software is structured in different modules, each with specific set of tools and functions designed to perform different types of analysis, such as de-novo genome assemblies, genetic variation analysis, differential expression analysis, and taxonomic classifications of microbiome data, including the functional interpretation and rich visualizations of results." . SCR:023677 a NLX:63400, owl:NamedIndividual ; @@ -164439,6 +164720,7 @@ SCR:023695 a NLX:63400, SCR:023696 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2509" ; rdfs:label "Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility" ; NIFRID:synonym "Stanford Biostatistics Shared Resource", "Stanford Cancer Institute Biostatistics Shared Resource" ; @@ -164496,14 +164778,14 @@ SCR:023705 a NLX:63400, "University of Miami U of Miami Biomarkers and Immunoassay Laboratory" ; definition: "Provides biomarker testing for human clinilcal research studies across multiple disciplines.Provides expertise with chemistry, special chemistry, radioimmunoassay, nephelometric and ELISA and multiplexing assay methods utilizing automated and manual procedures. Laboratory has Clinical Laboratory Improvement Act certification and follows guidelines established by CLIA for quality control and proficiency testing to ensure results. Core coordinates proper pre-analytical sample collection and processing procedures with project leaders; performs biochemical assays on samples submitted to the laboratory by investigators in manner that assures strict quality control both within and between assay runs; reports results to project staff in timely fashion; makes available expertise and technical assistance for establishing and validating new methodologies to support University of Miami investigators." . -SCR:023706 a NLX:63400, - owl:NamedIndividual ; +SCR:023706 a owl:NamedIndividual ; oboInOwl:hasDbXref "ABRF_710" ; rdfs:label "Northwestern University Analytical BioNanoTechnology Equipment Core Facility" ; NIFRID:synonym "Analytical BioNanoTechnology Equipment Core (ANTEC)", "Northwestern University Analytical BioNanoTechnology Equipment Core (ANTEC)" ; NIFRID:abbrev "ANTEC" ; - definition: "Core facility houses equipment for evaluation of materials and biological preparations in bionanotechnology laboratory.Equipment includes Zetasizer Nano ZSP for zeta potential measurements, molecular weight determination, and advanced characterization of proteins, polymers, and other macromolecules; a Cytation3 Automated Imager and Multimodal Plate Reader for fluorescence, luminescence, absorption assays and automatic cell imaging; two FreeZone 6 lyophilizers for freeze drying of biological and synthetic materials, SpectraMax M5 Microplate Reader, real-time CFX-Connect PCR detection system, Kodak gel imaging system, Azure300 Chemiluminescence Imager and refrigerated centrifuge.NanoSight NS300 with fluorescence detection capability for nanoparticle characterization, will be located in the J-Wing of Evanston Tech building." . + definition: """Facility houses research equipment for evaluating materials and biological preparations, and offers 3D printing and 3D scientific illustration services. Available instruments include +Cytation3 Automated Microscope Plate Reader, BioTek Inc.; Zetasizer Nano ZSP, Malvern Inc.; Lyophilizers FreeZone 6 and 6 Plus, Labconco; Azure300, Chemiluminescent Gel Imager, Azure Biosystems; Real-Time PCR I-cycler CFX-Connect, Bio-Rad Laboratories; Centrifuge Sorvall X1R, ThermoFisher; MCR302 Rheometer, Anton Paar Inc.; Plasma Cleaner, Harrick Plasma; NanoSight300, Malvern Instruments (Evanston); IncuCyte Live Cell Analysis System, Sartorius; Piuma Nanoindenter, Optics 11; Freezer/Mill, SPEX Sample Prep; J-1500 Circular Dichroism Spectrometer, JASCO.""" . SCR:023707 a NLX:63400, owl:NamedIndividual ; @@ -164698,9 +164980,8 @@ SCR:023738 a NLX:63400, SCR:023739 a NLX:63400, owl:NamedIndividual ; - rdfs:label "Alpaca" ; NIFRID:synonym "Automated Lightweight Provenance Capture" ; - definition: "Software Python package for capture of provenance information during execution of Python scripts that process data." . + definition: "Software Python package for the capture of provenance information during the execution of Python scripts that process data. Alpaca provides a simple API for recording the details of the functions being executed, the data flow, and a description of parameters used. Using simple Python decorators, this is accomplished with minimal code instrumentation and user intervention. Provenance information is structured and serialized according to a model based on the W3C PROV format. In addition, provenance information can be simplified and prepared for interactive visualization by the researcher." . SCR:023740 a NLX:63400, owl:NamedIndividual ; @@ -165394,8 +165675,10 @@ SCR:023863 a NLX:152328, SCR:023864 a NLX:63400, owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2447" ; rdfs:label "Pennsylvania State University Huck Institutes of Life Sciences Metabolomics Core Facility" ; - NIFRID:synonym "Penn State Huck Metabolomics Core Facility" ; + NIFRID:synonym "Huck Institues' Metabolomics Facility", + "Penn State Huck Metabolomics Core Facility" ; definition: "Core for conducting metabolomics studies on variety of biofluids and tissue extracts from plant and animal sources. Provided instruments include Agilent 5975C series GC-MSD, Bruker NEO 600 NMR, Thermo Exactive Plus, Thermo Orbitrap Exploris 120, Thermo Orbitrap Exploris 240, Thermo TSQ Quantis Plus, Thermo Orbitrap Fusion Lumos Tribrid." . SCR:023865 a NLX:63400, @@ -165500,4 +165783,6327 @@ SCR:023881 a NLX:63400, "Paris Human disease models core facility" ; definition: "Core Facility produces mice harboring human immune system and provides expertise for possible applications of this model. HIS mice engrafted with human Hematopoietic stem cells are advantageous in vivo models for long term studies in field of human immune cells biology, immune oncology and infectious disease. They constitute small animal model in which to analyze potency and safety of small animal model modulating immune system." . -### Serialized using the ttlser deterministic serializer v1.2.1 +SCR:023882 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bioawk" ; + definition: "Software tool as modified awk version for biodata. Extension to Brian Kernighan's awk, adding support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds few built-in functions and command line option to use TAB as the input/output delimiter." . + +SCR:023883 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MAKER" ; + NIFRID:synonym "maker", + "Maker2" ; + definition: "Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values." . + +SCR:023884 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "B-CALM" ; + definition: "Open source system for behavioral control based on Arduino Mega microcontroller and MATLAB based graphical interface and analysis code. Behavior controller optimized and customized for associative learning and memory tasks. Provided software should be able to control many different types of hardware for different task configurations." . + +SCR:023885 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Hierarchical Genome Assembly Process" ; + NIFRID:synonym "HGAP: Hierarchical Genome Assembly Process", + "PacBio Hierarchical Genome Assembly-Process (HGAP)" ; + NIFRID:abbrev "HGAP" ; + definition: "Software for High-quality de novo microbial genome assemblies using only single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing." . + +SCR:023886 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SpheroScan" ; + definition: "Software tool for analyzing images of spheroids. Designed to streamline process of spheroid segmentation, area calculation, and downstream analysis of spheroid image data, and can help to standardize and accelerate analysis of spheroid assay results." . + +SCR:023887 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_1817" ; + rdfs:label "University of California at Davis Bioinformatics Core Facility" ; + NIFRID:synonym "Davis UC Davis Bioinformatics Core", + "UC Davis Bioinformatics Core", + "University of California" ; + definition: "UC Davis Bioinformatics Core helps researchers with their projects, from experimental design, through all analyses and to publication.Provides expertise in analyzing data from omics technologies, and other projects. Regularly offers bioinformatics training." . + +SCR:023888 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Hitachi 16-bit 3-CCD color camera HV-F203GV / HV-F203SCL" ; + NIFRID:synonym "HV-F203GV / HV-F203SCL camera" ; + definition: "High resolution 1/1.8\" 3 CCD Progressive Scan Color Camera with 1600 x 1200 pixel (UXGA) that is installed in the ZEISS Axioscan Z1 slide scanner. Integrated functions include electronic shutter from 1/30s to 1/100000s, Long term Integration up to 4s, AGC, external Trigger, Auto Shading, 6 Colour Masking, Frame-On-Demand Function, White Balance, AGC, Black Level Adjustment and Partial Scan Function." . + +SCR:023890 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Automated Record Analysis" ; + NIFRID:synonym "ARA.v1.6.0", + "ARA:Automated Record Analysis" ; + NIFRID:abbrev "ARA" ; + definition: "Software automatic pipeline for exploration of Sequence Read Archive datasets with sequences as query." . + +SCR:023891 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "LW Scientific ZipCombo centrifuge" ; + NIFRID:synonym "ZipCombo Centrifuge" ; + definition: "Multi-function microcentrifuge available with choice of three rotors. The flat microhematocrit rotor spins shorter capillary tubes and eliminates angled separation lines, clay blow-outs, and broken tubes. The six place microtube rotor spins 1.5 to 2.0ml tubes for serum and urine separations and comes with adapters for smaller sized tubes (0.2ml-1.5ml). The optional 16-place PCR strip rotor spins two 8-place strips. The ZipCombo is well-suited to accomplish blood and urine separations, microfiltrations, and DNA preparations." . + +SCR:023892 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rainin Pipet-Lite LTS Pipette L-200XLS+" ; + NIFRID:synonym "Pipet-Lite™ XLS+", + "Rainin Pipet-Lite™ XLS+" ; + definition: """Pipet-Lite™ XLS+ manual single-channel pipette, 20-200 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-200XLS+) +""" . + +SCR:023893 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rainin Pipet-Lite LTS Pipette L-100XLS+" ; + NIFRID:synonym "Pipet-Lite LTS Pipette L-100XLS+" ; + definition: "Pipet-Lite™ XLS+ manual single-channel pipette, 10-100 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-100XLS+)" . + +SCR:023894 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rainin Pipet-Lite LTS Pipette L-1000XLS+" ; + NIFRID:synonym "Pipet-Lite LTS Pipette L-1000XLS+" ; + definition: "Pipet-Lite™ XLS+ manual single-channel pipette, 100-1000 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-1000XLS+)" . + +SCR:023895 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rainin Pipet-Lite LTS Pipette L-10XLS+" ; + NIFRID:synonym "Pipet-Lite LTS Pipette L-10XLS+" ; + definition: "Pipet-Lite™ XLS+ manual single-channel pipette, 0.5-10 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-10XLS+)." . + +SCR:023896 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "epitools" ; + NIFRID:synonym "Epidemiology Tools", + "epitools: Epidemiology Tools" ; + definition: "Software R package for training and practicing epidemiologists including methods for two-way and multi-way contingency tables." . + +SCR:023897 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Cell Ranger ARC " ; + NIFRID:synonym "10x Genomics Cell Ranger ARC" ; + definition: "Software analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate variety of analyses pertaining to gene expression , chromatin accessibility, and their linkage. Used to perform analyses that link chromatin accessibility and GEX." . + +SCR:023898 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GERONIMO" ; + NIFRID:synonym "GEnomic RNA hOmology aNd evolutIonary MOdeling" ; + definition: "Software pipeline to conduct high-throughput homology searches of structural genes using covariance models. Utilises covariance models to conduct homology searches of RNA sequences across wide range of gene families in broad evolutionary context." . + +SCR:023900 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rainin E4 Pipette Multi E8-1200XLS+" ; + NIFRID:synonym "E4 Pipette Multi E8-1200XLS+" ; + definition: "8-channel pipette, 100-1200 μL, uses LTS™ LiteTouch™ tips. Consistent sample pickup, all channels. Simple operation, advanced modes. Password-protection (E8-1200XLS+)." . + +SCR:023902 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VWR Lab Dancer Vortex Mixer" ; + definition: "Vortex mixer suitable for single, small containers up to 30 mm in diameter." . + +SCR:023903 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_1819" ; + rdfs:label "Leiden University Medical Center Flow Cytometry Core Facility" ; + NIFRID:synonym "Flow Cytometry Core Facility" ; + NIFRID:abbrev "LUMC FCF" ; + definition: "Provides flow cytometers for users from the LUMC, Leiden University and external companies.Instruments include conventional and spectral analyzers, cell sorters and mass cytometers. These instruments allow analysis and sorting up to biohazard level ML-II, while one analyzer is available for ML-III material. Provides support for all aspects of cytometry, including experimental design, instrument setup, data acquisition and data analysis." . + +SCR:023904 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SunTissuePrep Tissue Section Preparation System" ; + NIFRID:synonym "SunTissuePrep" ; + definition: "System automates all tissue section preparation steps that were previously performed manually. Deparaffinization, rehydration, antigen-retrieval and pH-adjustment steps are performed efficiently, reliably and fully automated." . + +SCR:023905 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SunDigest Incubator" ; + definition: """SunDigest incubation device provides fully software controlled and highly reproducible digestion process under standardized conditions. Feature includes Temperatures precisely adjustable between 4 °C and 50 °C; On-Tissue digestion process under optimal humidity; +Preservation of spatial resolution; High performance digestion at 50 °C; Full digestion process control.Essential for reproducible results.""" . + +SCR:023906 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SunCollect CF Spotter" ; + NIFRID:synonym "CF-Spotter for MALDI-TOF Microbial Identification" ; + definition: "CF-Spotter for MALDI-TOF microbial identification. Enables fast, efficient and reproducible sample preparation for MALDI-TOF microbial identification system and relieves your laboratory staff from tedious and time-consuming pipetting. Due to the non-contact application of the solutions, there is no carryover of the samples and the costs for consumables such as pipette tips are eliminated." . + +SCR:023907 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SunCollect MALDI Sprayer" ; + NIFRID:synonym "SunCollect Sprayer" ; + definition: """For tissue preparation for Imaging MALDI. The sprayer can handle fresh-frozen or FFPE tissue sections. Enzymes such as trypsin can be applied to the tissue for in situ digestion. +Sprayer offers the following key features: Automated delivery of matrix, enzyme or derivatization solutions; 6 port PEEK valve with low dead-volume to minimise liquid usage; +Automatic self-cleaning function at end of matrix application; 100 % biocompatible; +Compact unit 36 x 49 x 40 cm (w,d,h);Preprogrammed spray protocols;Up to 8 sample slides can be sprayed simultaneously;Easy to use software.""" . + +SCR:023908 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "SunChrom" ; + NIFRID:synonym "SunChrom Wissenschaftliche Geräte GmbH" ; + definition: "Develops and manufactures scientific instruments. Specialists for system solutions in liquid chromatography, development and optimization of front-end applications and sample preparation systems for MALDI and MALDI-MSI." . + +SCR:023909 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "nanoString CosMx Spatial Molecular Imager" ; + NIFRID:synonym "CosMx Spatial Molecular Imager", + "NanoString CosMx Spatial Molecular Imager" ; + definition: "Integrated system with mature cyclic fluorescent in situ hybridization chemistry, resolution imaging readout, interactive data analysis and visualization software. Analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded and fresh frozen tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes. Spatial single-cell imaging platform that drives deeper insights for cell atlasing, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery." . + +SCR:023910 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "10x Genomics Xenium Analyzer" ; + NIFRID:synonym "Xenium Analyzer" ; + definition: "Xenium Analyzer offers subcellular profiling of 100s to 1,000s of RNA targets alongside multiplexed protein, in fresh, frozen or FFPE tissue." . + +SCR:023911 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Resolve Biosciences" ; + NIFRID:synonym "Resolve Biosciences GmbH" ; + definition: "Biotechnology research company for molecular cartography. Applys the power of Molecular Cartography to enable scientists to gain new insights based on the highest-resolution view of single-cell spatial biology." . + +SCR:023912 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "NanoString Technologies" ; + NIFRID:synonym "NanoString" ; + definition: "Publicly held biotech company offering discovery and translational research solutions. NanoString's products include the nCounter® Gene Expression System, the GeoMx® Digital Spatial Profiler, the CosMx™ Spatial Molecular Imager, and the AtoMx™ Spatial Informatics Platform." . + +SCR:023913 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "epialleleR" ; + definition: "Software R package for calling hypermethylated variant epiallele frequencies at level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map files as input. Used for sensitive allele specific methylation analysis in next generation sequencing data. Used for sensitive detection, quantification and visualisation of mosaic epimutations in methylation sequencing data." . + +SCR:023914 a NLX:63400, + owl:NamedIndividual . + +SCR:023916 a NLX:63400, + owl:NamedIndividual . + +SCR:023917 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_53" ; + definition: "Scientific Instrument Services provides technical support functions including repair and maintenance of lab equipment; custom design and fabrication of new fixtures and devices using CAD, 3-D printing, and traditional machining; protocol development and performance optimization of wide variety of automated liquid handlers deployed in many of our institutions core services.Services are provided for JAX faculty." . + +SCR:023918 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Freibox" . + +SCR:023919 a owl:NamedIndividual ; + rdfs:label "commutator" ; + definition: """Affordable commutator that is equipped with novel sensing system that improves online tracking of cable rotations without impairing the 1-photon calcium imaging via Miniscope. +Commutator to allow freely moving behaviors while recording neural activity from platforms such as Miniscope V4 and OpenEphys. Used to perform calcium imaging.""" . + +SCR:023920 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "Molecular Devices SpectraMax iD3 multi-mode microplate reader", + "SpectraMax® iD3 multi-mode microplate reader" . + +SCR:023921 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "mONiTor" ; + definition: "Software tool monitors metrics available in sequencer, state of the computer to which the sequencer is connected, and the contents of the fast5 and fastq files. Real-time monitoring of Oxford Nanopore Technology sequencing run. Used for monitoring nanopore sequencing process." . + +SCR:023922 a NLX:63400, + owl:NamedIndividual . + +SCR:023923 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Collaborative Research Network Cloud" ; + NIFRID:abbrev "CRN Cloud" ; + definition: "MJFF in partnership with Aligning Science Across Parkinson’s are in the process of establishing data platform, CRN Cloud, leveraging Verily Workbench to share data generated by researcher labs funded through ASAP Collaborative Research Network. The data types include mainly raw and processed single cell RNA-seq, single nucleus RNA-seq, and bulk RNA-seq from both PD and healthy control samples." . + +SCR:023924 a NLX:63400, + owl:NamedIndividual ; + definition: "Curated data resource of protein carbonylation sites.Manually curated data resource of experimentally confirmed carbonylated proteins and sites.Provides information on other related resources such as list of other oxidative protein modification databases, list of protein oxidation and carbonylation prediction tools." . + +SCR:023925 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PKD Genome Browser" ; + NIFRID:synonym "Polycystic Kidney Disease Genome Browser" . + +SCR:023928 a owl:NamedIndividual ; + NIFRID:synonym "confgen" . + +SCR:023929 a NLX:63400, + owl:NamedIndividual . + +SCR:023930 a NLX:63400, + owl:NamedIndividual . + +SCR:023931 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "PDCM Finder", + "PDX Finder" . + +SCR:023932 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Molecular Operating Environment" ; + NIFRID:synonym "Chemical Computing Group ULC Molecular Operating Environment", + "Molecular Operating Environment (MOE)" ; + NIFRID:abbrev "MOE" . + +SCR:023934 a NLX:63400, + owl:NamedIndividual ; + NIFRID:abbrev "OAT" . + +SCR:023935 a owl:NamedIndividual ; + rdfs:label "NamSor" ; + definition: "A software tool useful for finding the name origin, ethnicity of a name. It can infer gender, translate Chinese names and Japanese names, format a phone number, and split a full name via user interface and an API." . + +SCR:023936 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "BioNovoGene Mzkit" . + +SCR:023937 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Agilent 6495 Triple Quadrupole LC/MS" ; + definition: "The Agilent 6495C triple quadrupole LC/MS system increases capacity and sensitivity for targeted quantitation applications. It positively impacts researchers� ability to investigate more diverse and biologically relevant groups of targeted peptides, small molecules and metabolites in a single experiment without compromising sensitivity, quantitative accuracy, or linearity." . + +SCR:023938 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Waters Select Series MRT" ; + definition: "The Multi Reflecting Time-of-Flight (MRT) features routine ppb mass accuracy and ultra-high resolution by extending the flight path via gridless electrostatic mirrors in the mass analyzer. It is equipped with DESI and MALDI sources for imaging mass spectrometry." . + +SCR:023939 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Waters Select Series Cyclic IMS" ; + definition: "The Cyclic IMS pairs unique cyclic ion mobility separation which enables separation based on shape, with time-of-flight separation based on mass to charge ratio (m/z). It is equipped with DESI and electrospray sources for surface and solution analyses." . + +SCR:023940 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bacmapping" ; + definition: "Software set of tools used in production and exploration of bacterial artificial chromosome restriction maps." . + +SCR:023941 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Customized Guide Cannulas" ; + definition: "Open source modular apparatus to produce guide cannulas exploiting 3D printing technology. Step by step procedure to realize hippocampal guide cannulas. 3D-printed guide cannula implant, as well as rotary tool based cutting station for fabrication of cannulae. Useful to conduct research in all the fields where access to brain areas is needed." . + +SCR:023942 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EBSCO SPORTDiscus" ; + NIFRID:synonym "SPORTDiscus" ; + definition: "Bibliographic database for sports and sports medicine research. Includes records from leading sports medicine journals. Includes rigorous curation and indexing of open access journals. Once validated and certified for inclusion, these journals are treated with subject indexing and full text linking." . + +SCR:023943 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Health Information National Trends Survey" ; + NIFRID:synonym "Health Information National Trends Survey (HINTS)", + "The Health Information National Trends Survey (HINTS)" ; + NIFRID:abbrev "HINTS" ; + definition: "Regularly collects nationally representative data about American public’s knowledge of, attitudes toward, and use of cancer and health related information. HINTS data are used to monitor changes in fields of health communication and health information technology and to create more effective health communication strategies across different populations. Weighted, nationally representative probability based survey of civilian, non-institutionalized adults administered by National Cancer Institute on knowledge of and attitudes toward cancer relevant information." . + +SCR:023944 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "CDC HPV and Cancer HPV-Associated Cancer", + "CDC HPV-Associated Cancer" . + +SCR:023945 a owl:NamedIndividual ; + NIFRID:synonym "Linked-Read ToolKit", + "Linked-Read ToolKit (LRTK)" . + +SCR:023946 a NLX:63400, + owl:NamedIndividual . + +SCR:023947 a NLX:63400, + owl:NamedIndividual ; + definition: "Comprehensive DNA methylation database. Provides genome wide mapping of methylation sites to target genes through integrating a large number of DNA methylation and gene expression profiles in human diseases, and to annotate methylation sites to abundant regulatory elements and TFs." . + +SCR:023948 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MAP Client" ; + NIFRID:synonym "MAP Client mapping tools", + "MAP Client mapping tools v0.19.1", + "MAP Client v0.19.1", + "Musculoskeletal Atlas Project Client" ; + definition: "Software Python cross platform framework for creating, managing, and sharing workflows. Workflow consists of number of connected workflow steps. Framework is plugin-based application where the plugins are workflow steps. Can be used for visualising and mapping anatomical structures." . + +SCR:023949 a NLX:63400, + owl:NamedIndividual . + +SCR:023950 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_SM2010 R" ; + NIFRID:synonym "Leica SM 2000R", + "SM2010 R Sliding Microtome" . + +SCR:023951 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_1822" ; + rdfs:label "University of Missouri Bioinformatics and Analytics Core Facility" ; + NIFRID:synonym "MU Bioinformatics and Analytics", + "University of Missouri MU Bioinformatics and Analytics Core" ; + definition: "Provides expert bioinformatics, analytical, and data science consulting and analysis solutions. Offers support for the management and analysis of large scale biological datasets." . + +SCR:023952 a owl:NamedIndividual ; + rdfs:label "University of Wisconsin-Madison Biochemistry Optical Core Facility" ; + definition: "Core provides instrumentation for light and fluorescence based microscopy, including epifluorescence, confocal, and super-resolution imaging.Provides access to and training on basic and advanced light microscopy techniques. Expertise and advice is available for the design of experiments involving these techniques." . + +SCR:023953 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GeneHancer" ; + definition: "Database of human regulatory elements like enhancers and promoters, and their inferred target genes which is embedded in GeneCards, human gene compendium. Associations between regulatory elements and target genes were based on multiple sources of linking molecular data, along with distance." . + +SCR:023956 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "simulation of Adaptive Immune Receptor Repertoire data" . + +SCR:023957 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_ST5010 XL" ; + rdfs:label "Leica Autostainer ST5010 XL" ; + definition: "Leica ST5010 Autostainer XL provides reproducible, consistent high quality staining, and increased workload throughput compared to manual staining." . + +SCR:023958 a NLX:63400, + owl:NamedIndividual . + +SCR:023959 a owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_1825" ; + rdfs:label "South Dakota State University Genomics Sequencing Core Facility" ; + NIFRID:synonym "SDState-Genomics Sequencing Facility", + "South Dakota State University SDState-Genomics Sequencing Facility" ; + definition: "Facility offers custom sequencing services from DNA/RNA extractions to sequencing using Illumina and Oxford Nanopore platforms. Projects examples include bulk RNAseq, 3\\'RNASeq, Single Cell transcriptomics (10X Genomics), Genome sequencing, and amplicon sequencing (ie 16SRNA, genotyping). Services include experimental design and bioinformatics data analysis." . + +SCR:023960 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Aeskulap" ; + NIFRID:synonym "aeskulap", + "Aeskulap - DICOM Viewer" ; + definition: "Software application as medical image viewer.Able to load series of special images stored in DICOM format for review. Able to query and fetch DICOM images from archive nodes (also called PACS) over the network. Designed to run under Linux." . + +SCR:023961 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "alleleCount" ; + NIFRID:synonym "allelecount" ; + definition: "Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings." . + +SCR:023962 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20869" ; + rdfs:label "Atropos" ; + NIFRID:synonym "atropos" ; + definition: "Software tool for specific, sensitive, and speedy trimming of NGS reads." . + +SCR:023963 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "assembly-stats" ; + definition: "Software to get assembly statistics from FASTA and FASTQ files." . + +SCR:023964 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Augur" ; + NIFRID:synonym "augur" ; + definition: "Software package to track evolution from sequence and serological data. Provides collection of commands which are designed to be composable into larger processing pipelines." . + +SCR:023965 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Aghermann" ; + NIFRID:synonym "aghermann" ; + definition: "Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection." . + +SCR:023966 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Auspice" ; + NIFRID:synonym "auspice" ; + definition: "Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data." . + +SCR:023967 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11402" ; + rdfs:label "Assemblytics" ; + NIFRID:synonym "assemblytics" ; + definition: "Web analytics tool for detection of variants from assembly. Used to detect and analyze structural variants from genome assembly by comparing it to reference genome." . + +SCR:023968 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "AxParafit" ; + NIFRID:synonym "Accelerated Parafit", + "axparafit" ; + definition: "Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Allows for rapid and much more thorough computation and analyses of large co-phylogenetic datasets." . + +SCR:023969 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bamkit" ; + definition: "Software tools for common BAM file manipulations." . + +SCR:023970 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bambamc" ; + definition: "Software package contains lightweight C implementation of name collating BAM file input and BAM file output." . + +SCR:023971 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "AxPcoords" ; + NIFRID:synonym "Accelerated DistPCoA", + "axpcoords" ; + definition: "Software tool for large scale co-phylogenetic analyses on several thousands of taxa. Faster than DistPCoA and numerically stable on large datasets." . + +SCR:023972 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BBHash" ; + NIFRID:synonym "bbhash" ; + definition: "Software library for building minimal perfect hash function. Designed to handle large scale datasets." . + +SCR:023973 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Biber" ; + NIFRID:synonym "biber" ; + definition: "Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX." . + +SCR:023974 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bibus" ; + NIFRID:synonym "bibus" ; + definition: "Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records." . + +SCR:023975 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_12164" ; + rdfs:label "BCALM 2" ; + NIFRID:synonym "bcalm" ; + definition: "Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution." . + +SCR:023976 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_03734" ; + rdfs:label "BAli-Phy" ; + NIFRID:synonym "bali-phy", + "BAli-Phy version 3" ; + definition: "Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously." . + +SCR:023977 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_19790" ; + rdfs:label "BioCocoa" ; + NIFRID:synonym "biococoa" ; + definition: "Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences." . + +SCR:023978 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_13504" ; + rdfs:label "BOLT-LMM" ; + NIFRID:synonym "bolt-lmm" ; + definition: "Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts." . + +SCR:023979 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BioImageXD" ; + NIFRID:synonym "bioimagexd" ; + definition: "Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once." . + +SCR:023980 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CLI for BioMAJ" ; + NIFRID:synonym "biomaj3-cli", + "biomaj-cli" ; + definition: "Software package to use BioMAJ providing biomaj-cli." . + +SCR:023981 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CAMP" ; + NIFRID:synonym "camp" ; + definition: """Software multi-purpose reflection library developped by Technogerma Systems France and then by Tegesoft. Provides extra layer of +flexibility to programs, and allows them to fully expose their data structures at runtime.""" . + +SCR:023982 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_24974" ; + rdfs:label "caftools" ; + definition: "Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site." . + +SCR:023983 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21717" ; + rdfs:label "BioMAJ" ; + NIFRID:synonym "BIOlogie Mise A Jour", + "BioMAJ3", + "biomaj3" ; + definition: "Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository." . + +SCR:023984 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CamiTK" ; + NIFRID:synonym "camitk", + "Computer Assisted Medical Intervention Tool Kit" ; + definition: "Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations." . + +SCR:023985 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CDK" ; + NIFRID:synonym "cdk", + "Chemistry Development Kit" ; + definition: "Open Source software modular Java libraries for cheminformatics." . + +SCR:023986 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08874" ; + rdfs:label "Change-O" ; + NIFRID:synonym "changeo" ; + definition: "Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences." . + +SCR:023987 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CHIME" ; + NIFRID:synonym "chime", + "COVID-19 Hospital Impact Model for Epidemics" ; + definition: "Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation." . + +SCR:023988 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CAT and BAT" ; + NIFRID:synonym "BAT", + "Bin Annotation Tool", + "CAT", + "cat-bat", + "CAT/BAT", + "Contig Annotation Tool" ; + definition: "Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies." . + +SCR:023989 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08756" ; + rdfs:label "CodonW" ; + NIFRID:synonym "codonw" ; + definition: "Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage." . + +SCR:023990 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11185" ; + rdfs:label "ChromImpute" ; + NIFRID:synonym "chromimpute" ; + definition: "Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally." . + +SCR:023991 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "conda-package-handling" ; + definition: "Software to create and extract conda packages of various formats." . + +SCR:023992 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Chemtool" ; + NIFRID:synonym "chemtool" ; + definition: "Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11." . + +SCR:023993 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Conquest DICOM" ; + NIFRID:synonym "conquest-common", + "conquest-dbase", + "conquest-dicom-server", + "conquest-mysql", + "conquest-postgres", + "conquest-sqlite" ; + definition: "Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation." . + +SCR:023994 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_03452" ; + rdfs:label "CONTRAfold" ; + NIFRID:synonym "CONditional TRAining for RNA Secondary Structure Prediction", + "contrafold" ; + definition: "Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction." . + +SCR:023995 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CARD" ; + NIFRID:synonym "card-rgi", + "Comprehensive Antibiotic Resistance Database", + "The Comprehensive Antibiotic Resistance Database" ; + definition: "Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes." . + +SCR:023996 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CiftiLib" ; + NIFRID:synonym "ciftilib" ; + definition: "Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files." . + +SCR:023997 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CTDopts" ; + NIFRID:synonym "ctdopts" ; + definition: "Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities." . + +SCR:023998 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "covtobed" ; + definition: "Software tool to generate BED coverage tracks from BAM files." . + +SCR:023999 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "C Thread Pool" ; + NIFRID:synonym "C-Thread-Pool", + "cthreadpool" ; + definition: "Software for minimal but powerful thread pool in ANSI C." . + +SCR:024000 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20006" ; + rdfs:label "cyvcf2" ; + definition: "Software Python library and software package for fast parsing and querying of VCF and BCF files and illustrate its speed, simplicity and utility. Used for variant analysis." . + +SCR:024001 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_30643" ; + rdfs:label "Deepbinner" ; + NIFRID:synonym "deepbinner" ; + definition: "Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads." . + +SCR:024002 a owl:NamedIndividual ; + rdfs:label "CTK" ; + NIFRID:synonym "ctk", + "CTK - The Common Tool Kit" ; + definition: "Software to support biomedical image computing." . + +SCR:024003 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_04266" ; + rdfs:label "Dendroscope3" ; + NIFRID:synonym "dendroscope", + "dendroscope3" ; + definition: "Software Java program for analyzing and visualizing rooted phylogenetic trees and networks." . + +SCR:024004 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CTSim" ; + NIFRID:synonym "ctsim", + "Open Source Computed Tomography Simulator" ; + definition: "Software tool to simulate process of transmitting X-rays through phantom objects. Reconstructs original phantom image from projections. Has wide array of image analysis and image processing functions." . + +SCR:024005 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DEXTRACTOR" ; + NIFRID:synonym "dextractor", + "Dextractor and Compression Command Library" ; + definition: "Software as Bax file decoder and data compressor." . + +SCR:024006 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "dicompyler" ; + definition: "Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer." . + +SCR:024007 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CTDConverter" ; + NIFRID:synonym "ctdconverter" ; + definition: "Software Python scripts to convert CTD files into other formats such as Galaxy, CWL." . + +SCR:024008 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Dicom3tools" ; + NIFRID:synonym "dicom3tools" ; + definition: "Software package provides DICOM medical image files manipulation and conversion tools. Command line utilities for creating, modifying, dumping and validating DICOM files." . + +SCR:024009 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_13264" ; + rdfs:label "DNApi" ; + NIFRID:synonym "dnapi" ; + definition: "Software de novo adapter prediction algorithm for small RNA sequencing data." . + +SCR:024010 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EDFlib" ; + NIFRID:synonym "edflib" ; + definition: "Software programming library for C/C++ to read/write EDF+/BDF+ files.It also reads old-type EDF/BDF files." . + +SCR:024011 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_24617" ; + rdfs:label "ELPH" ; + NIFRID:synonym "elph", + "Estimated Locations of Pattern Hits" ; + definition: "Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs)." . + +SCR:024012 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08871" ; + rdfs:label "EMMAX" ; + NIFRID:synonym "Efficient Mixed-Model Association eXpedited", + "emmax" ; + definition: "Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model." . + +SCR:024013 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EMPeror" ; + NIFRID:synonym "EMPEROR", + "Emperor", + "emperor" ; + definition: "Web browser enabled tool with versatile command line interface to perform exploratory investigations of 3D visualizations of microbial community data, such as principal coordinates plots. EMPeror includes set of controllers to modify features as function of metadata. Web interactive next generation tool for analysis, visualization and understanding of high throughput microbial ecology datasets." . + +SCR:024014 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EMBOSS explorer" ; + NIFRID:synonym "emboss-explorer" ; + definition: "Web based graphical user interface to the EMBOSS suite of bioinformatics tools." . + +SCR:024015 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Entangle" ; + NIFRID:synonym "entangle" ; + definition: "Software tool provides graphical interface for tethered shooting, aka taking photographs with digital camera completely controlled from the computer." . + +SCR:024016 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_19988" ; + rdfs:label "Epigrass" ; + NIFRID:synonym "Epidemiological Geo-referenced Analysis and Simulation system", + "epigrass" ; + definition: "Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior." . + +SCR:024017 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_23387" ; + rdfs:label "EpiFire" ; + NIFRID:synonym "epifire" ; + definition: "Open source C++ library and application for contact network epidemiology. Application programming interface that models the spread of infectious disease in population and generates and manipulates networks of nodes and edges." . + +SCR:024018 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FFP" ; + NIFRID:synonym "Feature Frequency Profile Phylogeny", + "ffp" ; + definition: "Softwaare alignment free comparison tool for phylogenetic analysis and text comparison. Can be applied to nucleotide sequences, complete genomes, proteomes and for text comparison." . + +SCR:024019 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_10303" ; + rdfs:label "ExaBayes" ; + NIFRID:synonym "exabayes" ; + definition: "Software package for Bayesian tree inference. Used for large-scale analyses on computer clusters." . + +SCR:024020 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Filtlong" ; + NIFRID:synonym "filtlong" ; + definition: "Software tool for filtering long reads by quality.Can take set of long reads and produce smaller, better subset. Uses both read length and read identity when choosing which reads pass the filter." . + +SCR:024021 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EDFbrowser" ; + NIFRID:synonym "edfbrowser" ; + definition: "Open source, multiplatform, universal viewer, annotator and toolbox intended for time-series storage files like EEG, EMG, ECG, BioImpedance, etc." . + +SCR:024022 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FreeImage" ; + NIFRID:synonym "freeimage" ; + definition: "Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications." . + +SCR:024023 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29589" ; + rdfs:label "Fast5 Library" ; + NIFRID:synonym "Fast5", + "fast5" ; + definition: "Software C++ library for accessing Oxford Nanopore Technologies sequencing data." . + +SCR:024024 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_04834" ; + rdfs:label "GATB" ; + NIFRID:synonym "GATB-CORE", + "gatb-core", + "GATB-TOOLS", + "The Genome Analysis Toolbox with de-Bruijn graph" ; + definition: "Software genome analysis toolbox with de-Bruijn graph. Library dedicated to genome assembly and analysis." . + +SCR:024025 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "foreign" ; + NIFRID:synonym "r-cran-foreign" ; + definition: "Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files." . + +SCR:024026 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_02363w" ; + rdfs:label "GenomeTester4" ; + NIFRID:synonym "genometester" ; + definition: "Software toolkit for performing set operations - union, intersection and complement on k-mer lists." . + +SCR:024027 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GDCM" ; + NIFRID:synonym "gdcm", + "Grassroots DICOM library" ; + definition: "GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly." . + +SCR:024028 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GCLib" ; + NIFRID:synonym "gclib", + "genome-code-lib" ; + definition: "Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time." . + +SCR:024029 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GNUmed" ; + NIFRID:synonym "gnumed", + "gnumed-client", + "gnumed-server" ; + definition: "Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists." . + +SCR:024030 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_19577" ; + rdfs:label "GfaPy" ; + NIFRID:synonym "Gfapy", + "gfapy" ; + definition: "Software library for handling sequence graphs in Python." . + +SCR:024031 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Ginkgo CADx" ; + NIFRID:synonym "ginkgocadx" ; + definition: "Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files." . + +SCR:024032 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_05314" ; + rdfs:label "GramAlign" ; + NIFRID:synonym "gramalign" ; + definition: "Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences." . + +SCR:024033 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "IDeFIX" ; + NIFRID:synonym "idefix" ; + definition: "Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s)." . + +SCR:024034 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Htscodecs" ; + NIFRID:synonym "htscodecs" ; + definition: "Software repository implements the custom CRAM codecs used for \"EXTERNAL\" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data." . + +SCR:024035 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GraphMap2" ; + NIFRID:synonym "graphmap2" ; + definition: "Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices" . + +SCR:024036 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "HTSJDK" ; + NIFRID:synonym "htsjdk" ; + definition: "Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data." . + +SCR:024037 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_16456" ; + rdfs:label "IgDiscover" ; + NIFRID:synonym "igdiscover" ; + definition: "Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)." . + +SCR:024038 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_02397" ; + rdfs:label "InsPecT" ; + NIFRID:synonym "Inspect", + "inspect" ; + definition: "Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed." . + +SCR:024039 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ImageTooth" ; + NIFRID:synonym "imagetooth" ; + definition: "Software library to generate images for odontograms.Allows to choose between png or jpg images." . + +SCR:024040 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Insight Toolkit" ; + NIFRID:synonym "insighttoolkit4", + "ITK" ; + definition: "Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions." . + +SCR:024041 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_31218" ; + rdfs:label "InSilicoSeq" ; + NIFRID:synonym "insilicoseq", + "InSilicoSeq- A sequencing simulator" ; + definition: "Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome." . + +SCR:024042 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Intake" ; + NIFRID:synonym "intake", + "Intake: A general interface for loading data" ; + definition: "Software package for finding, investigating, loading and disseminating data." . + +SCR:024043 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ISMRMRD" ; + NIFRID:synonym "ISMRM Raw Data Format", + "ismrmrd" ; + definition: "Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format." . + +SCR:024044 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08188" ; + rdfs:label "IVA" ; + NIFRID:synonym "Iterative Virus Assembler - de novo virus assembler of Illumina paired reads.", + "iva" ; + definition: "Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth." . + +SCR:024045 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "iVar" ; + NIFRID:synonym "ivar" ; + definition: "Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files." . + +SCR:024046 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_27932" ; + rdfs:label "Kaptive" ; + NIFRID:synonym "kaptive" ; + definition: "Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies." . + +SCR:024047 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "JabRef" ; + NIFRID:synonym "jabref", + "JabRef Bibliography Management" ; + definition: "Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research." . + +SCR:024048 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "KBibTeX" ; + NIFRID:synonym "kbibtex" ; + definition: "Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported." . + +SCR:024049 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_18309" ; + rdfs:label "kineticsTools" ; + NIFRID:synonym "kineticstools" ; + definition: "Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol." . + +SCR:024050 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20021" ; + rdfs:label "JAligner" ; + NIFRID:synonym "jaligner" ; + definition: "Open source software Java implementation of the Needleman�Wunsch and Smith-Waterman algorithms for biological pairwise sequence alignment with the affine gap penalty model." . + +SCR:024051 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Kleborate" ; + NIFRID:synonym "KLEBORATE", + "kleborate" ; + definition: "Software tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for MLST sequence type, species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.), ICEKp associated virulence loci (yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)), virulence plasmid associated loci (salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)), antimicrobial resistance determinants (acquired genes, SNPs, gene truncations and intrinsic ?-lactamases), and K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive." . + +SCR:024052 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08009" ; + rdfs:label "Lambda" ; + NIFRID:synonym "LAMBDA", + "lambda-align", + "Lambda: the Local Aligner for Massive Biological DatA" ; + definition: "Software tool as local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools." . + +SCR:024053 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_18534" ; + rdfs:label "IGoR" ; + NIFRID:synonym "igor", + "Inference and Generation Of Repertoires" ; + definition: "C++ software designed to infer V(D)J recombination related processes from sequencing data." . + +SCR:024054 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_31606" ; + rdfs:label "KMA" ; + NIFRID:synonym "kma" ; + definition: "Software mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.Used for aligning high quality reads against highly redundant databases, where unique matches often does not exist. Works for long low quality reads as well, such as those from Nanopore. Non-unique matches are resolved using the \"ConClave\" sorting scheme, and a consensus sequence are outputtet in addition to other common attributes, based on users demands." . + +SCR:024055 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "kempbasu" ; + definition: "Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts." . + +SCR:024056 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-ASN1-EntrezGene" ; + NIFRID:synonym "Bio-ASN1-EntrezGene - Regular expression-based Perl Parser for NCBI Entrez Gene", + "libbio-asn1-entrezgene-perl" ; + definition: "Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record." . + +SCR:024057 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "AcePerl" ; + NIFRID:synonym "ACE", + "Ace", + "Ace - Object-Oriented Access to ACEDB Databases", + "Ace-Perl", + "ace-perl", + "libace-perl" ; + definition: "Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously." . + +SCR:024058 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "KmerResistance" ; + NIFRID:synonym "kmerresistance" ; + definition: "Software tool to correlate mapped genes with the predicted species of WGS samples, where this allows for identification of genes in samples which have been poorly sequenced or high accuracy predictions for samples with contamination. KmerResistance has one dependency, namely KMA to perform the mapping, which is also freely available." . + +SCR:024059 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-Chado-Schema" ; + NIFRID:synonym "Bio-Chado-Schema - A standard DBIx-Class layer for the Chado database schema", + "libbio-chado-schema-perl" ; + definition: "Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module." . + +SCR:024060 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "AI-FANN" ; + NIFRID:synonym "AI-FANN - Perl wrapper for the Fast Artificial Neural Network library", + "libai-fann-perl" ; + definition: "Software Perl wrapper for the Fast Artificial Neural Network library" . + +SCR:024061 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-Graphics" ; + NIFRID:synonym "Bio-Graphics - Generate GD images of Bio-Seq objects", + "libbio-graphics-perl" ; + definition: "Software package to generate GD images of Bio::Seq objects." . + +SCR:024062 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20057" ; + rdfs:label "BioD" ; + definition: "Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations." . + +SCR:024063 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-Coordinate" ; + NIFRID:synonym "Bio-Coordinate - Modules for working with biological coordinates", + "libbio-coordinate-perl" ; + definition: """Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. + +""" . + +SCR:024064 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-EUtilities" ; + NIFRID:synonym "Bio-EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils", + "libbio-eutilities-perl" ; + definition: "Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic." . + +SCR:024065 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bioparser" ; + NIFRID:synonym "bioparser", + "libbioparser-dev" ; + definition: "Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files." . + +SCR:024066 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-SamTools" ; + NIFRID:synonym "libbio-samtools-perl" ; + definition: "Software Perl interface to SamTools library for DNA sequencing." . + +SCR:024067 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-Tools-Run-Alignment-Clustalw" ; + NIFRID:synonym "Bio-Tools-Run-Alignment-Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program", + "libbio-tools-run-alignment-clustalw-perl" ; + definition: "Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program." . + +SCR:024068 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-SCF" ; + NIFRID:synonym "Bio-SCF - Perl extension for reading and writting SCF sequence files", + "libbio-scf-perl" ; + definition: "Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back." . + +SCR:024069 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-Tools-Phylo-PAML" ; + NIFRID:synonym "baseml", + "basemlg", + "Bio-Tools-Phylo-PAML - Parses output from the PAML programs codeml", + "codemlsites and yn00", + "libbio-tools-phylo-paml-perl" ; + definition: "Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output." . + +SCR:024070 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-Tools-Run-Alignment-TCoffee" ; + NIFRID:synonym "libbio-tools-run-alignment-tcoffee-perl" ; + definition: "Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program." . + +SCR:024071 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Libchipcard" ; + NIFRID:synonym "libchipcard", + "libchipcard-dev", + "libchipcard-tools" ; + definition: "Software library for generic access to chipcard readers and cards" . + +SCR:024072 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libdisorder" ; + definition: "Software C library for entropy measurement of byte streams and other data." . + +SCR:024073 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Chado" ; + NIFRID:synonym "libchado-perl" ; + definition: "Relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny. It has been designed to handle complex representations of biological knowledge and should be considered one of the most sophisticated relational schemas currently available in molecular biology. The price of this capability is that the new user must spend some time becoming familiar with its fundamentals." . + +SCR:024074 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FAST Analysis of Sequences Toolbox" ; + NIFRID:synonym "fast", + "FAST - FAST Analysis of Sequences Toolbox", + "Fast Analysis of Sequences Toolbox", + "libfast-perl" ; + NIFRID:abbrev "FAST" ; + definition: "Software Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records.FAST workflows are designed for serial processing of flatfile biological sequence record databases per-sequence, rather than per-line, through UNIX pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FASTQ format is supported. FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm." . + +SCR:024075 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libGDF" ; + NIFRID:synonym "gdf-tools", + "libgdf", + "libgdf-dev", + "octave-gdf" ; + definition: "Software library for processing of biomedical signals. Provides generic storage for biosignals, such as EEG, ECG, MEG. C++ implementation of GDF - \" general dataformat for biosignals\" version V2.20." . + +SCR:024076 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "JLODA" ; + NIFRID:synonym "jloda", + "libjloda-java" ; + definition: "Software Java library of data structures and algorithms.Provides some basic data structures and algorithms used by SplitsTree, Dendroscope and MEGAN." . + +SCR:024077 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libmaus2" ; + definition: "Software collection of data structures and algorithms. Contains I/O classes (single byte and UTF-8), bitio classes (input, output and various forms of bit level manipulation), text indexing classes (suffix and LCP array, fulltext and minute (FM), ...), BAM sequence alignment files input/output (simple and collating) and many lower level support classes." . + +SCR:024078 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_15611" ; + rdfs:label "Edlib" ; + NIFRID:synonym "Edib: A lightweight and super fast C/C++ library for sequence alignment using edit distance.", + "libedlib" ; + definition: "Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance." . + +SCR:024079 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libdivsufsort" ; + NIFRID:synonym "libdivsufsort: A lightweight suffix-sorting library" ; + definition: "Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string." . + +SCR:024080 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20523" ; + rdfs:label "libncl" ; + NIFRID:synonym "NCL", + "ncl", + "NCL - the NEXUS Class Library" ; + definition: "Software C++ class library for interpreting data files in NEXUS format. NEXUS Class Library software package is collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses.NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored." . + +SCR:024081 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MIA" ; + NIFRID:synonym "libmia-2.4-dev", + "libmialm", + "libmialm-dev", + "libmiaviewit-dev", + "libvistaio-dev", + "mia-tools", + "mia-viewit", + "mialmpick", + "python3-mia" ; + definition: "Software toolkit for gray scale medical image analysis. Provides combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in command shell and prototype algorithms as shell scripts. MIA is build around a plug-in structure that makes it easy to add functionality without compromising the original code base, and it makes use of wide variety of external libraries that provide additional functionality." . + +SCR:024082 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Bio-PrimerDesigner" ; + NIFRID:synonym "Bio-PrimerDesigner - Design PCR Primers using primer3 and epcr", + "libbio-primerdesigner-perl" ; + definition: "Software package provides low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio-PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported." . + +SCR:024083 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20524" ; + rdfs:label "libqes" ; + definition: "Software C library with bioinformatic focus optimised for speed and clean API." . + +SCR:024084 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Java NeXML libraries and tools" ; + NIFRID:synonym "libnexml-java", + "nexml.java" ; + definition: "Software repository contains java code for NeXML processing." . + +SCR:024085 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libics" ; + NIFRID:synonym "libics- Image Cytometry Standard file reading and writing" ; + definition: "Software reference library for Image Cytometry Standard, an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.Image Cytometry Standard file reading and writing." . + +SCR:024086 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libminc" ; + NIFRID:synonym "Medical Image NetCDF library" ; + definition: "Software core library and API of the Medical Image NetCDF toolkit." . + +SCR:024087 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Core Wrapper" ; + NIFRID:synonym "CORE-WRAPPER", + "core-wrapper" ; + definition: "Software library that exports C++ mmCIF accessors to Python." . + +SCR:024088 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libqc++" ; + NIFRID:synonym "libqcpp" ; + definition: "Software C++11 library for next-gen sequence quality control and assessment." . + +SCR:024089 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20525" ; + rdfs:label "SSW Library" ; + NIFRID:synonym "Complete-Striped-Smith-Waterman-Library", + "libssw", + "SIMD Smith-Waterman Library" ; + definition: "SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages." . + +SCR:024090 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "TaxonomyTree" ; + NIFRID:synonym "librdp-taxonomy-tree-java" ; + definition: "Software library used by other RDP tools.TaxonomyTree building and traversal utility classes." . + +SCR:024091 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14682" ; + rdfs:label "SeqLib" ; + NIFRID:synonym "libseqlib" ; + definition: "Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data" . + +SCR:024092 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Sort-Key-Top" ; + NIFRID:synonym "libsort-key-top-perl", + "Sort-Key-Top - select and sort top n elements" ; + definition: "Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures." . + +SCR:024093 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libStatGen" ; + NIFRID:synonym "C++ Library: libStatGen", + "libstatgen" ; + definition: "Software library as set of classes for creating statistical genetic programs." . + +SCR:024094 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ThreadPool" ; + NIFRID:synonym "libthread-pool", + "Thread pool" ; + definition: "Software C++ thread pool library." . + +SCR:024095 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Lighter" ; + NIFRID:synonym "lighter" ; + definition: "Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors." . + +SCR:024096 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Libxdf" ; + NIFRID:synonym "libxdf", + "Libxdf � a C++ library for loading XDF files" ; + definition: "Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications." . + +SCR:024097 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "limereg" ; + definition: "Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image." . + +SCR:024098 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11266" ; + rdfs:label "LTRsift" ; + NIFRID:synonym "LTRSIFT", + "ltrsift" ; + definition: "Software graphical desktop tool for semi-automatic postprocessing of de novopredicted LTR retrotransposon annotations, such as the ones generated by LTRharvestand LTRdigest. Interface displays LTR retrotransposon candidates, their putative families and their internal structure in a hierarchical fashion allowing the user to \"sift\" through results of de novo prediction software. It also offers customizable filtering and classification functionality." . + +SCR:024099 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14823" ; + rdfs:label "Lucy" ; + NIFRID:synonym "lucy", + "Lucy DNA sequence quality and vector trimming tool" ; + definition: "Software tool to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses." . + +SCR:024100 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VIGRA" ; + NIFRID:synonym "libvigraimpex", + "The VIGRA Computer Vision Library", + "Vision with Generic Algorithms" ; + definition: "Software image processing and analysis library that puts its main emphasis on customizable algorithms and data structures. VIGRA is especially strong for multi-dimensional images. By using template techniques similar to those in the C++ Standard Template Library, you can easily adapt any VIGRA component to the needs of your application, without thereby giving up execution speed. As of version 1.7.1, VIGRA also provides extensive Python bindings on the basis of the popular numpy framework." . + +SCR:024101 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Tab2MAGE" ; + NIFRID:synonym "ArrayExpress Tab2MAGE", + "mage2tab" ; + definition: "Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange." . + +SCR:024102 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_18310" ; + rdfs:label "Mapsembler2" ; + NIFRID:synonym "Mapsembler", + "mapsembler2" ; + definition: "Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants." . + +SCR:024103 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MAXFLOW" ; + NIFRID:synonym "maxflow" ; + definition: "Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph." . + +SCR:024104 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20118" ; + rdfs:label "Logol" ; + NIFRID:synonym "logol" ; + definition: "Pattern matching grammar language and set of tools to search pattern in sequence nucleic or proteic." . + +SCR:024105 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_06743" ; + rdfs:label "MafFilter" ; + NIFRID:synonym "maffilter", + "MafFilter a genome alignment processor" ; + definition: "Software tool for analysis of genome alignments. It parses and manipulates MAF files as well as more simple fasta files. Despite various filtering options and format conversion tools, MafFilter can compute a wide range of statistics including phylogenetic trees, nucleotide diversity, inferrence of selection, etc." . + +SCR:024106 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20116" ; + rdfs:label "MacSyFinder" ; + NIFRID:synonym "macsyfinder" ; + definition: "Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search." . + +SCR:024107 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "tabixpp" ; + NIFRID:synonym "libtabixpp" ; + definition: "Software C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.Wrapper to tabix indexer" . + +SCR:024108 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Maude" ; + NIFRID:synonym "maude" ; + definition: "Software high performance reflective language and system supporting both equational and rewriting logic specification and programming for wide range of applications.Supports equational specification and programming, rewriting logic computation." . + +SCR:024109 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MCL" ; + NIFRID:synonym "Markov Cluster Algorithm", + "mcl" ; + definition: "Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs." . + +SCR:024110 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20187" ; + rdfs:label "Metastudent" ; + NIFRID:synonym "metastudent", + "metastudent-data" ; + definition: "Software tool to predict gene ontology terms for protein sequences through homology." . + +SCR:024111 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "metaBIT" ; + NIFRID:synonym "metabit" ; + definition: "Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing." . + +SCR:024112 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_17085" ; + rdfs:label "MicrobeGPS" ; + NIFRID:synonym "microbegps" ; + definition: "Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates." . + +SCR:024113 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_13515" ; + rdfs:label "MHAP" ; + NIFRID:synonym "mhap", + "MinHash Alignment Process" ; + definition: "Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data." . + +SCR:024114 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11366" ; + rdfs:label "Miniasm" ; + NIFRID:synonym "miniasm" ; + definition: "Software OLC-based de novo assembler for noisy long reads." . + +SCR:024115 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_05472" ; + rdfs:label "MindTheGap" ; + NIFRID:synonym "mindthegap" ; + definition: "Software tool to perform detection and assembly of DNA insertion variants in NGS read datasets with respect to reference genome.Used to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome." . + +SCR:024116 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_31718" ; + rdfs:label "mirtop" ; + definition: "Command lines tool to annotate miRNAs with standard mirna/isomir naming." . + +SCR:024117 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "medicalterms" ; + NIFRID:synonym "hunspell-de-med", + "wgerman-medical" ; + definition: "Software package to create specialized dictionaries for medical terms used in various languages.German medical dictionary words." . + +SCR:024118 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_33146" ; + rdfs:label "mPSQed" ; + NIFRID:synonym "mpsqed" ; + definition: "Software tool for the design of multiplex pyrosequencing assays." . + +SCR:024119 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_20188" ; + rdfs:label "SMILE" ; + NIFRID:synonym "mlv-smile" ; + definition: "Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths." . + +SCR:024120 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "mmtf-python" ; + definition: "Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries." . + +SCR:024121 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_15264" ; + rdfs:label "mPTP" ; + NIFRID:synonym "mptp", + "multi-rate Poisson Tree Processes" ; + definition: "Software tool for single locus species delimitation. Implements fast method to compute the ML delimitation from inferred phylogenetic tree of the samples.Used to handle very large biodiversity datasets." . + +SCR:024122 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Molekel" ; + NIFRID:synonym "molekel" ; + definition: "Open source multi platform molecular visualization program." . + +SCR:024123 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MRtrix3" ; + NIFRID:synonym "mrtrix3" ; + definition: "Software tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses." . + +SCR:024124 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11495" ; + rdfs:label "Nanocall" ; + NIFRID:synonym "nanocall" ; + definition: "Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller." . + +SCR:024125 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NanoLyse" ; + NIFRID:synonym "nanolyse" ; + definition: "Software package to remove reads mapping to the lambda phage genome from a fastq file." . + +SCR:024126 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_03642" ; + rdfs:label "Mustang" ; + NIFRID:synonym "MUltiple (protein) STructural AligNment alGorithm", + "MUSTANG", + "mustang" ; + definition: "Software tool for structural alignment of multiple protein structures. Used to produce sequence alignment. Reports multiple sequence alignment and corresponding superposition of structures." . + +SCR:024127 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29732" ; + rdfs:label "NanoSV" ; + NIFRID:synonym "nanosv" ; + definition: "Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers." . + +SCR:024128 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NanoPlot" ; + NIFRID:synonym "nanoplot" ; + definition: "Software package as plotting tool for long read sequencing data and alignments." . + +SCR:024129 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_15907" ; + rdfs:label "MView" ; + NIFRID:synonym "mview" ; + definition: "Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats." . + +SCR:024130 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NCBI accession download script" ; + NIFRID:synonym "ncbi-acc-download" ; + definition: "Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API." . + +SCR:024131 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21450" ; + rdfs:label "NeoBio" ; + NIFRID:synonym "neobio" ; + definition: "Software library of sequence alignment algorithms implemented in Java." . + +SCR:024132 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11714" ; + rdfs:label "Murasaki" ; + NIFRID:synonym "murasaki" ; + definition: "Software language-theory based homology detection tool across multiple large genomes." . + +SCR:024133 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_03695" ; + rdfs:label "Ngila" ; + NIFRID:synonym "ngila" ; + definition: "Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties." . + +SCR:024134 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_30332" ; + rdfs:label "NextSV" ; + NIFRID:synonym "nextsv", + "NextSV3" ; + definition: "Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling." . + +SCR:024135 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Nextflow" ; + NIFRID:synonym "nextflow" ; + definition: "Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more." . + +SCR:024136 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Entrez Direct" ; + NIFRID:synonym "EDirect", + "Entrez Direct: E-utilities on the Unix Command Line", + "ncbi-entrez-direct" ; + definition: "Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats." . + +SCR:024137 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_04815" ; + rdfs:label "NJplot" ; + NIFRID:synonym "njplot" ; + definition: "Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods." . + +SCR:024138 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NW-align" ; + NIFRID:synonym "nw-align" ; + definition: "Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm." . + +SCR:024139 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21452" ; + rdfs:label "NORSp" ; + NIFRID:synonym "NOn-Regular Secondary Structure predictor", + "norsp", + "NORSp - predictor of NOn-Regular Secondary Structure" ; + definition: "Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions." . + +SCR:024140 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Odil" ; + NIFRID:synonym "odil" ; + definition: "Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard." . + +SCR:024141 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_32696" ; + rdfs:label "OBITools" ; + NIFRID:synonym "obitools" ; + definition: "Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses." . + +SCR:024142 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14951" ; + rdfs:label "OpenCFU" ; + NIFRID:synonym "opencfu" ; + definition: "Software to count cell colonies and other circular objects. Used to facilitate enumeration of colony forming unit." . + +SCR:024143 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_31719" ; + rdfs:label "omegaMap" ; + NIFRID:synonym "omegamap" ; + definition: "Software tool for detecting natural selection and recombination in DNA or RNA sequences." . + +SCR:024144 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "OpenEMR" ; + NIFRID:synonym "openemr" ; + definition: "Open source software for electronic health records and medical practice management solution." . + +SCR:024145 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Orthanc" ; + NIFRID:synonym "orthanc" ; + definition: "Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases." . + +SCR:024146 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_16034" ; + rdfs:label "NORSnet" ; + NIFRID:synonym "Norsnet", + "norsnet" ; + definition: "Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data." . + +SCR:024147 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "OpenSurgSim" ; + NIFRID:synonym "opensurgsim" ; + definition: "Open source software framework that includes the necessary building blocks for surgical simulations, such as native device support, haptic feedback, graphics, discrete collision detection and physics simulation. Developers can refactor the physics engine, swap models, ODE solvers, or linear system solvers." . + +SCR:024148 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "OpenIGTLink" ; + NIFRID:synonym "Open Network Interface for Image-Guided Therapy Link", + "openigtlink" ; + definition: "Open source software network communication interface for image guided interventions.Provides plug-and-play unified real-time communications in operating rooms for image-guided interventions, where imagers, sensors, surgical robots,and computers from different vendors work cooperatively to ensure seamless data flow among those components and enable a closed loop process of planning, control, delivery, and feedback." . + +SCR:024149 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_33123" ; + rdfs:label "OptimiR" ; + NIFRID:synonym "optimir" ; + definition: "Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis." . + +SCR:024150 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "parallel-fastq-dump" ; + definition: "Software wrapper to speed up downloading process by dividing the work into multiple threads." . + +SCR:024151 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PAIPline" ; + definition: "Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples." . + +SCR:024152 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pbcopper" ; + definition: "Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications." . + +SCR:024153 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21461" ; + rdfs:label "Parsnp" ; + NIFRID:synonym "parsnp" ; + definition: "Software to align the core genome of hundreds to thousands of bacterial genomes. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction." . + +SCR:024154 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Patristic" ; + NIFRID:synonym "patristic" ; + definition: "Software Java program for calculating patristic distances and graphically comparing the components of genetic change." . + +SCR:024155 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14370" ; + rdfs:label "PDB2PQR" ; + NIFRID:synonym "pdb2pqr" ; + definition: "Software interface for running PDB2PQR web service. Used to prepare structures for further calculations by reconstructing missing atoms, adding hydrogens, assigning atomic charges and radii from specified force fields, and generating PQR files." . + +SCR:024156 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14997" ; + rdfs:label "PCMA" ; + NIFRID:synonym "pcma", + "Profile Consistency Multiple Sequence Alignment" ; + definition: "Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences." . + +SCR:024157 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PartitionFinder" ; + NIFRID:synonym "partitionfinder", + "PartitionFinder 2" ; + definition: "Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data." . + +SCR:024158 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29588" ; + rdfs:label "PfTools" ; + NIFRID:synonym "pftools" ; + definition: "Software suite of tools to build and search generalized profiles." . + +SCR:024159 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21686" ; + rdfs:label "PhySamp" ; + NIFRID:synonym "physamp" ; + definition: "Software package dedicated to phylogenetic sampling. Used to sample sequence alignment according to its corresponding phylogenetic tree." . + +SCR:024160 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_33677" ; + rdfs:label "PiGx-RNAseq" ; + NIFRID:synonym "pigx-rnaseq" ; + definition: "Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables." . + +SCR:024161 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "picopore" ; + definition: "Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality." . + +SCR:024162 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PHYLOViZ" ; + definition: "Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods." . + +SCR:024163 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21460" ; + rdfs:label "ParsInsert" ; + NIFRID:synonym "parsinsert" ; + definition: "Software C++ implementation of Parsimonious Insertion algorithm. Used to produce phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis." . + +SCR:024164 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_02387" ; + rdfs:label "Phyx" ; + definition: "Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects." . + +SCR:024165 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pipasic" ; + definition: "Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor." . + +SCR:024166 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PlasmidID" ; + NIFRID:synonym "plasmidid" ; + definition: "Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences." . + +SCR:024167 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_28371" ; + rdfs:label "PlasmidSeeker" ; + NIFRID:synonym "plasmidseeker" ; + definition: "Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads." . + +SCR:024168 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Plastimatch" ; + definition: "Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images." . + +SCR:024169 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pngquant" ; + definition: "Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems." . + +SCR:024170 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_06498" ; + rdfs:label "PLAST" ; + NIFRID:synonym "parallel local alignment search tool", + "plast" ; + definition: "Software parallel local alignment search tool for database comparison. NGS sequence similarity search tool providing significant accelerations of seeds based heuristic comparison methods." . + +SCR:024171 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21692" ; + rdfs:label "ProDA" ; + NIFRID:synonym "proda" ; + definition: "Software for multiple alignment of protein sequences with repeated and shuffled elements.Used for automated detection and alignment of homologous regions in collections of proteins with arbitrary domain architectures." . + +SCR:024172 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14254" ; + rdfs:label "POA" ; + NIFRID:synonym "Partial Order Alignment", + "poa" ; + definition: "Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment." . + +SCR:024173 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08028" ; + rdfs:label "PLIP" ; + NIFRID:synonym "plip", + "Protein-Ligand Interaction Profiler" ; + definition: "Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures." . + +SCR:024174 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_12425" ; + rdfs:label "PRANK" ; + NIFRID:synonym "prank" ; + definition: "Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences." . + +SCR:024175 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29592" ; + rdfs:label "Populations" ; + NIFRID:synonym "populations" ; + definition: "Population genetic software for individuals or populations distances based on allelic frequencies, phylogenetic trees, file conversions." . + +SCR:024176 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11487" ; + rdfs:label "Placnet" ; + NIFRID:synonym "placnet", + "plasmid constellation networks" ; + definition: "Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools." . + +SCR:024177 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_05355" ; + rdfs:label "Proteinortho" ; + definition: "Software tool to detect orthologous genes within different species. Stand-alone tool for large datasets for orthology analysis." . + +SCR:024178 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PRINSEQ" ; + NIFRID:synonym "prinseq-lite" ; + definition: "Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format." . + +SCR:024179 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_13706" ; + rdfs:label "PROFisis" ; + NIFRID:synonym "profisis" ; + definition: "Software tool that identifies interacting residues from sequence alone. Developed using transient protein�protein interfaces from complexes of experimentally known 3D structures." . + +SCR:024180 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PyBEL" ; + NIFRID:synonym "pybel" ; + definition: "Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J." . + +SCR:024181 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pssh2" ; + definition: "Software tools for creating the sequence-to-structure alignment database PSSH2." . + +SCR:024182 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pyepl" ; + NIFRID:synonym "Python Experiment-Programming Library" ; + definition: "Software library for coding psychology experiments in Python.Supports presentation of both visual and auditory stimuli, and supports both manual and sound input as responses." . + +SCR:024183 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "purple" ; + NIFRID:synonym "Picking Unique Relevant Peptides for viraL Experiments" ; + definition: "Software tool for selecting target specific peptide candidates directly from given proteome sequence data." . + +SCR:024184 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pufferfish" ; + definition: "Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph." . + +SCR:024185 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pycoqc" ; + definition: "Software application to compute metrics and generate interactive QC plots for Oxford Nanopore technologies sequencing data." . + +SCR:024186 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pyFAI" ; + NIFRID:synonym "pyFai", + "pyfai" ; + definition: "Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments." . + +SCR:024187 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "python-airr" ; + definition: "Software airr reference library provides basic functions and classes for interacting with AIRR Community Data Representation Standards, including tools for read, write and validation." . + +SCR:024188 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pyomo" ; + definition: "Open source Python-based optimization modeling language with diverse set of optimization capabilities." . + +SCR:024189 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_15419" ; + rdfs:label "pynast" ; + NIFRID:synonym "Python Nearest Alignment Space Termination tool" ; + definition: "Software tool for aligning sequences to template alignment." . + +SCR:024190 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21694" ; + rdfs:label "pyscanfcs" ; + definition: "Software application for perpendicular line scanning fluorescence correlation spectroscopy." . + +SCR:024191 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pyranges" ; + definition: "Software application for efficient comparison of genomic intervals in Python." . + +SCR:024192 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14006" ; + rdfs:label "PyCogent" ; + NIFRID:synonym "COmparative GENomic Toolkit", + "python-cogent" ; + definition: "Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics." . + +SCR:024193 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "python-biom-format" ; + definition: "Software provides command line interface and Python API for working with Biological Observation Matrix files." . + +SCR:024194 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Cooler" ; + NIFRID:synonym "python-cooler" ; + definition: "Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays." . + +SCR:024195 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "qcat" ; + definition: "Software Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files." . + +SCR:024196 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "psignifit" ; + definition: "Software toolbox to fit psychometric functions and to test hypotheses about psychometric data." . + +SCR:024197 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08877" ; + rdfs:label "DendroPy" ; + NIFRID:synonym "python-dendropy" ; + definition: "Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA." . + +SCR:024198 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_10013" ; + rdfs:label "rambo-k" ; + definition: "Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data." . + +SCR:024199 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "qtlreaper" ; + definition: "Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL." . + +SCR:024200 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_18457" ; + rdfs:label "qtltools" ; + definition: "Software tool set for molecular Quantitative Trait Loci discovery and analysis. Allows to go from raw sequence data to collection of molecular Quantitative Trait Loci in few easy-to-perform steps." . + +SCR:024201 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21300" ; + rdfs:label "raccoon" ; + definition: "Software graphical interface for preparing AutoDock virtual screenings.Automates some of the most common operations performed when preparing virtual screening." . + +SCR:024202 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_18239" ; + rdfs:label "python-bx" ; + definition: "Software Python library and associated set of scripts for rapid implementation of genome scale analyses." . + +SCR:024203 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "qcumber" ; + definition: "Software for quality control, quality trimming, adapter removal and sequence content check of NGS data." . + +SCR:024204 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_10349" ; + rdfs:label "rapmap" ; + NIFRID:synonym "RapMap" ; + definition: "Software tool for mapping RNA-seq reads to transcriptomes. Used for rapid sensitive and accurate read mapping via quasi-mapping" . + +SCR:024205 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "quicktree" ; + definition: "Software application as implementation of Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments." . + +SCR:024206 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_07883" ; + rdfs:label "ragout" ; + NIFRID:synonym "Reference-Assisted Genome Ordering UTility" ; + definition: "Software tool for chromosome level scaffolding using multiple references. Given initial assembly fragments and one or multiple related references it produces chromosome scale assembly." . + +SCR:024207 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_33016" ; + rdfs:label "rampler" ; + definition: "Standalone software for sampling genomic sequences.Supports two modes, random subsampling of sequencing data to desired depth and file splitting to desired size in bytes." . + +SCR:024208 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_05076" ; + rdfs:label "rasmol" ; + NIFRID:synonym "RasMol" ; + definition: "Software package for molecular graphics visualisation.Used for visualisation of molecules." . + +SCR:024209 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Moodle LMS" ; + NIFRID:synonym "Moodle", + "moodle", + "moodle (LMS)" ; + definition: "Open source learning platform to provide educators, administrators and learners with integrated system to create personalised learning environments. Designed to help educators create online courses based on pedagogical principles." . + +SCR:024210 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MorePower" ; + NIFRID:synonym "MorePower 6.0", + "MorePower calculator" ; + definition: "Software tool as flexible freeware statistical calculator that computes sample size, effect size, and power statistics for factorial ANOVA designs." . + +SCR:024211 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Epworth Sleepiness Scale" ; + NIFRID:abbrev "ESS" ; + definition: "New method for measuring daytime sleepiness. Self administered questionnaire to provide measurement of subject's general level of daytime sleepiness. Subjects are to rate the chances that they would doze off or fall asleep when in eight different situations commonly encountered in daily life.Used to give valid measurements of sleep propensity in adults." . + +SCR:024212 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Karolinska Sleepiness Scale" ; + definition: "The scale measures subjective level of sleepiness at particular time during the day. On this scale subjects indicate which level best reflects the psycho-physical sate experienced in the last 10 min.KSS is measure of situational sleepiness." . + +SCR:024213 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Psychomotor Vigilance Task system" ; + NIFRID:synonym "Psychomotor Vigilance Task", + "PVT-192 Psychomotor Vigilance Task Monitor" ; + definition: "System includes PVT-192 monitor and REACT software. Used for reaction time testing for long-term, large-scale testing of vigilance, effects of sleep deprivation, and drug effects. Used for PVT test wherever measures of performance or sleepiness effects are needed." . + +SCR:024214 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GenomeMUSter" ; + definition: "Web and programmatically accessible data service comprising allelic data covering strains at segregating sites. Mouse genetic variation service enables multi-trait, multi-population data integration and analyses. Interoperation with phenotype databases, analytic tools and other resources enable wealth of applications including multi-trait, multi-population meta-analysis. Mouse genetic resource that includes typed, sequenced, and imputed allelic states of 657 inbred mouse strains and their derivatives at 106.8M sites." . + +SCR:024215 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rocker " ; + definition: """Software suite of Docker images with customized R environments for particular tasks. +Docker containers for R to create, distribute, deploy, and run software applications +using containers.""" . + +SCR:024216 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ensemblQueryR" ; + definition: "Software R package allowing integration of Ensembl querying with R workflow. Used to seemlessly integrate querying of Ensembl databases into your R workflow." . + +SCR:024217 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Multiome Pipeline" ; + NIFRID:synonym "Multiome GEX and scATAC Pipeline" ; + definition: "Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Atlas Network, and SCORCH. Supports processing of 10x 3' single-cell and single-nucleus gene expression and single-cell chromatin accessibility data generated with 10x Genomics Multiome assay." . + +SCR:024220 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_05054" ; + rdfs:label "Raster3D" ; + NIFRID:synonym "raster3d" ; + definition: "Software tools for generating high quality raster images of proteins or other molecules. Photorealistic molecular graphics. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing." . + +SCR:024221 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "annotate" ; + definition: "Software R package for using R enviroments for annotation." . + +SCR:024222 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_06940" ; + rdfs:label "Rate4Site" ; + NIFRID:synonym "rate4site" ; + definition: "Software tool for detecting conserved amino-acid sites by computing relative evolutionary rate for each site in multiple sequence alignment. Used for identification of functional regions in proteins." . + +SCR:024223 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29381" ; + rdfs:label "affyio" ; + definition: "Software R package as routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing CEL and CDF file formats." . + +SCR:024224 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Biobase" ; + definition: "Software R package provides functions that are needed by many other packages or which replace R functions. Base functions for Bioconductor." . + +SCR:024225 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "altcdfenvs" ; + NIFRID:synonym "alternative CDF environments" ; + definition: "Software R package contains convenience data structures and functions to handle cdfenvs." . + +SCR:024226 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BiocGenerics" ; + definition: "Software R package defines many S4 generic functions used in Bioconductor." . + +SCR:024227 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29380" ; + rdfs:label "AnnotationHub" ; + definition: "Software R package to provide a client for the Bioconductor AnnotationHub web resource. AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered." . + +SCR:024228 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "biomformat" ; + definition: "Software R package for interfacing with BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, limited support for writing biom-object back to biom-format file." . + +SCR:024229 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "biovizBase" ; + definition: "Software R package to provide set of utilities, color schemes and conventions for genomic data. Used for various high-level packages for biological data visualization." . + +SCR:024230 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bsgenome" ; + definition: "Software R package provides infrastructure shared by all the Biostrings-based genome data packages." . + +SCR:024231 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bridgedbr" ; + definition: "Software R pacakge provides functions and load identifier mapping databases in R. Uses GitHub, Zenodo, and Figshare if you use this package to download identifier mappings files." . + +SCR:024232 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ctc" ; + definition: "Software R package for export and import classification trees and clusters to other programs." . + +SCR:024233 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_33013" ; + rdfs:label "CNEr" ; + definition: "Software R package provides large scale identification and advanced visualization of sets of conserved noncoding elements." . + +SCR:024234 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_15854" ; + rdfs:label "geneplotter" ; + definition: "Software R package provides functions for plotting genomic data" . + +SCR:024235 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "genomeinfodb" ; + definition: "Software R package contains data and functions that define and allow translation between different chromosome sequence naming conventions, including function that attempts to place sequence names in their natural, rather than lexicographic order." . + +SCR:024236 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "genomicalignments" ; + definition: "Software R package provides efficient containers for storing and manipulating short genomic alignments. This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments." . + +SCR:024237 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_07953" ; + rdfs:label "groHMM" ; + NIFRID:synonym "grohmm" ; + definition: "Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data" . + +SCR:024238 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29382" ; + rdfs:label "genefilter" ; + definition: "Software R package provides some basic functions for filtering genes." . + +SCR:024239 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_17191" ; + rdfs:label "gviz" ; + definition: "Software R package to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package." . + +SCR:024240 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "hypergraph" ; + definition: "Software R package that implements some simple capabilities for representing and manipulating hypergraphs." . + +SCR:024241 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_22608" ; + rdfs:label "go.db" ; + definition: "Software R package provides set of annotation maps describing entire Gene Ontology assembled using data from GO." . + +SCR:024242 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "htsfilter" ; + definition: "Software R package implements filtering procedure for replicated transcriptome sequencing data based on global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions." . + +SCR:024243 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "impute" ; + definition: "Software R package for imputation for microarray data." . + +SCR:024244 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_12862" ; + rdfs:label "mergeomics" ; + definition: "Software R pacakage for multidimensional data integration to identify pathogenic perturbations to biological systems. Used for integrating multidimensional omics disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. Includes Marker set enrichment analysis and Weighted Key Driver Analysis parts." . + +SCR:024245 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_19308" ; + rdfs:label "multiassayexperiment" ; + definition: "Software R package to harmonize data management of multiple experimental assays performed on overlapping set of specimens.Provides user experience by extending concepts from SummarizedExperiment, supporting open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis." . + +SCR:024246 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_07813" ; + rdfs:label "metagenomeseq" ; + definition: "Software R package to determine features that are differentially abundant between two or more groups of multiple samples. Used to address the effects of both normalization and under-sampling of microbial communities on disease association detection and testing of feature correlations." . + +SCR:024247 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "mutationalpatterns" ; + definition: "Software R package provides set of flexible functions to evaluate and visualize multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells." . + +SCR:024248 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "makecdfenv" ; + definition: "Software R package has two functions. One reads Affymetrix chip description file and creates hash table environment containing location/probe set membership mapping. The other creates package that automatically loads that environment." . + +SCR:024249 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pwmenrich" ; + definition: "Software toolkit of high level functions for DNA motif scanning and enrichment analysis built upon Biostrings. Used for PWM enrichment analysis of already known PWMs. Also implements high-level functions for PWM scanning and visualisation." . + +SCR:024250 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "nanostringqcpro" ; + definition: "Software R package to assess quality of NanoString mRNA gene expression data, to identify outlier probes and outlier samples. Provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and easily sharable html quality control output." . + +SCR:024251 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rbgl" ; + definition: "Software R package as interface to the graph algorithms contained in the BOOST library." . + +SCR:024252 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14344" ; + rdfs:label "pcaMethods" ; + NIFRID:synonym "pcamethods" ; + definition: "Software R package providing PCA methods for incomplete data. Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and conventional SVD PCA. Cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation." . + +SCR:024253 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rcpi" ; + definition: "Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery." . + +SCR:024254 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "preprocesscore" ; + definition: "Software library of core preprocessing routines." . + +SCR:024255 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "qusage" ; + NIFRID:synonym "Quantitative Set Analysis for Gene Expression" ; + definition: "Software R package is implementation Quantitative Set Analysis for Gene Expression method. Used to provide faster, more accurate, and easier to understand test for gene expression studies." . + +SCR:024256 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rgsepd" ; + definition: "Software R package to help disambiguate transcriptome samples by automating differential expression, then gene set enrichment, and finally N-dimensional projection to quantify in which ways each sample is like either treatment group." . + +SCR:024257 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rsamtools" ; + definition: "Software R package provides interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating Sequence Alignment Map, FASTA, binary variant call and compressed indexed tab-delimited files." . + +SCR:024258 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_15992" ; + rdfs:label "savr" ; + definition: "Software R package to parse Illumina Sequence Analysis Viewer files, access data, and generate QC plots." . + +SCR:024259 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ade4" ; + definition: "Software R package for multivariate data analysis. Used for analysis of one-table, two-table, three-table and K-table." . + +SCR:024260 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11082" ; + rdfs:label "tfbstools" ; + NIFRID:synonym "TFBSTools" ; + definition: "Software R package for analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software." . + +SCR:024261 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21399" ; + rdfs:label "alakazam" ; + definition: "Software R package for high-throughput adaptive immune receptor repertoire sequencing analysis. In particular, immunoglobulin sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage." . + +SCR:024262 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "beeswarm" ; + NIFRID:synonym "an Alternative to Stripchart", + "beeswarm: The Bee Swarm Plot", + "r-cran-beeswarm", + "The Bee Swarm Plot" ; + definition: "Software R package implementing bee swarm plots. Bee swarm plot is one-dimensional scatter plot like \"stripchart\", but with closely packed, non overlapping points." . + +SCR:024263 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "xvector" ; + definition: "Software R package provides memory efficient S4 classes for storing sequences externally." . + +SCR:024264 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_06963" ; + rdfs:label "BoolNet" ; + NIFRID:synonym "BoolNet: Construction", + "r-cran-boolnet", + "Simulation and Analysis of Boolean Networks" ; + definition: "Software R package provides functions to reconstruct, generate, and simulate synchronous, asynchronous, probabilistic, and temporal Boolean networks. Provides also functions to analyze and visualize attractors in Boolean networks." . + +SCR:024265 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "cmprsk" ; + NIFRID:synonym "cmprsk: Subdistribution Analysis of Competing Risks", + "r-cran-cmprsk" ; + definition: "Software R package for estimation, testing and regression modeling of subdistribution functions in competing risks." . + +SCR:024266 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_12577" ; + rdfs:label "bio3d" ; + NIFRID:synonym "bio3d: Biological Structure Analysis", + "r-cran-bio3d" ; + definition: "Softwar R package for comparative analysis of protein structures. Used to process, organize and explore protein structure, sequence and dynamics data. Used to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. Enables statistical and graphical power of R environment to work with biological sequence and structural data." . + +SCR:024267 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08682" ; + rdfs:label "adephylo" ; + definition: "Software R package provides multivariate tools to analyze comparative data. Analysis of comparative evolutionary data. Used for investigating phylogenetic signal in biological traits." . + +SCR:024268 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DoseFinding" ; + NIFRID:synonym "DoseFinding: Planning and Analyzing Dose Finding Experiments", + "r-cran-dosefinding" ; + definition: "Software R package provides functions for design and analysis of dose finding experiments. Used for multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and implementation of MCPMod methodology." . + +SCR:024269 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_33012" ; + rdfs:label "distory" ; + NIFRID:synonym "distory: Distance Between Phylogenetic Histories", + "r-cran-distory" ; + definition: "Software R package for geodesic distance between phylogenetic trees and associated functions." . + +SCR:024270 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DT" ; + NIFRID:synonym "DataTables", + "DT: A Wrapper of the JavaScript Library 'DataTables'", + "r-cran-dt" ; + definition: "Software R package for data objects in R to render as HTML tables using JavaScript library DataTables. DataTables library has been included in this R package." . + +SCR:024271 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "biwt" ; + NIFRID:synonym "biwt: Compute the Biweight Mean Vector and Covariance & Correlation Matrice", + "r-cran-biwt" ; + definition: "Software R package for compute multivariate location, scale, and correlation estimates based on Tukey's biweight M-estimator." . + +SCR:024272 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Epi" ; + NIFRID:synonym "Epi: Statistical Analysis in Epidemiology", + "r-cran-epi" ; + definition: "Software R package provides functions for demographic and epidemiological analysis in Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and function for interval censored data and some useful functions for tabulation and plotting, as well as number of epidemiological data sets." . + +SCR:024273 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "fitbitscraper" ; + definition: "Software R package to scrape data from Fitbit to generate graphs." . + +SCR:024274 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "fitdistrplus" ; + definition: "Software R package extends fitdistr function to help the fit of parametric distribution to non-censored or censored data." . + +SCR:024275 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "epibasix" ; + NIFRID:synonym "epibasix: Elementary Epidemiological Functions for Epidemiology and Biostatistics", + "r-cran-epibasix" ; + definition: "Software R package for analysis of common epidemiological problems, ranging from sample size estimation, through 2x2 contingency table analysis and basic measures of agreement." . + +SCR:024276 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "incidence" ; + definition: "Software R package provides functions and classes to compute, handle and visualise incidence from dated events for defined time interval. Dates can be provided in various standard formats." . + +SCR:024277 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "forecast" ; + definition: "Software R package for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling." . + +SCR:024278 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "lexrankr" ; + definition: "Software R package as implementation of LexRank algorithm. Used for computing sentence importance based on concept of eigenvector centrality in graph representation of sentences." . + +SCR:024279 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "genetics" ; + definition: "Software R package for handling genetic data. Includes classes to represent genotypes and haplotypes at single markers up to multiple markers on multiple chromosomes. Function include allele frequencies, flagging homo/heterozygotes, flagging carriers of certain alleles, estimating and testing for Hardy-Weinberg disequilibrium, estimating and testing for linkage disequilibrium." . + +SCR:024280 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_23803" ; + rdfs:label "dynamicTreeCut" ; + NIFRID:synonym "dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering Dendrograms", + "r-cran-dynamictreecut" ; + definition: "Software R package contains methods for detection of clusters in hierarchical clustering dendrograms." . + +SCR:024281 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "mediana" ; + definition: "Software R package for clinical trial simulations based on Clinical Scenario Evaluation approach. The package supports broad class of data models, analysis strategies and commonly used evaluation criteria." . + +SCR:024282 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "itertools" ; + definition: "Software R package for creating iterators, many patterned after functions in the Python itertools module, and others patterned after functions in the 'snow' package." . + +SCR:024283 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "optimalcutpoints" ; + definition: "Software R package to compute optimal cutpoints for diagnostic tests or continuous markers.Used for selecting optimal cutoffs, analysis and diagnostic test accuracy measures." . + +SCR:024284 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "nmf" ; + definition: "Software R package provides framework to perform Non-negative Matrix Factorization.Used for nonnegative matrix factorization.Implements set of already published algorithms and seeding methods, and provides framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines." . + +SCR:024285 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_16887" ; + rdfs:label "parmigene" ; + NIFRID:synonym "Parallel Mutual Information Estimation for Gene Network Reconstruction" ; + definition: "Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks." . + +SCR:024286 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_17528" ; + rdfs:label "proc" ; + definition: "Software R tools for visualizing, smoothing and comparing receiver operating characteristic. Partial area under curve AUC can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves." . + +SCR:024287 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pcapp" ; + definition: "Software R package provides functions for principal component analysis by projection pursuit." . + +SCR:024288 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "psychotree" ; + definition: "Software R package for recursive partitioning based on psychometric models, employing general MOB algorithm to obtain Bradley-Terry trees, Rasch trees, rating scale and partial credit trees, and MPT trees, trees for 1PL, 2PL, 3PL and 4PL models and generalized partial credit models." . + +SCR:024289 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "psyphy" ; + definition: "Software R package useful in analyzing data from psychophysical experiments.Includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice data to be used with binomial family in glm and self-Start functions for estimating gamma values for CRT screen calibrations." . + +SCR:024290 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rncl" ; + definition: "Software R package provides interface to Nexus Class Library which allows parsing of NEXUS, Newick and other phylogenetic tree file formats. Provides elements of file that can be used to build phylogenetic objects such as ape's 'phylo' or phylobase's 'phylo4(d)'." . + +SCR:024291 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rnexml" ; + definition: "Software R package provides access to phyloinformatic data in 'NeXML' format." . + +SCR:024292 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "phylobase" ; + definition: "Software R package provides base S4 class for comparative methods, incorporating one or more trees and trait data. Used for phylogenetic analysis." . + +SCR:024293 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_12451" ; + rdfs:label "qqman" ; + definition: "Software R package to create Q-Q and manhattan plots for GWAS data from PLINK output files." . + +SCR:024294 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "hms" ; + definition: "Software R package implements S3 class for storing and formatting time-of-day values, based on the 'difftime' class." . + +SCR:024295 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "psychometric" ; + NIFRID:synonym "Applied Psychometric Theory" ; + definition: "Software R package for measurement theory, meta-analysis, reliability, item analysis, inter-rater reliability, classical utility, and correlation" . + +SCR:024296 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rniftilib" ; + definition: "Software R package provides R-interface to the NIfTI reference implementation the niftilib C-library." . + +SCR:024297 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rann" ; + definition: "Software R package finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3)." . + +SCR:024298 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rook" ; + definition: "Web server for R with documented API to interface between R and the server. The documentation contains the Rook specification and details for building and running Rook applications." . + +SCR:024299 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "robustrankaggreg" ; + NIFRID:synonym "Robust Rank Aggregation" ; + NIFRID:abbrev "RRA" ; + definition: "Software R package for aggregating ranked lists, especially lists of genes. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking." . + +SCR:024300 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rpact" ; + definition: "Software R package for design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints." . + +SCR:024301 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29370" ; + rdfs:label "shazam" ; + definition: "Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis." . + +SCR:024302 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rwave" ; + definition: "Software R package provides environment for Time-Frequency analysis of 1-D signals." . + +SCR:024303 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rsvd" ; + NIFRID:synonym "randomized singular value decomposition" ; + definition: "Software R package used to compute near optimal low-rank singular value decomposition of massive data sets with high accuracy. Provides several randomized matrix algorithms such as randomized singular value decomposition (rsvd), randomized principal component analysis (rpca), randomized robust principal component analysis (rrpca), randomized interpolative decomposition (rid), and the randomized CUR decomposition (rcur). In addition several plot functions are provided." . + +SCR:024304 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "surveillance" ; + definition: "Software R package for modeling and monitoring of time series of counts, proportions and categorical data, as well as for modeling of continuous-time point processes of epidemic phenomena." . + +SCR:024305 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "tsne" ; + definition: "Softare R package as implementation of the t-SNE algorithm." . + +SCR:024306 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_28401" ; + rdfs:label "rotl" ; + definition: "Software R package provides interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling comprehensive phylogenetic tree for all named species." . + +SCR:024307 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "sjplot" ; + definition: "Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data." . + +SCR:024308 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "waveslim" ; + definition: "Software R package for basic wavelet routines for time series 1D, image 2D and array 3D analysis." . + +SCR:024309 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "snowfall" ; + definition: "Software R package usability wrapper around snow for easier development of parallel R programs. This package offers e.g. extended error checks, and additional functions. All functions work in sequential mode if no cluster is present or wished. Package is also designed as connector to the cluster management tool sfCluster, but can also used without it." . + +SCR:024310 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_07533" ; + rdfs:label "tigger" ; + definition: "Software R package infers V genotype of individual from immunoglobulin repertoire sequencing data like AIRR-Seq, Rep-Seq. Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among sample sequences." . + +SCR:024311 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "wavethresh" ; + definition: "Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation." . + +SCR:024312 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_02222" ; + rdfs:label "webgestaltr" ; + NIFRID:synonym "WebGestaltR" ; + definition: "Software R package to support gene set enrichment analysis, network topology analysis.Can be integrated into other pipeline or simultaneously analyze multiple gene lists. The user-friendly output report allows interactive and efficient exploration of enrichment results." . + +SCR:024313 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "readseq" ; + definition: "Software package as Java based common sequence file format reader and sequence file manipulation." . + +SCR:024314 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "resfinder" ; + NIFRID:synonym "ResFinder" ; + definition: "Software tool identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. Used for identification of acquired antimicrobial resistance genes in whole-genome data." . + +SCR:024315 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "readucks" ; + definition: "Software package as Nanopore read de-multiplexer." . + +SCR:024316 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "roguenarok" ; + definition: "Software tool as versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index." . + +SCR:024317 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "recan" ; + definition: "Software tool as genetic distance plotting for recombination events analysis." . + +SCR:024318 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21698" ; + rdfs:label "roadtrips" ; + NIFRID:synonym "ROADTRIPS 2.0" ; + definition: "Software C program that performs single SNP, case control association testing in samples with partially or completely unknown population and pedigree structure." . + +SCR:024319 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "stringi" ; + definition: "Software R package as collection of character string/text/natural language processing tools for pattern searching, random string generation, case mapping, string transliteration, concatenation, sorting, padding, wrapping, Unicode normalisation, date time formatting and parsing." . + +SCR:024320 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_28979" ; + rdfs:label "rtax" ; + definition: "Software tool for rapid and accurate taxonomic classification of short paired-end sequence reads from the 16S ribosomal RNA gene." . + +SCR:024321 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "runcircos-gui" ; + definition: "GUI tool to run circos" . + +SCR:024322 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ruby-bio" ; + definition: "Software tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO." . + +SCR:024323 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_19578" ; + rdfs:label "rgfa" ; + definition: "Ruby library for handling GFA files." . + +SCR:024324 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_16243" ; + rdfs:label "saint" ; + NIFRID:synonym "Significance Analysis of INTeractome" ; + NIFRID:abbrev "SAINT" ; + definition: "Software package for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments." . + +SCR:024325 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "crb-blast" ; + NIFRID:synonym "Conditional Reciprocal Best Blast" ; + definition: "Software tool for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation." . + +SCR:024326 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_03939" ; + rdfs:label "sailfish" ; + definition: "Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads." . + +SCR:024327 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "sepp" ; + definition: "Ensemble of HMM methods.Repository includes code for SEPP, TIPP, UPP, HIPPI. Methods use ensembles of Hidden Markov Models in different ways, each focusing on different problem." . + +SCR:024328 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_07586" ; + rdfs:label "sambamba" ; + definition: "Software tools for working with SAM/BAM data" . + +SCR:024329 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_06013" ; + rdfs:label "sbmltoolbox" ; + definition: "Software toolbox provides set of basic functions allowing SBML models to be used in both MATLAB and Octave." . + +SCR:024330 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "samclip" ; + definition: "Software tool to filter SAM file for soft and hard clipped alignments" . + +SCR:024331 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11290" ; + rdfs:label "seqmagick" ; + definition: "Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO." . + +SCR:024332 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "seqwish" ; + definition: "Software tool for alignment to variation graph inducer." . + +SCR:024333 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21700" ; + rdfs:label "seqsero" ; + definition: "Software pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies." . + +SCR:024334 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "shiny-server" ; + definition: "Open Source platform to host multiple Shiny applications on single server." . + +SCR:024335 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "shapeit4" ; + NIFRID:synonym "SHAPEIT", + "SHAPEIT4" ; + definition: "Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features." . + +SCR:024336 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11719" ; + rdfs:label "sibelia" ; + definition: "Software comparative genomics tool to assist biologists in analysing genomic variations that correlate with pathogens, or genomic changes that help microorganisms adapt in different environments. Used for evolutionary and genome rearrangement studies for multiple strains of microorganisms." . + +SCR:024337 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_29594" ; + rdfs:label "sigma-align" ; + NIFRID:synonym "Simple greedy multiple alignment" ; + definition: "Software alignment program with new algorithm and scoring scheme designed specifically for non-coding DNA sequence. This problem is now growing in importance with the increasing number of fully-sequenced species. In particular, studies of gene regulation seek to take advantage of comparative genomics, and recent algorithms (such as PhyloGibbs) for finding regulatory sites in phylogenetically-related intergenic sequence require alignment as a preprocessing step." . + +SCR:024338 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21290" ; + rdfs:label "sibsim4" ; + definition: "Software tool designed to align expressed DNA sequence with genomic sequence, allowing for introns." . + +SCR:024339 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "signalalign" ; + definition: "Software tool to align ionic current from MinION to reference sequence using trainable hidden Markov model. HMM-HDP models for MinION signal alignments," . + +SCR:024340 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "sigviewer" ; + definition: "Software viewing application for biosignals such as EEG or MEG time series. In addition to viewing raw data, SigViewer can also create, edit, and display event information such as annotations or artifact selections." . + +SCR:024341 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "skesa" ; + NIFRID:synonym "SKESA" ; + definition: "Software de-novo sequence read assembler for microbial genomes.Designed to create breaks at repeat regions in the genome. This leads to excellent sequence quality without significantly compromising contiguity.SKESA contigs could be connected into GFA graph using GFA connector." . + +SCR:024342 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_12011" ; + rdfs:label "sistr" ; + NIFRID:synonym "Salmonella In Silico Typing Resource" ; + NIFRID:abbrev "SISTR" ; + definition: "SISTR command-line tool. Open web accessible tool for rapidly typing and subtyping draft salmonella genome assemblies." . + +SCR:024343 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "seq-seq-pan" ; + definition: "Software workflow for SEQuential alignment of SEQuences to build PAN-genome data structure and whole-genome-alignment." . + +SCR:024344 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "sitplus" ; + NIFRID:synonym "SITPLUS" ; + definition: "Software framework to provide ludic-therapeutic activities for people with disabilities.Offers new forms of interaction based on computer vision, voice and other peripherals to produce result in form of image and sound. Used for continuous and remote interaction, attainable to majority of people with cognitive, sensory and physical disabilities." . + +SCR:024345 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_05427" ; + rdfs:label "spaced" ; + definition: "Software for alignment free sequence comparison. Uses pattern of care and don't care positions. Compares frequencies of spaced words according to pre-defined pattern." . + +SCR:024346 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "sofa-apps" ; + NIFRID:synonym "SOFA" ; + definition: "Open source software framework targeting at real-time simulation, with emphasis on medical simulation." . + +SCR:024347 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21832" ; + rdfs:label "sourmash" ; + definition: "Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets." . + +SCR:024348 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_15114" ; + rdfs:label "snpomatic" ; + NIFRID:synonym "SNP-o-matic" ; + definition: "Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping," . + +SCR:024349 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "sparta" ; + NIFRID:synonym "SPARTA" ; + definition: "Software workflow aimed at analyzing single-end Illumina RNA-seq data. The software is supported on Windows, Mac OS X, and Linux platforms." . + +SCR:024350 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_03771" ; + rdfs:label "sra-toolkit" ; + NIFRID:synonym "NCBI SRA Toolkit" ; + definition: "Software collection of tools and libraries for using data in the INSDC Sequence Read Archives.Used for long term storage of the next-generation sequence traces." . + +SCR:024351 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "strap-base" ; + definition: "Software tool as Intuitive Editor for annotated multiple Sequence and Structure Alignments." . + +SCR:024352 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_19112" ; + rdfs:label "sumaclust" ; + definition: "Software tool aims to cluster sequences in a way that is fast and exact at the same time." . + +SCR:024353 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21293" ; + rdfs:label "sprai" ; + NIFRID:synonym "single pass read accuracy improver" ; + definition: "Software tool to correct sequencing errors in single pass reads for de novo assembly." . + +SCR:024354 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "streamlit" ; + definition: "Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps." . + +SCR:024355 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_09480" ; + rdfs:label "surankco" ; + definition: "Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet." . + +SCR:024356 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "libswiss-perl" ; + definition: "Software object oriented Perl library to handle Swiss-Prot entries" . + +SCR:024357 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_08598" ; + rdfs:label "sweed" ; + definition: "Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps." . + +SCR:024358 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14578" ; + rdfs:label "swarm" ; + definition: "Software tool as clustering method for amplicon-based studies." . + +SCR:024359 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "tab2mage" ; + NIFRID:synonym "Tab2MAGE" ; + definition: "Software package written and supported by ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets to our public repository database." . + +SCR:024360 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_21299" ; + rdfs:label "zAlign" ; + NIFRID:synonym "zalign" ; + definition: "Software tool as local sequence aligner intended for use with large biological DNA sequences, with more than 1 Millions of base pairs." . + +SCR:024361 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "tiddit" ; + NIFRID:synonym "TIDDIT" ; + definition: "Software tool as structural variant calling." . + +SCR:024362 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Yanagiba" ; + NIFRID:synonym "yanagiba" ; + definition: "Software tool to filter and slice Nanopore reads which have been basecalled with Albacore." . + +SCR:024363 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Yanosim" ; + NIFRID:synonym "yanosim", + "yet another nanopore simulator" ; + definition: "Software tool as read simulator for nanopore DRS datasets." . + +SCR:024364 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Workrave" ; + NIFRID:synonym "workrave" ; + definition: "Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage." . + +SCR:024365 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_04675" ; + rdfs:label "yaha" ; + NIFRID:synonym "YAHA" ; + definition: "Software tool as fast and flexible long read alignment with optimal breakpoint detection." . + +SCR:024366 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "XMedCon" ; + NIFRID:synonym "xmedcon" ; + definition: "Open source software toolkit for medical image conversion." . + +SCR:024367 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VolPack" ; + NIFRID:synonym "volpack" ; + definition: "Portable software library for volume rendering." . + +SCR:024368 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VMD" ; + NIFRID:synonym "vmd" ; + definition: "Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code." . + +SCR:024369 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "variation graph" ; + NIFRID:synonym "variationgraph" ; + NIFRID:abbrev "vg" ; + definition: "Software toolkit to improve read mapping by representing genetic variation in reference.Provides succinct encoding of sequences of many genomes." . + +SCR:024370 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VisIt" ; + NIFRID:synonym "visit" ; + definition: "Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations." . + +SCR:024371 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_17862" ; + rdfs:label "VirulenceFinder" ; + NIFRID:synonym "virulencefinder" ; + definition: "Software tool for detection of E. coli virulence genes. Used to identify viruelnce genes in total or partial sequenced isolates of bacteria. E. coli, Enterococcus, S. aureus and Listeria are available.for detection of E. coli virulence genes." . + +SCR:024372 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11863" ; + rdfs:label "vcfanno" ; + definition: "Software tool for flexible annotation of genetic variants.Extracts and summarizes attributes from multiple annotation files and integrates annotations within INFO column of the original VCF file." . + +SCR:024373 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_04455" ; + rdfs:label "VARNA" ; + NIFRID:synonym "varna", + "Visualization Applet for RNA" ; + definition: "Software tool for automated drawing, visualization and annotation of secondary structure of RNA, designed as companion software for web servers and databases.Allows manual modification and structural annotation of resulting drawing using either interactive point and click approach, within web server or through command-line arguments." . + +SCR:024374 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "tacg" ; + definition: "Software tool as command line program that performs many of the common routines in pattern matching in biological strings. It was originally designed for restriction enzyme analysis and while that still forms core of the program, it has been expanded to fill more roles, sort of 'grep' for DNA." . + +SCR:024375 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14435" ; + rdfs:label "VarMatch" ; + NIFRID:synonym "varmatch" ; + definition: "Software tool for variant matching problem.Used for robust matching of small variant datasets using flexible scoring schemes" . + +SCR:024376 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14601" ; + rdfs:label "VelvetOptimiser" ; + NIFRID:synonym "perl-velvetoptimiser", + "velvetoptimiser" ; + definition: "Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile." . + +SCR:024377 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VADR" ; + NIFRID:synonym "ushahidi" ; + definition: "Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families." . + +SCR:024378 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_11724" ; + rdfs:label "FISH" ; + definition: "Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps." . + +SCR:024379 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_26281" ; + rdfs:label "CCS" ; + NIFRID:synonym "ccs ; unanimity" ; + definition: "Software to generate highly accurate single molecule consensus reads." . + +SCR:024380 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_14591" ; + rdfs:label "Unicycler" ; + NIFRID:synonym "unicycler" ; + definition: "Software assembly pipeline for bacterial genomes. Used for resolving bacterial genome assemblies from short and long sequencing reads. Can assemble Illumina only read sets where it functions as SPAdes-optimiser. Can assembly long read only sets for PacBio or Nanopore where it runs miniasm+Racon pipeline." . + +SCR:024381 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_12783" ; + rdfs:label "umis" ; + definition: "Software tools for estimating expression in RNA-Seq data which performs sequencing of end tags of transcript, and incorporate molecular tags to correct for amplification bias." . + +SCR:024382 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_18458" ; + rdfs:label "TREE-PUZZLE" ; + NIFRID:synonym "tree-puzzle" ; + definition: "Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set." . + +SCR:024383 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "TopHat-Recondition" ; + definition: "Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat." . + +SCR:024384 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Trinculo" ; + NIFRID:synonym "trinculo" ; + definition: "Software toolkit for carrying out genetic association for multi-catagory phenotypes. Implements multinomial and ordinal association incorporating covariates, conditional analysis, empirical and non-emperical priors and fine-mapping." . + +SCR:024385 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_07268" ; + rdfs:label "toppred" ; + definition: "Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins." . + +SCR:024386 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_33039" ; + rdfs:label "trace2dbEST" ; + definition: "Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST." . + +SCR:024387 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Tn-seq explorer" ; + NIFRID:synonym "Tn-seq Explorer", + "tn-seqexplorer" ; + definition: "Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions." . + +SCR:024388 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Tombo" ; + NIFRID:synonym "ont-tombo" ; + definition: "Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal." . + +SCR:024389 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_10215" ; + rdfs:label "TRANSIT" ; + NIFRID:synonym "tnseq-transit" ; + definition: "Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions." . + +SCR:024390 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_03646" ; + rdfs:label "TM-align" ; + definition: "Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons." . + +SCR:024391 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "OMICS_25666" ; + rdfs:label "toil" ; + definition: "Software pipeline management system, written in Python. Enables reproducible, open source, big biomedical data analyses." . + +SCR:024392 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FTA32" ; + NIFRID:synonym "First Ten Angstrom FTA32", + "FTA32 2.0" ; + definition: "Software tool for tensiometry measurements and contact angle hysteresis." . + +SCR:024393 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Galileo Tissue Microarray CK Series" ; + NIFRID:synonym "Galileo computer assisted tissue microarray", + "Galileo Fully Automated Tissue Microarray", + "Galileo Tissue Microarray", + "Galileo TMA CK", + "Galileo TMA CK Series" ; + definition: "Galileo computer assisted Tissue Microarray instrument allows TMA preparation with different paraffin block sizes, producing digital excel format reporting and possibility of data transfer to several Digital TMA Slide Scanners for complete tracking of Tissue Microarray process." . + +SCR:024394 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Gate" ; + NIFRID:synonym "GATE", + "GATE V6", + "Geant4 Application for Tomographic Emission" ; + definition: "Software toolkit for PET and SPECT. Simulation platform for medical imaging and radiotherapy. Used for modelling of planar scintigraphy, single photon emission computed tomography (SPECT) and positron emission tomography (PET) acquisitions, this platform is widely used to assist PET and SPECT research. Extension of this platform, released by OpenGATE collaboration as GATE V6, enables modelling of x-ray computed tomography and radiation therapy experiments." . + +SCR:024395 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "scNTImpute" ; + NIFRID:synonym "single-cell Neural Topic Imputation" ; + definition: "Software imputation model for scRNA-seq data. Used to accurately and efficiently identify dropout values and impute them precisely, which helps to improve downstream analyses of single-cell RNA sequencing data." . + +SCR:024396 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BrainWAVE" ; + NIFRID:synonym "Brain Wide-spectrum Audio/Visual Exposure", + "BrainWAVE: Noninvasive Rhythm Stimulation" ; + definition: "Code to program and run flicker stimulation on BrainWAVE stimulator device. This brain oscillation stimulating software can be adapted across subjects and integrated into variety of experimental designs like electrophysiology, neuroimaging, EEG, MRI. Flexible method for noninvasive stimulation of brain rhythms across species. Used to measure effects of rhythmic brain activity on behavior." . + +SCR:024397 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ChrAccR" ; + NIFRID:synonym "Chromatin Accessibility data in R" ; + definition: "Software R package for comprehensive analysis chromatin accessibility data. Analyzing chromatin accessibility data in R. Used for data quality control, exploratory analyses including unsupervised methods for dimension reduction, clustering and quantifying transcription factor activities, and identification and characterization of differentially accessible regions. Used for analysis of large bulk datasets comprising hundreds of samples as well as for single cell datasets." . + +SCR:024398 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Indiana University Bloomington Flow Cytometry Core Facility" ; + NIFRID:synonym "IUB Flow Cytometry Core Facility" ; + NIFRID:abbrev "FCCF" ; + definition: "Core offers flow cytometry analysis and cell sorting services. It houses FACS Aria II 5-laser, 14-color sorter, SH800 2-laser, 6-color user-run cell sorter, COPAS Select, Drosophila embryo and large particle sorter, LSRII, 4-laser, 14-color analyzer, MACSQuant VYB 3-laser, 8-color analyzer with 96-well plate option, as well as Moxi Z cell counter technology used for determining cell concentration and size distribution and Miltenyi QuadroMACS separator. Services include technician assisted sorting, as well as training for analyzers, SH800 and Moxi instruments. Help with experimental design is available.Facility maintains workstation with flow cytometry data analysis software, and has copy of this software as well as site license for use outside of facility." . + +SCR:024399 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Efficient and Adaptive Gaussian Smoothing" ; + NIFRID:abbrev "EAGS" ; + definition: "Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell." . + +SCR:024400 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_1826" ; + rdfs:label "National Autonomous University of Mexico Materials Research Institute Electron Microscopy University Laboratory Core Facility" ; + NIFRID:synonym "National Autonomous University of Mexico Materials Research Institute Electron Microscopy University Laboratory", + "Universidad Nacional Autonoma de Mexico LUME" ; + NIFRID:abbrev "LUME" ; + definition: "Core covers main techniques of electron microscopy, from scanning electron microscopy to scanning transmission electron microscopy, for characterization of morphology and structure of materials at micrometer and nanometer scale.Provides equipment for preparing samples for analysis by different electron microscopy techniques." . + +SCR:024401 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Learning Locker" ; + NIFRID:synonym "Learning Record Store" ; + NIFRID:abbrev "LRS" ; + definition: "Open source software Learning Record Store implementing the xAPI (Tin Can API) e-learning standard.Type of data repository designed to store learning activity statements generated by xAPI (Tin Can) compliant learning activities." . + +SCR:024402 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Brainways" ; + definition: """Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat +atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices.""" . + +SCR:024403 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FindTelomeres" ; + definition: "Software Python tool for finding telomeric repeats (TTAGGG/CCCTAA) in FASTA files." . + +SCR:024404 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2446" ; + rdfs:label "University of British Columbia Advanced Research Computing Core Facility" ; + NIFRID:synonym "UBC Advanced Research Computing", + "University of British Columbia Advanced Research Computing" ; + definition: "Core supports high performance computing and data management needs of UBC researchers by providing consultation, expertise, and access to digital research infrastructure such as high performance computing clusters and storage." . + +SCR:024405 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_1827" ; + rdfs:label "Jackson Laboratory JAX Scientific Research Services Microscopy Services Core Facility" ; + NIFRID:synonym "JAX Microscopy Services", + "The Jackson Laboratory JAX Microscopy Services" ; + definition: "Jackson Laboratory Microscopy Services, located in Bar Harbor, Maine and Farmington, Connecticut, provides essential support to their faculty labs. Service includes standard widefield microscopy; advanced fluorescent microscopy, including confocal and spinning disk; 2-photon and fluorescence lifetime microscopy ; longitudinal observation or live cell imaging, including imaging of iPS and ES cells under various environmental conditions; laser capture microdissection, image analysis and 3D visualization; high throughput cell based screening; brightfield slide scanning; automated fluorescence slide scanning." . + +SCR:024406 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RiboToolkit" ; + definition: "Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs." . + +SCR:024407 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Acute Kidney Injury Data Portal" ; + definition: "UK Renal Registry collection of data from acute kidney injury patients in England." . + +SCR:024408 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ramr" ; + NIFRID:synonym "rare aberrantly methylated regions" ; + definition: "Software R package for detection of low frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. Provides functions to visualize found aberrantly methylated regions, to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms." . + +SCR:024409 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "BioImaging North America" ; + NIFRID:abbrev "BINA" ; + definition: "US-based non-profit engaging bioimaging scientists across Canada, Mexico, the US and its territories by creating inclusive and supportive community to support bioimaging scientists through on-line events, registration assistance for professional development opportunities and the chance to visit peer imaging facilities to learn new techniques, develop or expand management skills, and/or image data management and analysis skills., through Exchange of Experience program." . + +SCR:024410 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Healthcare Cost and Utilization Project" ; + NIFRID:abbrev "HCUP" ; + definition: "Family of healthcare databases and related software tools and products developed through Federal-State-Industry partnership. Databases bring together data collection of State data organizations, hospital associations, private data organizations, and Federal government to create national information resource of encounter-level healthcare data. HCUP includes largest collection of longitudinal hospital care data in the United States, with all-payer, encounter-level information beginning in 1988. These databases enable research on broad range of health policy issues, including cost and quality of health services, medical practice patterns, access to healthcare programs, and outcomes of treatments at the national, State, and local market levels." . + +SCR:024411 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SoftCite" ; + NIFRID:synonym "Software Citation" ; + definition: "Gold standard dataset of software mentions in research publications. Provides dataset of annotated software mentions from full text academic literature in biomedicine and economics directly converted from published PDFs with reproducible infrastructure. Includes provenance, and is formatted for immediately usefulness in NLP. Useful for supervised learning at scale." . + +SCR:024412 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ctregistries" ; + NIFRID:synonym "Clinical Trial Registries", + "clinical trial registries" ; + definition: "Software R package to facilitate detection and analysis of clinical trial registration numbers. Data package of regular expressions and provides some R functions for implementing the regexes. Data Package and R Functions for Clinical Trial Registries and other MEDLINE Databanks." . + +SCR:024413 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MRIcroGL" ; + definition: "Medical image viewer that allows to load overlays and draw regions of interest. Runs on Windows, Linux and OSX. Allows to view 2D slices and renderings of your brain imaging data. It can display many image formats and includes graphical interface for dcm2nii to convert DICOM images to NIfTI format. Allows to draw regions of interest which can aid lesion mapping and fMRI analysis." . + +SCR:024414 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ProteinPilot" ; + definition: "Software tool for protein identification and protein expression analysis. Used to identify proteins and search large numbers of post translational modifications, without increasing search time or false positives. Compatible with all proteomics MS/MS systems." . + +SCR:024415 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "survivalROC" ; + NIFRID:synonym "survival Receiver Operating Characteristic" ; + definition: "Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data." . + +SCR:024416 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GIFT" ; + NIFRID:synonym "GIFT:Group ICA Of fMRI Toolbox" ; + definition: "Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group and single subject functional magnetic resonance imaging data." . + +SCR:024417 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pRRophetic" ; + definition: "Software R package for prediction of clinical chemotherapeutic response from tumor gene expression levels. Used to predict phenotypes from gene expression microarray data, gene expression microarray data," . + +SCR:024418 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RNALocate" ; + NIFRID:synonym "RNALOCATE", + "RNALocate v2.0" ; + definition: "Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation." . + +SCR:024419 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GOplot" ; + NIFRID:synonym "R GOplot" ; + definition: "Software R package for visually combining expression data with functional analysis." . + +SCR:024420 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ROCit" ; + NIFRID:synonym "Receiver Operating Characteristic it" ; + definition: "Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot." . + +SCR:024421 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PyWavelets" ; + definition: "Software Python package for wavelet analysis." . + +SCR:024422 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rgdal" ; + NIFRID:synonym "R geospatial data abstraction library", + "rgdal" ; + definition: "Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats." . + +SCR:024423 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pyPCcazip" ; + definition: "Software PCA-based toolkit for compression and analysis of molecular simulation data. Used for compression and analysis of molecular dynamics (MD) simulation data." . + +SCR:024424 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "riskRegression" ; + definition: "Software R package provides risk regression models and prediction scores for survival analysis with competing risks." . + +SCR:024425 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ScanProsite" ; + NIFRID:abbrev "PMID:16845026" ; + definition: "Web tool for detecting PROSITE signature matches in protein sequences." . + +SCR:024426 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RapGreen" ; + NIFRID:abbrev "PMID:34568824" ; + definition: "Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package." . + +SCR:024427 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RNAfold" ; + definition: "Web server predict secondary structures of single stranded RNA or DNA sequences." . + +SCR:024428 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "LFP Monitoring" ; + NIFRID:synonym "Local Field Potential video Monitoring" ; + definition: "Low cost platform for multianimal chronic Local Field Potential video monitoring with Graphical User Interface for seizure detection and behavioral scoring. Enables chronic monitoring of several animals simultaneously, synchronizes bilateral local field potential and video streams in real time, and parses recorded data into manageable file sizes. Hardware solution leverages Intan and Open Ephys acquisition systems and software solution is implemented in Bonsai. Data are synchronized and parsed in Bonsai, allowing for flexibility and scalability of up to 128 channels per animal. The use of Intan adapter board for LFP video recordings allows compatibility with large variety of recording devices. Custom made electrodes and cables were components for the chronic LFP recordings. Used as acquisition system for long term video neurophysiology recordings." . + +SCR:024429 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NutritionQuest Questionnaires and Screeners" ; + definition: "NutritionQuest provides questionnaires and screeners for assessment of diet and physical activity. Questionnaires are derived from and based on Dr. Block's landmark research into the development of valid, user-friendly assessment methods. Questionnaires and dietary analysis services are available to nutritional epidemiologists and public health researchers." . + +SCR:024430 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Ecocyte Bioscience Xenopus laevis oocytes delivery service" ; + NIFRID:synonym "Ecocyte Bioscience Xenopus laevis defolliculated oocytes", + "Xenopus laevis defolliculated oocytes", + "Xenopus laevis oocytes delivery service" ; + definition: "Ecocyte Bioscience offers weekly delivery service of Xenopus laevis oocytes for expression studies. Products include defolliculated and ready to use Xenopus Laevis oocytes used for mRNA or cDNA injections or other electrophysiological experiments." . + +SCR:024431 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rockd" ; + definition: "Map database allows to record your geological observations and uses your location to provide spatially informed suggestions for nearby geologic units, time intervals, and fossils." . + +SCR:024432 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Sparrow-data" ; + definition: "Software for managing geochemical data created by individual geochronology laboratory. Designed for flexibility and extensibility, so that it can be tailored to the needs of individual analytical labs that manage wide variety of data. Database set up for metadata tracking." . + +SCR:024433 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Olympus FV10-ASW Viewer" ; + NIFRID:synonym "FV10-ASW Viewer software v4.2b" ; + definition: "Software for image processing. Reads data captured by FV1200/FV1000/FV500/FV300 microscopes. Images saved with FV file format (OIF, OIB, FV Multi-Tiff) can be read." . + +SCR:024434 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "XDD" ; + definition: "Software digital library and cyberinfrastructure facilitating discovery and utilization of data and knowledge in published documents." . + +SCR:024435 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Cerner Enviza" ; + definition: "American healthcare company that provides data, analytics, and research to the life sciences industry, with particular focus on oncology and rare diseases." . + +SCR:024437 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "National Cancer Institute Cancer Statistics Cancer Stat Facts" ; + definition: "Collection of statistical summaries for number of common cancer types. They were developed to provide quick overview of frequently requested cancer statistics. Available statistics may include incidence, mortality, survival, stage, prevalence, and lifetime risk. Links to additional resources from NCI including risk factors, treatment, and clinical trials are also provided. The statistics will be updated annually to coincide with the SEER data release." . + +SCR:024438 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "StereoCell v2.0" ; + NIFRID:synonym "StereoCell" ; + definition: "Enhanced application on generating single cell gene expression profile for high resolution spatial transcriptomics. Registers spatial gene expression map and cell membrane/wall staining image with nuclei staining image as intermediary, thus cell membrane/wall outlines can be directly segmented from cell membrane/wall staining image without correcting nuclei boundaries." . + +SCR:024439 a NLX:63400, + owl:NamedIndividual ; + NIFRID:abbrev "MLme" ; + definition: "Software toolkit for Machine Learning Driven Data Analysis. Simplifies machine learning for data exploration, visualization and analysis." . + +SCR:024440 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Allen Brain Cell Atlas" ; + NIFRID:synonym "ABC Atlas", + "Allen Brain Cell (ABC) Atlas", + "The Allen Brain Cell Atlas" ; + definition: "Provides platform for visualizing multimodal single cell data across mammalian brain and aims to empower researchers to explore and analyze multiple whole brain datasets simultaneously. Allen Institute and its collaborators continue to add new modalities, species, and insights to the ABC Atlas. Atlas as part of Brain Knowledge Platform will enable neuroscience community to identify more cell types in brain; Investigate spatial location of cell types; Investigate gene expression and co-expression patterns in cell types; Refine boundaries and knowledge of brain regions defined by gene expression." . + +SCR:024441 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SCKAN Composer" ; + NIFRID:synonym "SPARC Connectivity Knowledge Base of the Autonomic Nervous system Composer" ; + definition: "Web application authoring interface that permits users to display, inspect, survey, and formulate knowledge statements to be added to SCKAN, as well as the ability to query and augment knowledge information within SCKAN, the SPARC Connectivity Knowledge Base of the Autonomic Nervous system." . + +SCR:024443 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Metabox" ; + NIFRID:synonym "metabox", + "metabox2", + "Metabox 2.0" ; + definition: "Software R toolbox for thorough metabolomic data analysis, integration and interpretation. Metabox 2.0 is updated version of R package Metabox and includes several methods for data processing, statistical analysis, biomarker analysis, integrative analysis and data interpretation." . + +SCR:024444 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "INFRAFRONTIER" ; + NIFRID:synonym "European Research Infrastructure for Modelling Human Diseases" ; + definition: "Non-profit organisation dedicated to advancing disease, understanding and treatment through cutting-edge models. Provides mouse model resources for modelling human diseases. Provides research infrastructure for generation, phenotyping, archiving, and distribution of mouse models in Europe. Through collaboration with other infrastructures, it fosters global data sharing and contributes to tackling significant health challenges." . + +SCR:024445 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Cancer Information Service" ; + NIFRID:synonym "Cancer Information Service in Japan" ; + definition: "Portal provides information on Cancer Statistics in Japan. Official website operated by National Cancer Center for cancer information." . + +SCR:024446 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Thermo Scientific Maps Software" ; + NIFRID:synonym "Maps Software" ; + definition: "Correlative electron microscopy and cross-platform imaging automation software. Imaging and correlative workflow software suite compatible with full line of Thermo Scientific SEM, DualBeam (FIB SEM) and TEM platforms." . + +SCR:024447 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "OsteoMetrics OsteoMeasure" ; + NIFRID:synonym "OsteoMeasure", + "OsteoMetrics Osteomeasure" ; + definition: "Software for semi-automatic bone histomorphometry. Used for manual tracing of bone surfaces." . + +SCR:024448 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ZEISS Lightsheet 7" ; + NIFRID:synonym "ZEISS Lightsheet 7 imaging system" ; + definition: "System for imaging of living and cleared specimens. Used to image large optically cleared specimens in toto with subcellular resolution. Dedicated optics, sample chambers and holders allow adaption to the refractive index of your chosen clearing method." . + +SCR:024449 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Resolve Biosciences Molecular Cartography" ; + NIFRID:synonym "Molecular Cartography", + "Resolve Biosciences Molecular Cartography platform" ; + definition: "Platform is multi-analyte, multiplex spatial analysis technology that enables scientists to resolve complex biological challenges in areas such as oncology, neuroscience, and infectious disease. Platform produces contextual data sets that illuminate molecular interactions at subcellular resolution, while preserving the sample tissue." . + +SCR:024450 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "vhlab-microscopyimageanalysis-matlab" ; + definition: "Software Matlab app for analysis of high density imaging data like that from Array Tomography." . + +SCR:024451 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MOBFinder" ; + NIFRID:synonym "Mobilization Finder" ; + definition: "Software tool for MOB typing for plasmid metagenomic fragments based on language model." . + +SCR:024453 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PyMouseTracks" ; + NIFRID:abbrev "PMT" ; + definition: "Open source, adaptable tracking system for multiple rodents. Scalable and customizable system for tracking and behavior assessment consists of Raspberry Pi based video and RFID acquisition. Maximum of six rodents of any coat color can be tracked simultaneously in any user defined arena with few restrictions. For pose estimation and travel trajectory analysis, PyMouseTracks supports interfacing with open source packages such as DeepLabCut and Traja." . + +SCR:024456 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2448" ; + rdfs:label "Pennsylvania State University Huck Institutes Cryo-Electron Microscopy Core Facility" ; + NIFRID:synonym "Huck Institutes' Cryo-Electron Microscopy Facility" ; + definition: "Cryo-Electron Microscopy Facility houses FEI Titan Krios microscope that offers data collection for life sciences while incorporating materials science applications. Used for creating super high definition 3D images of atoms and molecules. Facility allows for fully automated atomic resolution single particle and high contrast tomography tilt-series data collection. Additional microscopy components permit a full range of materials science applications, including EELS, STEM, and DPC. Facility also houses ThermoFisher Arctica G2." . + +SCR:024457 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2449" ; + rdfs:label "Pennsylvania State University Huck Institutes Microscopy Core Facility" ; + NIFRID:synonym "Huck Institutes' Microscopy Facility" ; + definition: "Microscopy facility specializes in areas of optical microscopy, electron microscopy, and histology. Facility is equipped with confocal microscopes, research fluorescence microscopes, and transmission and scanning electron microscopes. Research staff engage in experimentation, training, project collaboration, and consultation." . + +SCR:024458 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2450" ; + rdfs:label "Pennsylvania State University Huck Institutes Automated Biological Calorimetry Core Facility" ; + NIFRID:synonym "Huck Institutes' Automated Biological Calorimetry Facility" ; + definition: "Automated Biological Calorimetry Facility provides infrastructure and support for individual investigators to undertake studies of macromolecule binding and folding, as well as protein and lipid quantification. Our calorimetry instruments are fully automated and require the least amount of sample of any commercially available instruments.Provides instrumentation and collaborative assistance for Isothermal titration calorimetry for studying ligand-macromolecule binding; Differential scanning calorimetry for investigating stability and folding thermodynamics. Staff is available to assist with project development and research." . + +SCR:024459 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2451" ; + rdfs:label "Pennsylvania State University Huck Institutes CSL Behring Fermentation Core Facility" ; + NIFRID:synonym "Huck Institutes CSL Behring Fermentation Facility" ; + definition: "Biotechnology pilot plant capable of research and pilot scale production of microbial cells, recombinant proteins, and other microbial products over wide range of controlled conditions. Facility provides equipment and expertise to university affiliated and independent government and industry researchers interested in fermentation and related technologies, including cell separation and disruption, biomolecule production and purification, and process monitoring." . + +SCR:024460 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2452" ; + rdfs:label "Pennsylvania State University Huck Institutes Flow Cytometry Core Facility" ; + NIFRID:synonym "Huck Institutes' Flow Cytometry Facility" ; + definition: "Facility is equipped with flow cytometers and cell sorters to examine cell samples within range of micron. Staff engage in experimentation, training, project collaboration, and consultation." . + +SCR:024461 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2453" ; + rdfs:label "Pennsylvania State University Huck Institutes High Field Magnetic Resonance Imaging Core Facility" ; + NIFRID:synonym "Huck Institutes' High-Field Magnetic Resonance Imaging Facility" ; + definition: "Facility for investigating samples at micrometer scale using in vivo imaging and magnetic resonance microscopy. Facility houses Bruker BioSpec 70/30 horizontal magnet and Agilent 14.1 Tesla vertical magnet." . + +SCR:024462 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2454" ; + rdfs:label "Pennsylvania State University Huck Institutes Proteomics and Mass Spectrometry Core Facility" ; + NIFRID:synonym "Huck Institutes' Proteomics and Mass Spectrometry Core Facility" ; + definition: "Facility offers highly sensitive and accurate mass spectrometry analysis, including identification and quantitation of proteins by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS) or by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-TOF-MS)." . + +SCR:024463 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2455" ; + rdfs:label "Pennsylvania State University Huck Institutes Sartorius Cell Culture Core Facility" ; + NIFRID:synonym "Huck Institutes Sartorius Cell Culture Facility" ; + definition: "Sartorius Cell Culture Facility delivers hands-on training in cell culture to students, faculty, staff, and external personnel, while providing researchers across numerous Penn State disciplines access to the lab environment." . + +SCR:024464 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2456" ; + rdfs:label "Pennsylvania State University Huck Institutes X-Ray Crystallography Core Facility" ; + NIFRID:synonym "Huck Institutes' X-Ray Crystallography Facility" ; + definition: """Facility provides infrastructure and support for investigators to undertake single crystal X-ray structural studies. Provides instrumentation, training, and collaboration for Protein characterization, including dynamic light scattering, differential scanning calorimetry, bio-layer interferometry, and circular dichroism; Binding studies using isothermal titration calorimetry; Robotic crystallization, incubators, UV, and digital microscopes;Robotic imaging; +Diffraction data collection and processing; Structure determination and analysis; Molecular modeling; Small angle X-ray scattering. Staff is available to train researchers to use equipment and to assist with project development and research.""" . + +SCR:024465 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CURTAIN" ; + definition: """Web tool for exploration and sharing of mass spectrometry based proteomics data. +Used for analysis and sharing of proteomics data, data visualization, export of plots in SVG format, assessment of experimental quality by correlation matrix and profile plot. User can analyze domain structure, AlphaFold predicted structure, reported interactors, relative expression, disease and pharmaceutical links, and mutagenesis information on all selected hits.""" . + +SCR:024466 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SIMA" ; + definition: "Software Python package for analysis of dynamic fluorescence microscopy data." . + +SCR:024467 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Ocular" ; + NIFRID:synonym "Teledyne Photometrics Ocular" ; + definition: "Photometrics acquisition software to capture, save and publish images and movies. Allows users of color and monochrome cameras to capture high quality images and videos from their microscope or lens system." . + +SCR:024468 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Pattern Health Digital Research Platform" ; + definition: "Platform for researchers to economically create and manage digital health programs. Platform built for research management and digital interventions. Helps researchers collect data and engage participants." . + +SCR:024469 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FAIRassist.org" ; + NIFRID:synonym "FAIR Assist", + "FAIRassist" ; + definition: "Portal that aggregates tools that assist users ascertain FAIR-ness. Offers guidance to discover standards and repositories in FAIRsharing, which should be used to make data FAIR, as well as signpost other resources that enable FAIRness." . + +SCR:024470 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2457" ; + rdfs:label "Karolinska Institute Biomedicum Flow Cytometry Core Facility" ; + NIFRID:synonym "Biomedicum Flow Cytometry (BFC) Core Facility", + "Biomedicum Flow Cytometry Core Facility Karolinska Institutet" ; + NIFRID:abbrev "BFC" ; + definition: "Facility is shared resource laboratory providing comprehensive suite of services to support research needs in flow cytometry. Offers conventional and full spectral cytometry for multi-parametric analysis, as well as multiparameter fluorescence activated cell sorting." . + +SCR:024471 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Science-Metrix" ; + definition: "Independent research evaluation firm, based in the U.S. and Canada. Provider of research analytics services and data. Provides science research evaluation and analytics to assess science and technology activities. Headquartered in Montréal, Canada, Science-Metrix is known for independent bibliometric analysis and research evaluation and bibliometric and informetrics expertise. Science-Metrix was an early adopter of Elsevier’s abstract database Scopus and has worked closely with Elsevier. Elsevier has acquired Science-Metrix Inc. in 2018." . + +SCR:024472 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pyEulerCurves" ; + definition: "Software Python package to compute Euler Characteristic Curves of point cloud or image data." . + +SCR:024473 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_AIA-900" ; + rdfs:label "TOSOH AIA-900 Automated Immunoassay Analyzer" ; + definition: """AIA immunoassay analyzer offers automation for immunoassay testing with flexible expansion capabilities. AIA-900 features: 90 tests/hour throughput; Load 10 racks on board; +Load up to 5 tests/patient; First result in 18 minutes; Random access; Continuous processing; Simple touch screen operation; Bar coded primary tube sampling; Clot detection; Unit Dose Test Cup; Automated pretreatment; Automated dilution from 2 to 1000.""" . + +SCR:024474 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CARGO" ; + NIFRID:synonym "Cellular Autophagy Regulation and GOlgiphagy" ; + definition: "Web browser for analysis of proteomic data. ShinyApp interface generated in R and RStudio." . + +SCR:024475 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "CNS Vital Signs" ; + NIFRID:synonym "CNS Vital Signs LLC" ; + definition: "Designs and develops neurocognitive and behavioral assessment tools and technologies. Provides clinicians and researchers with leading-edge technologies for improved neurocognitive and behavioral evaluation and management capabilities. Provides CNS Vital Signs which is reimbursable assessment procedure that utilizes scientifically validated, objective, and reliable computerized neuropsychological tests to evaluate neurocognitive status of patients and covers a range of mental processes from simple motor performance, attention, memory, to executive functions. CNS Vital Signs is available as both web/cloud platform and local platform." . + +SCR:024478 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Planet Microbe" ; + definition: "Web based platform that enables data discovery from curated historical and on going oceanographic sequencing efforts. Enables discovery and integration of oceanographic ‘omics, environmental and physiochemical data layers. Used to centralize and standardize contextual data associated with major marine 'omic datasets. Used for marine microbiology to discover and analyze interconnected 'omics and environmental data." . + +SCR:024479 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2458" ; + rdfs:label "University of Arizona Molecular Clinical Core Facility" ; + NIFRID:synonym "Arizona Molecular Clinical Core", + "UA-Arizona Molecular Clinical Core", + "University of Arizona UA-Arizona Molecular Clinical Core" ; + NIFRID:abbrev "AZClinCore" ; + definition: "Core is CLIA certified/CAP accredited laboratory specializing in high complexity genetic and serological clinical testing and research. Provides inpatient and outpatient diagnostic testing services as well as support for clinical trial and clinical research activities for physicians, researchers and industry clients. The AZClinCore has aided in development of novel genetic testing and clinical trial protocols as well as providing evaluations for new technology and testing platforms. Supports end-to-end clinical testing as well as reference lab services." . + +SCR:024480 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Lightning Pose" ; + definition: "Software video centric package for direct video manipulation. Semi supervised animal pose estimation algorithm, Bayesian post processing approach and deep learning package. Improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools." . + +SCR:024481 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DNA Amplicon" ; + NIFRID:synonym "Illumina DNA Amplicon" ; + definition: "Local Run Manager DNA Amplicon analysis module aligns amplicon reads against reference specified in the manifest file. Variants are called for the targeted regions." . + +SCR:024482 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2459" ; + rdfs:label "Florida State University Innovation Hub Core Facility" ; + NIFRID:synonym "Florida State University Innovation Hub", + "FSU-Innovation Hub" ; + definition: "Hosts makerspaces, labs, and promotes design based frameworks toward iteration and innovation. Acts as open intersection of university departmental collaboration and provides access to low barrier prototyping tools. Supports FSU student, staff, and faculty research initiatives." . + +SCR:024483 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NGmerge" ; + definition: "Software tool for merging paired-end reads via novel empirically derived models of sequencing errors. Used for merging paired-end reads and removing adapters. Corrects errors and ambiguous bases and assigns quality scores for merged bases that accurately reflect the error rates." . + +SCR:024484 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NOTUNG" ; + NIFRID:synonym "Notung 2.9" ; + definition: "Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses." . + +SCR:024485 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "OMNISEC" ; + definition: "Software for OMNISEC instrument control, data acquisition, analysis and reporting. Used for advanced analysis of proteins and polymers by GPC/SEC, and is specifically designed for control of OMNISEC RESOLVE and OMNISEC REVEAL." . + +SCR:024486 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Optimization Toolbox" ; + definition: "Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations." . + +SCR:024487 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PHYLDOG" ; + definition: "Software tool to simultaneously build gene and species trees when gene families have undergone duplications and losses. Can analyze thousands of gene families in dozens of genomes simultaneously." . + +SCR:024488 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "OpenBUGS" ; + NIFRID:synonym "Open Bayesian inference Using Gibbs Sampling" ; + definition: "Software for analysing complex statistical models using Markov chain Monte Carlo methods." . + +SCR:024489 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ProgRes Capture Pro" ; + NIFRID:synonym "Jenoptic ProgRes Capture Pro" ; + definition: "Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras." . + +SCR:024490 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Ocular" ; + NIFRID:synonym "Teledyne Photometrics Ocular" ; + definition: "Scientific image acquisition software. Software allows color and monochrome cameras to capture high quality images and videos from their microscope or lens system." . + +SCR:024491 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Agilent Seahorse Wave" ; + NIFRID:synonym "Seahorse Wave" ; + definition: "Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis." . + +SCR:024492 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Umediation" ; + definition: "Software R package that examines the role of unmeasured confounding in mediation analysis allowing for normally distributed or Bernoulli distributed exposures, outcomes, mediators, measured confounders, and unmeasured confounders. Umediation also accommodates multiple measured confounders, multiple unmeasured confounders, and allows for mediator exposure interaction on the outcome. Enables to simulate unmeasured confounding in mediation analysis in order to see how the results of the mediation analysis would change in the presence of unmeasured confounding." . + +SCR:024493 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Nano Measurer" ; + definition: "Software tool to process micrograph images for particle size." . + +SCR:024494 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VSEARCH" ; + definition: "Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data." . + +SCR:024495 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "WHONET" ; + definition: "Software free desktop Windows application for the management and analysis of microbiology laboratory data with a particular focus on antimicrobial resistance surveillance developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance at the Brigham and Women's Hospital in Boston, Massachusetts. WHONET, available in 44 languages, supports local, national, regional, and global surveillance efforts in over 2,300 hospital, public health, animal health, and food laboratories in over 130 countries worldwide." . + +SCR:024496 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ToposPro" ; + definition: "Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters." . + +SCR:024497 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Treerecs" ; + definition: "Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree." . + +SCR:024498 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "TomoStudio" ; + definition: "Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data." . + +SCR:024499 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Stem" ; + NIFRID:synonym "Short Time-series Expression Miner" ; + definition: "Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology." . + +SCR:024500 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SRAMP" ; + NIFRID:synonym "Sequence-based Rna Adenosine Methylation site Predictor" ; + definition: "Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features." . + +SCR:024501 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SimPhy" ; + definition: "Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees." . + +SCR:024502 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Mutation Assessor" ; + definition: "Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs." . + +SCR:024503 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CRISPResso2" ; + definition: "Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments." . + +SCR:024504 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "WinNonlin" ; + NIFRID:synonym "Phoenix WinNonlin" ; + definition: "Software to automate repetitive analysis steps and is widely considered the industry standard for NCA, TK, and PK/PD modeling. Used as non-compartmental analysis (NCA), pharmacokinetic/pharmacodynamic (PK/PD), and toxicokinetic (TK) modeling tool." . + +SCR:024505 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FastMulRFS" ; + definition: "Software pipeline for estimating species trees from multi copy gene trees." . + +SCR:024506 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Evalue" ; + definition: "Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences." . + +SCR:024507 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "gamm4" ; + definition: "Software R package to estimate generalized additive mixed models." . + +SCR:024508 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Inference of CRISPR Edits" ; + NIFRID:synonym "Synthego Inference of CRISPR Edits" ; + NIFRID:abbrev "ICE" ; + definition: "Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data." . + +SCR:024509 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DAGitty" ; + definition: "Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models." . + +SCR:024510 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "geepack" ; + NIFRID:synonym "generalized estimating equations pack" ; + definition: "Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data." . + +SCR:024511 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ggridges" ; + definition: "Software R package enables creation of Ridgeline plots in 'ggplot2'" . + +SCR:024512 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CopyKAT" ; + NIFRID:synonym "Copynumber Karyotyping of Aneuploid Tumors" ; + definition: "Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data." . + +SCR:024513 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "AutoRT" ; + definition: "Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides." . + +SCR:024514 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CMplot" ; + NIFRID:synonym "Circle Manhattan Plot" ; + definition: "Software drawing R package designed for Manhattan plot of genomic analysis." . + +SCR:024515 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "classInt" ; + NIFRID:synonym "Class Intervals" ; + definition: "Software R package for choosing univariate class intervals for mapping or other graphics purposes." . + +SCR:024516 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "mitml" ; + definition: "Software R package for multiple imputation of missing data in multilevel modeling." . + +SCR:024517 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MetaPSICOV" ; + definition: "Software tool for accurate prediction of contacts and long range hydrogen bonding in proteins." . + +SCR:024518 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ModFOLD" ; + NIFRID:synonym "ModFOLD6", + "ModFOLD8" ; + definition: "Web server for the global and local quality estimation of 3D protein models" . + +SCR:024519 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "maftools" ; + definition: "Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files." . + +SCR:024520 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ASTRAL-Pro" ; + NIFRID:synonym "ASTRAL for PaRalogs and Orthologs", + "ASTRAL-Pro 2" ; + definition: "Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy." . + +SCR:024521 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Kaplan Meier Plotter" ; + NIFRID:synonym "Kaplan-Meier Plotter", + "KM Plotter" ; + definition: "Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma." . + +SCR:024522 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MADOKA" ; + definition: "Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library." . + +SCR:024523 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "IntFOLD" ; + definition: "Web integrated protein structure and function prediction server. Integrated server for modelling protein structures and functions from amino acid sequences." . + +SCR:024524 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "lDDT" ; + NIFRID:synonym "Local Distance Difference Test" ; + definition: "Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility." . + +SCR:024525 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "LaCyTools" ; + definition: "Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides." . + +SCR:024526 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bedr" ; + definition: "Software R package for genomic interval processing.Genomic regions processing using open-source command line tools to perform genome arithmetic e.g indexing, formatting and merging." . + +SCR:024527 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2510" ; + rdfs:label "Stanford University Microfluidics Foundry Core Facility" ; + NIFRID:synonym "Stanford Microfluidics Foundry", + "Stanford University Stanford Microfluidics Foundry" ; + NIFRID:abbrev "SMF" ; + definition: "Core in part of Bioengineering Department at Stanford University and is the main service provider of integrated microfluidic devices on Stanford campus servicing universities and academic institutions." . + +SCR:024528 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2512" ; + rdfs:label "Stanford University Koret Human Neurosciences Community Laboratory Core Facility" ; + NIFRID:synonym "Koret Human Neurosciences Community Laboratory", + "Stanford University Koret Human Neurosciences Community Laboratory" ; + NIFRID:abbrev "HNCL" ; + definition: "Core for collaborative human neuroscience research provides access to technology and expertise to high density electroencephalography recording and transcranial magnetic stimulation studies in human subjects." . + +SCR:024529 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2511" ; + rdfs:label "Stanford University Additive Manufacturing and Printing Core Facility" ; + NIFRID:synonym "Additive Manufacturing and Printing Facility", + "Stanford University Additive Manufacturing and Printing Facility" ; + NIFRID:abbrev "AMPF" ; + definition: "Advanced 3D printing facility enables digital design, prototyping, and small scale production as integrated innovation hub and shared use facility for innovation and commercialization for investigators spanning the Stanford campus and Silicon Valley." . + +SCR:024530 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2513" ; + rdfs:label "Pennsylvania State University Huck Institutes Genomics Research Incubator Core Facility" ; + NIFRID:synonym "Pennsylvania State University Huck Institutes Genomics Research Incubator" ; + NIFRID:abbrev "GRI" ; + definition: """Provides access to highly specialized and custom genomics and epigenomics assays that Genomics Core Facility does not currently support. Examples include ATAC sequencing; +RUN sequencing;Tag sequencing;Chromatin immunoprecipitation;Custom assays. Offers hands-on experiences and training for researchers in genomic technologies, methodologies, and instrumentation.""" . + +SCR:024531 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ms-variability-analysis" ; + definition: "Variability analysis of proteomics data used for deep learning." . + +SCR:024532 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Splice AI" ; + definition: "Software package annotates genetic variants with their predicted effect on splicing. Used to identify splice variants." . + +SCR:024533 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MediBeacon Transdermal GFR Monitor" ; + definition: "Transdermal Glomerular Filtration Rate monitor used to assess renal function in mouse and rat models of acute kidney injury and chronic kidney disease." . + +SCR:024534 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "3D ImageJ Suite" ; + definition: "Software suite provides plugins to enhance 3D capabilities of ImageJ." . + +SCR:024535 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_TP1020" ; + rdfs:label "Leica TP1020 Automatic Benchtop Tissue Processor Semi Enclosed" ; + NIFRID:synonym "Leica TP1020 tissue processor" ; + definition: "Leica TP1020 tissue processor is available in four configurations: basic instrument, basic instrument with vacuum, basic instrument with fume control system and basic instrument with both vacuum and fume control. Used for gentle specimen processing and high level of specimen safety at all stages of processing run." . + +SCR:024536 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "10X Genomics Chromium iX Single Cell Analyzer" ; + NIFRID:synonym "Chromium iX", + "Chromium iX Single Cell Analyzer" ; + definition: "Chromium iX offers cost effective, lower throughput single cell analysis, and can be upgraded to the high throughput full-range Chromium X.Chromium iX does not run high-throughput (HT) assays." . + +SCR:024537 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "10X Genomics Chromium X Single Cell Analyzer" ; + NIFRID:synonym "10X Genomics Chromium X", + "Chromium X", + "Chromium X Single Cell Analyzer" ; + definition: "Analyzer used for high throughput full range single cell analysis. Chromium X runs high-throughput assays. It runs all single cell assays, including high-throughput assays for Single Cell Immune Profiling and Single Cell Gene Expression." . + +SCR:024538 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "TADA-A" ; + NIFRID:synonym "TADA-Annotations" ; + definition: "Software statistical framework for mapping risk genes from de novo mutations in whole genome sequencing studies." . + +SCR:024539 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BioThings API" ; + definition: "FAIR API ecosystem for inter-connected biomedical knowledge. Provides three components in its API development ecosystem: family of high-performance APIs for accessing up-to-date annotations for genes, genetic variants, chemicals and drugs; provides BioThings API packages its API-development best practice into reusable Software Development Kit to help other bioinformaticians to build same high-quality API to distribute their own specific knowledge; BioThings API provides platform to foster findability and interoperability across community developed biomedical APIs. Provides tools for authoring API metadata following community supported OpenAPI standard and hosts standardized interactive API documentation. Defines set of OpenAPI extensions to provide biomedical specific semantic annotations." . + +SCR:024540 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Playbook Workflow Builder" ; + definition: "Web based platform that facilitates knowledge resolution by enabling users to traverse growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by the ecosystem. Via user friendly web based user interface, workflows can be constructed from these building blocks without technical expertise." . + +SCR:024541 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Luna" ; + definition: "Software package for analysis of sleep signal data. Open source C/C++ software for manipulating and analyzing polysomnographic recordings, with focus on sleep EEG." . + +SCR:024542 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Moonlight" ; + definition: "Web Luna based interactive viewer for EDF signal and annotations, specifically designed for polysomnographic data. Supports visualization, analyses and manipulation of sleep signals, range of summary statistics and hypnogram based analyses including automated staging." . + +SCR:024543 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ImageTwin" ; + definition: "AI based software for detecting integrity issues in figures of scientific articles. Used for detecting integrity issues in life science articles. Detects inappropriate manipulation and duplication in many figure types, including blots, microscopy images, and light photography." . + +SCR:024544 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2469" ; + rdfs:label "University of California at Berkeley Electron Microscope Laboratory Core Facility" ; + NIFRID:synonym "Electron Microscope Laboratory", + "UC Berkeley Electron Microscope Laboratory", + "University of California at Berkeley Electron Microscope Laboratory", + "University of California Berkeley UC Berkeley Electron Microscope Laboratory" ; + NIFRID:abbrev "EML" ; + definition: "Imaging core and shared resource facility. Provides electron microscopy services, education, and training. Equipped with high resolution transmission electron microscopes, scanning electron microscopes, high pressure freezer and ancillary sample preparation equipment. The equipment can provide nanometer scale analysis for biological, chemical and materials science. Offers Project consultation, Education and training for new users, Equipment for trained users who anticipate having long term EM projects, Full service microscopy." . + +SCR:024545 a owl:NamedIndividual ; + rdfs:label "Molecular Property Diagnostic Suite Covid-19" ; + NIFRID:synonym "Galaxy MPDS COVID-19" ; + NIFRID:abbrev "MPDS-Covid19" ; + definition: "Galaxy based disease specific web portal for drug discovery research of COVID-19. Open access disease specific drug discovery portal." . + +SCR:024546 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BatchEval" ; + definition: "Software tool for evaluating batch effects in data integration. Tool to improve accuracy and reliability of experimental results. Used to evaluate batch effect of dataset integration and output comprehensive report." . + +SCR:024547 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Franklin by Genoox" ; + definition: "Platform as clinical knowledge base to search information to answer genomic questions. Connects clinicians, genetic counselors, and healthcare organizations by sharing genetic insights, enabling platform users to make impactful discoveries providing better patient care." . + +SCR:024548 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Kassandra" ; + definition: "Software bulk RNA-seq cellular deconvolution tool. Used for analysis of healthy tissue and tumor biopsies. Based on RNA-seq NGS data of biological sample, Kassandra predicts cellular composition including stromal and immune elements by analyzing gene expression." . + +SCR:024549 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "OSS Research and Community Activity" ; + NIFRID:synonym "Emerging Technology Observatory Open Source Software Research and Community Activity", + "Open Source Software Research and Community Activity" ; + NIFRID:abbrev "ORCA" ; + definition: "Platform for data on open source software (OSS) used in science and technology research. Drawing on Github Archive, ETO’s Merged Academic Corpus, and many other data sources, ORCA tracks OSS usage, health, development activity, and community engagement across software projects and research subjects. Use ORCA to compare OSS projects in particular research area, track trends over time, and sort and filter projects by different metrics." . + +SCR:024550 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RediVis" ; + definition: "Data platform for academic research. Redivis provides organizations with central hub where researchers can easily discover, access, and analyze their data." . + +SCR:024551 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Customizable Multielectrode Array" ; + NIFRID:synonym "16-channel customizable multielectrode array", + "CMEA: Customizable Multielectrode Arrays" ; + NIFRID:abbrev "CMEA" ; + definition: "Simple, lightweight, and low cost customizable multielectrode array for Local Field Potential recordings. Used to collect LFP data from different brain regions simultaneously in rats. Can be modified to record single unit and multiunit activity in addition to LFP activity using both wired and wireless neural data acquisition systems." . + +SCR:024552 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Berkeley Seismological Laboratory" ; + NIFRID:synonym "Berkeley Seismological Lab" ; + definition: "Acts as part of statewide earthquake monitoring system, the California Integrated Seismic Network. Conducts essential research on earthquakes and solid earth processes while collecting and delivering high quality geophysical data. Data from these geophysical networks are recorded digitally and are archived at the Northern California Earthquake Data Center, which is located at the Berkeley Seismological Lab." . + +SCR:024553 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Biocode Commons" ; + definition: "Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO." . + +SCR:024554 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "California Coastal Atlas" ; + definition: "Resource designed to publish information and data about California coast reflecting current scientific understanding and data for the purpose of informing public policy and advancing the understanding of coastal processes." . + +SCR:024555 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2472" ; + rdfs:label "University of Florida Scripps Institute for Biomedical Innovation and Technology Structural Biology Cryo Electron Microscopy Core Facility" ; + NIFRID:synonym "Structural Biology Cryo Electron Microscopy Core", + "The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology Structural Biology Cryo Electron Microscopy Core" ; + definition: "Provides scientists with cryo-electron microscopy utilization, skills and knowledge to aid in their research." . + +SCR:024556 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2514" ; + rdfs:label "Yale University Wu Tsai Institute BrainWorks Core Facility" ; + NIFRID:synonym "Wu Tsai Institute-BrainWorks" ; + definition: "Service core arm of Center for Neurocognition and Behavior. Used for measuring healthy human brain and behavior in action. Facility houses equipment, including MRI, SQUID and triaxial OPM MEG, EEG, NIRS, TMS, VR, eye-tracking, and body motion tracking." . + +SCR:024557 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Comprehensive Everglades Restoration Plan" ; + NIFRID:synonym "South Florida Water Management District Comprehensive Everglades Restoration Plan" ; + NIFRID:abbrev "CERP" ; + definition: "Platform provides framework for restoring, protecting and preserving the greater Everglades ecosystem. The plan is partnership between State of Florida and federal government." . + +SCR:024558 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_B15" ; + rdfs:label "Heraeus B 15 Compact Incubator" ; + definition: "Compact incubator total volume is 15 litres and it operates at temperatures from 5 °C above ambient to 50 °C. Temperature is displayed in increments of 0.2 °C. Air circulation system ensures heat distribution and minimizes the drying out of samples. Incubator can be set up directly on any counter top or work bench and is made of plastic that can be sterilised with standard disinfectants. Small opening on the housing can be used to accommodate cables for electrical devices placed inside the incubator. Reservoir for collecting spilled liquids is provided for additional safety." . + +SCR:024559 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_Cobas_C311" ; + rdfs:label "Roche Cobas C311" ; + definition: "Autoanalyzer is standalone system that provides consolidated testing from range of clinical chemistry applications. Allows determination of sodium, potassium and chloride in serum, plasma and urine using ion selective electrodes. Measurement of HbA1c levels in whole blood can also be performed." . + +SCR:024560 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_Infinite_M200" ; + rdfs:label "Tecan Infinite M200" ; + NIFRID:synonym "Infinite M200", + "TECAN Infinite M200" ; + definition: "TECAN Infinite M200 is laboratory device and accessory for multiplex luminescence and fluorescence applications. Device features automated robotic arm for dispensing samples or reagents onto cuvettes or microplates, as well as range of high speed and throughput sample injection capabilities. Infinite M200 is integrated with TECAN's proven laser-based multi-channel detection technology, to measure multiple biological responses simultaneously. System features graphical user interface to configure instrument for single or multiple sample injection processes. Accommodates range of different cuvette and microplate vessels, suitable for both 1.5ml and 0.2ml tubes as well as plates up to 384 wells. Multichannel optical detector can detect up to four different signals in parallel, with wide range of detection wavelengths. Designed for high-throughput applications with sensitive fluorescence and luminescence. Features automated sample injection unit that enables hands-free operation of 96 or 1,536 up to eight-channel multipoint experiments, providing maximum flexibility. Comes with range of software, including intuitive data collection and analysis interface. Designed with automated calibration settings, providing reliable, accurate and reproducible results." . + +SCR:024561 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_NanoQuantPlate" ; + rdfs:label "Tecan NanoQuantPlate" ; + definition: "Device designed for simultaneous measurement of multiple low volume samples. Consists of 16 precision manufactured quartz optics in user friendly format, offering precise, straightforward absorbance and fluorescence based measurements from sample volumes as low as 2 µl. Combined with Tecan’s Infinite series readers – the Infinite 200 PRO, Infinite F500 and Infinite M1000 PRO – the NanoQuant Plate provides solution for DNA or RNA quantification, allowing detection of concentrations down to 1 ng/µl for wide variety of applications." . + +SCR:024562 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Tecan i-Control" ; + NIFRID:synonym "i-Control", + "Tecan i-Control software" ; + definition: "Microplate reader software as user friendly interface for control of Tecan's Infinite series of microplate readers designed for professional use." . + +SCR:024563 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Leica TCS SP8 DLS LightSheet microscope" ; + NIFRID:synonym "Leica DLS TCS SP8" ; + definition: "Digital LightSheet full confocal with gentle single plane illumination microscope for easy light sheet imaging. TwinFlect mirror deflects illuminating light sheet at 90° angle, which allows integration of illumination and detection beam path into vertical axis of every inverted, Leica TCS SP8 confocal." . + +SCR:024564 a NLX:63400, + owl:NamedIndividual ; + definition: "Software R package to predict drug functional similarity to drug repurposing." . + +SCR:024565 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2516" ; + rdfs:label "Griffith University Compounds Australia Core Facility" ; + NIFRID:synonym "Compounds Australia - Griffith University" ; + definition: "Core for compound management and logistics. Through specialist infrastructure and expertise, we enable health researchers worldwide to outsource their sample logistics. Securely stores and curates suite of compound libraries (>1.5 million compounds), which are provided to researchers in flexible, assay-ready formats." . + +SCR:024566 a NLX:152328, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Crossref Funder ID 501100001791", + "GRID grid.1022.1", + "ISNI 0000 0004 0437 5432", + "Wikidata Q1202292" ; + rdfs:label "Griffith University; Brisbane; Australia" ; + definition: "Griffith University, Brisbane, Queensland, Australia is public research university in South East Queensland on the east coast of Australia. One of Australia's leading universities. The university offers undergraduate, postgraduate, and research programs across range of disciplines, including business, law, science, health, education, engineering, and arts." . + +SCR:024567 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "miRNet" ; + NIFRID:synonym "miRNet 2.0" ; + definition: "Web based tool that offers statistical, visual and network based approaches to understand miRNAs functions and regulatory mechanisms. Used for dissecting miRNA-target interactions and functional associations through network-based visual analysis.miRNet 2.0 is network based visual analytics for miRNA functional analysis and systems biology." . + +SCR:024568 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Illumina NovaSeq X Plus" ; + NIFRID:synonym "NovaSeq X Plus", + "NovaSeq X Plus Sequencing System" ; + definition: """NovaSeq X Plus Sequencing System has ability to sequence more than 128 genomes per run. Provides faster run times, and the ability to process data directly on the instrument. +Uses dual flow cells. Production scale sequencing system can also perform broad range of data intensive applications, from single-cell analysis to exome and circulating tumor DNA sequencing.""" . + +SCR:024569 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Illumina NovaSeq X" ; + NIFRID:synonym "NovaSeq X", + "NovaSeq X Sequencing System" ; + definition: "Updated NovaSeq to NovaSeq X. NovaSeq X Sequencing System achieves lower cost per genome by packing more genomes per flowcell, and that is because each flowcell has more wells for more fragments. NovaSeq X uses single flow cell." . + +SCR:024570 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Visium CytAssist" ; + NIFRID:synonym "10XGenomics Visium CytAssist" ; + definition: """Compact, benchtop instrument that enables transfer of transcriptomic probes from +standard glass slides to Visium slides, enabling spatial profiling insights to be gained from even more samples. Enables whole transcriptomic spatial profiling insights across entire tissue section, and expanded compatibility with FFPE and/or FF samples.""" . + +SCR:024571 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "lubridate" ; + definition: "Software R package to work with date-times and time-spans. Used for fast and user friendly parsing of date-time data, extraction and updating of components of date-time, algebraic manipulation on date-time and time-span objects." . + +SCR:024573 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2517" ; + rdfs:label "University of Pennsylvania Institute for RNA Innovation Targeting Core Facility" ; + NIFRID:synonym "Targeting Core", + "University of Pennsylvania Institute for RNA InnovationTargeting Core", + "University of Pennsylvania Targeting Core" ; + definition: "Core to support advancement of RNA biotherapeutics via enabling swift and low failure solutions of targeting related aspects. Provides methodologies, equipment, reagents, expertise and support in identification of epitopes and ligands, molecular design and testing of targeting RNA to diverse multitudes of desirable addresses in the body." . + +SCR:024574 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2518" ; + rdfs:label "University of Pennsylvania Institute for Immunology and Immune Health I3H Core Facility" ; + NIFRID:synonym "Immune Health Platforms", + "PennMedicine Immune Health" ; + NIFRID:abbrev "I3H" ; + definition: "Core provides infrastructure and technical support for scaling clinical immune profiling of large scale clinical cohorts. Provides biospecimen processing, sample storage, high dimensional immune assays, computational analysis, and project management. Services are only available to investigators and teams whose cohorts have been approved by the Immune Health leadership." . + +SCR:024575 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DataMares " ; + definition: "Open source, and interactive platform to resolve trans disciplinary problems related to coastal and marine ecosystem. Data sharing and science communication portal holds amounts of fishery, reef, and mangrove data pertaining to Gulf of California and Mexico specific oceans, and delivers this information in interactive and easily digestible manner. Consistently expands library of datasets while improving functionality and overall usability of the platform. Facilitate access to scientific knowledge and data to promote transparency, education, and deeper understanding of Mexico’s ecosystems and their biodiversity to bridge gap between science and design process of conservation and resource management programs." . + +SCR:024576 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EarthCube" ; + definition: "Platform provides tools, data, services, apps and community resources for geoscience researchers. EarthCube community works together to influence how data will be collected accessed, analyzed, visualized, shared and archived; participate in interdisciplinary and collaborative research; and contribute to transformation of geoscience research through emerging practices of digital scholarship, data and software stewardship, and open science." . + +SCR:024577 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EarthRef" ; + definition: "Platform for Earth reference data and models supported by San Diego Supercomputer Center and Scripps Institution of Oceanography. Provides webservices and database." . + +SCR:024578 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Engineering Biology Research Consortium" ; + NIFRID:synonym "The Engineering Biology Research Consortium (EBRC)" ; + NIFRID:abbrev "EBRC" ; + definition: "Non-profit, public-private partnership dedicated to bringing together inclusive community committed to advancing engineering biology to address national and global needs. We showcase cutting-edge research in engineering biology, identify pressing challenges and opportunities in research and application, articulate compelling research roadmaps and programs to address them, and provide timely access to other key developments in engineering biology." . + +SCR:024579 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Geotechnical Extreme Events Reconnaissance" ; + NIFRID:abbrev "GEER" ; + definition: "Leading global organization for investigation and collection of highly valuable and perishable geotechnical insights and data and timely distillation and provision of that information to public through reports." . + +SCR:024580 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Kavli Institute for Theoretical Physics Online Talks" ; + NIFRID:synonym "KITP Online Talks" ; + NIFRID:abbrev "KITP" ; + definition: "Most seminars, conferences, colloquia, and lectures at KITP since late 1997 have been archived on this website, in the form of slides, audio, video, and podcasts. Portal to foster scientific communication, education, and outreach." . + +SCR:024581 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "LBNL OpenMSI" ; + NIFRID:synonym "Open Mass Spectrometry Imaging", + "OpenMSI" ; + definition: "Web-based platform for mass spectrometry imaging. Used for visualization, analysis and management of mass spectrometry imaging data. Used for management and storage of MSI data, visualization of hyper-dimensional contents of data, and statistical analysis." . + +SCR:024583 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Biobank@VITO" ; + definition: "Population biobank hosts heterogeneous collection of samples from general population spread across Flanders and over time and covers different ages. Biobank in which bio-specimen including human peripheral blood, cord blood, serum, plasma, cells, RNA, DNA), urine, hair, nails, exhaled breath condensate, saliva DNA, and human breast milk collected from non-diseased populations are preserved. These biospecimen were collected since 2002 in different human biomonitoring studies comprising European (e.g., DEMOCOPHES, HBM4EU), national (e.g., WHO human breastmilk studies), Flemish (Flemish Environment and Health Study (FLEHS) campaigns), and local (e.g., hotspots, 3xG project) well-defined and ethically approved research projects." . + +SCR:024584 a owl:NamedIndividual ; + rdfs:label "ProPlot" ; + definition: "Software tool as succinct matplotlib wrapper for making publication quality graphics." . + +SCR:024585 a "Oganization", + owl:NamedIndividual ; + oboInOwl:hasDbXref "Crossref Funder ID 100007058", + "GRID grid.261128.e", + "ISNI 0000 0000 9003 8934", + "Wikidata Q1191344" ; + rdfs:label "Northern Illinois University; DeKalb; USA" ; + definition: "Northern Illinois University is a public research university in DeKalb, Illinois. It was founded as Northern Illinois State Normal School in 1895 by Illinois Governor John P. Altgeld to provide the state with college-educated teachers." . + +SCR:024586 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2551" ; + rdfs:label "Northern Illinois University Molecular Analysis Core facility" ; + NIFRID:synonym "Molecular Analysis Core Facility", + "Northern Illinois University MAC core facility", + "Northern Illinois University MAC facility" ; + NIFRID:abbrev "NIU MAC" ; + definition: "Molecular Analysis Core offers analytical and instructional expertise in mass spectrometry. Provides instruments for spectroscopy, chromatography, and thermal analysis. Located in La Tourette Hall 304 and managed and supported by the Division of Research and Innovation Partnerships" . + +SCR:024587 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Cartopy" ; + definition: "Software Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. Cartographic library with matplotlib support." . + +SCR:024588 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bayesplot" ; + definition: "Software R package providing extensive library of plotting functions for use after fitting Bayesian models.Plotting functions for posterior analysis, MCMC diagnostics, prior and posterior predictive checks, and other visualizations to support the applied Bayesian workflow." . + +SCR:024589 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Waters" ; + NIFRID:synonym "Waters Corporation" ; + definition: "Publicly traded analytical laboratory instrument and software company headquartered in Milford, Massachusetts. Leading provider of lab equipment, supplies and software. Has pioneered chromatography, mass spectrometry, and thermal analysis innovations." . + +SCR:024590 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Evosep" ; + definition: "Business Services and Biotechnology Research company in Odense, Denmark." . + +SCR:024591 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2519" ; + rdfs:label "Weill Cornell Medical College Department of Pathology and Laboratory Medicine Multiparametric In Situ Imaging Laboratory Core Facility" ; + NIFRID:synonym "Weill Cornell Medical College MISI WCM" ; + NIFRID:abbrev "MISI WCM" ; + definition: "Core focuses on providing immunohistochemistry, multiplex immunofluorescence and high-plex histological imaging.Provides in situ-based profiling of cellular microenvironments at single cell resolution, in tumor and non-tumor tissues." . + +SCR:024592 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Live Mouse Tracker Toolkit Analysis" ; + NIFRID:synonym "Live Mouse Tracker Toolkit", + "LMT Toolkit", + "LMT toolkit analysis", + "lmt toolkit analysis", + "LMT-toolkit", + "LMT-Toolkit Analysis" ; + definition: "Open source web application created to analyze Live Mouse Tracker data easily and intuitively. Used to check reliability and to make some analysis of data from Live Mouse Tracker experiments. LMT stores data in SQLite files that requires some computer skills, but LMT-toolkit makes it easy to compute and extract behavioral profiles for each animal tested following step-by-step process." . + +SCR:024593 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "IonOpticks" ; + definition: "Innovative Australian company that develops, manufactures and distributes advanced proteomics tools. Produces high performance nanoflow chromatography solutions for global research community." . + +SCR:024594 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "windrose" ; + definition: "Software Python library to manage wind data, draw windroses also known as polar rose plots, and fit Weibull probability density functions." . + +SCR:024595 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "scikit-learn-intelex" ; + definition: "Software tool as Intel(R) Extension for Scikit-learn to speed up Scikit-learn application. Used to accelerate existing scikit-learn code. Accelerates Scikit-learn applications and still have full conformance with all Scikit-Learn APIs and algorithms. Software AI accelerator brings over 10-100X acceleration across variety of applications." . + +SCR:024596 a NLX:152328, + owl:NamedIndividual ; + oboInOwl:hasDbXref "GRID grid.462422.4", + "ISNI 0000 0001 2109 9028", + "Wikidata Q6291683" ; + rdfs:label "Marine and Coastal Research Institute of Columbia; Santa Marta; Colombia" ; + NIFRID:abbrev "INVEMAR" ; + definition: "Nonprofit marine and coastal research institute of Colombia linked to Ministry of Environment and Sustainable Development. Provides basic and applied scientific research on marine and coastal issues related to biodiversity, geosciences, resource use assessment, environmental quality and management of marine and coastal information. Coordinates Environmental Information System in marine and coastal aspects. Infrastructure has specialized laboratories with cutting-edge technology and Museum of Marine Natural History of Colombia. INVEMAR is recognized nationally and internationally for quality and leadership in its basic and applied research activities and its commitment to sustainable use of marine and coastal resources." . + +SCR:024597 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Crossref Funder ID 100014585", + "GRID grid.507579.9", + "ISNI 0000 0001 2190 7056", + "Wikidata Q6971323" ; + rdfs:label "National Center for Ecological Analysis and Synthesis" ; + NIFRID:abbrev "NCEAS" ; + definition: "Synthesis science center to help to transform ecology and environmental science to generate bigger insights. Leader in environmental data science, has led development of technological solutions to improve data access and management and efficiency of analyses, and helped set scientific standards in data ethics." . + +SCR:024598 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "Nightingale" ; + NIFRID:abbrev "NGSCI" . + +SCR:024599 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Arctic Data Center" ; + NIFRID:synonym "NSF Arctic Data Center" ; + definition: "Data and software repository for Arctic section of National Science Foundation’s Office of Polar Programs. Repository has CoreTrustSeal certification so that the data can be used, shared, and preserved over long timespan. Helps research community reproducibly preserve and discover all products of NSF funded science in Arctic, including data, metadata, software, documents, and provenance that link these in coherent knowledge model. Initiative is the partnership between National Center for Ecological Analysis and Synthesis at UC Santa Barbara, DataONE, and National Centers for Environmental Information." . + +SCR:024600 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Ocean Protection Council" ; + NIFRID:abbrev "OPC" ; + definition: "Cabinet level state body that works jointly with state and federal agencies, NGOs, tribes and public to ensure that California maintains healthy, resilient, and productive ocean and coastal ecosystems. The mission is to protect California’s coast and ocean by advancing innovative, science based policy and management, making strategic investments, and catalyzing action through partnerships and collaboration. Provides global model for ecosystem based protection and conservation." . + +SCR:024601 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CodeMeta Generator" ; + definition: "Web application that creates CodeMeta files." . + +SCR:024602 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Software Heritage" ; + definition: "Software Heritage provides service for archiving and referencing historical and contemporary software with focus on human readable source code. The site was unveiled in 2016 by Inria and is supported by UNESCO. The project itself is structured as non‑profit multi‑stakeholder initiative." . + +SCR:024603 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Open Tree of Life" ; + definition: "Project aims to construct comprehensive, dynamic and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data." . + +SCR:024604 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Open Context" ; + definition: "Publishes documentation and data to make them discoverable and searchable on the Web. Publishing service archives data by integrating analyses, maps, media, and journals together. Open Context editors clean data and organize content. Every item receives unique identifier that allows citation of individual items. Your data publication receives DOI. Creative Commons licenses facilitate reuse. All Open Context data publications are preserved with California Digital Library." . + +SCR:024605 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rstanarm" ; + definition: "Software R package for Bayesian applied regression modeling via Stan." . + +SCR:024606 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2521" ; + rdfs:label "Tulane University TNPRC Anatomic Pathology Core Facility" ; + NIFRID:synonym "TNPRC Anatomic Pathology Core", + "Tulane University TNPRC Anatomic Pathology Core" ; + NIFRID:abbrev "APC" ; + definition: "Anatomic Pathology Core is responsible for post-mortem examinations, tissue collection and distribution, fixation, processing, slide preparation, routine and special staining, and diagnostic gross and histologic pathology services. Processes and interprets biopsy specimens for both research and diagnostic purposes and provides tissue trimming, paraffin processing, sectioning, and routine and special staining for clinical and research staff and faculty. APC works closely with clinical veterinarians, and through diagnostic pathology on biopsies and necropsies, plays major role in monitoring and maintaining health of animals in breeding colonies." . + +SCR:024607 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2522" ; + rdfs:label "Tulane University TNPRC Immunology Assay Core Facility" ; + NIFRID:synonym "TNPRC Immunology Assay Core", + "Tulane University TNPRC Immunology Assay Core" ; + NIFRID:abbrev "IAC" ; + definition: "Immunology Assay Core provides several immunology services to core and affiliate investigators. Offers multicolor staining for flow cytometry, access to inventory of commonly used antibodies, reagent compounding, sample processing such as cell isolation, automated cell separation through RoboSep, and irradiation of biological samples.Offers multiplex assays using MESO QuickPlex SQ 120 Imager to investigators." . + +SCR:024608 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2523" ; + rdfs:label "Tulane University TNPRC Infectious Disease Aerobiology Core Facility" ; + NIFRID:synonym "TNPRC Infectious Disease Aerobiology Core", + "Tulane University TNPRC Infectious Disease Aerobiology Core" ; + definition: "Core focuses on infectious disease aerobiology. Core facilitates biomedical research efforts that require unique demands of aerosol and aerobiology in their respective performance." . + +SCR:024609 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2526" ; + rdfs:label "Tulane University TNPRC Clinical Pathology Core Facility" ; + NIFRID:synonym "TNPRC Clinical Pathology Core", + "Tulane University TNPRC Clinical Pathology Core" ; + NIFRID:abbrev "CPC" ; + definition: "Clinical Pathology Core performs clinical diagnostic testing for all research and colony animals. This includes complete blood counts, routine chemistry panels, and microbial culture workups. The lab is equipped with Sysmex XN1000v veterinary hematology analyzer, Beckman AU480 chemistry analyzer, and Matrix assisted laser desorption ionization time of flight MALDI-TOF instrument for microbe identification. CPC is staff with American Society of Clinical Pathologist certified licensed Medical Technologists." . + +SCR:024610 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2525" ; + rdfs:label "Tulane University TNPRC Unit of Collaborative Research Core Facility" ; + NIFRID:synonym "TNPRC Unit of Collaborative Research", + "Tulane University TNPRC Unit of Collaborative Research" ; + NIFRID:abbrev "UCR" ; + definition: "Core serves as regional and national resource and center of excellence for biomedical research using Nonhuman Primate Models. Unit is staffed by personnel with expertise in veterinary medicine, research study design, budgeting, database management, IACUC issues, sample acquisition, processing, performing laboratory base assays and shipping." . + +SCR:024611 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2528" ; + rdfs:label "Tulane University TNPRC Flow Cytometry Core Facility" ; + NIFRID:synonym "TNPRC Flow Cytometry", + "Tulane University TNPRC Flow Cytometry" ; + definition: "Core provides analytical flow cytometry services and live cell sorting under enhanced Biosafety Level 2 conditions. Instruments available include six analyzers ranging from 4-30 color acquisition and three sorters using 1-,2-,4-way, and plate sorting between 6-18 colors. Provides experimental and panel design consultation. Provides continued education in seminar format and one-on-one sessions with user." . + +SCR:024612 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2531" ; + rdfs:label "Tulane University TNPRC High Containment Research Performance Core Facility" ; + NIFRID:synonym "TNPRC High Containment Research Performance Core", + "Tulane University TNPRC High Containment Research Performance Core" ; + NIFRID:abbrev "HCRPC" ; + definition: "Provides full or partial support for researchers seeking to perform BSL3 and BSL2/BSL3 Select Agent studies and provides services for bacterial/viral culture and propagation, sample preparation, and processing of blood, BAL, single cell isolation, flow cytometry, and more. Offers project management assistance in study design, budgeting, and IACUC and IBC preparation. Our standard operating procedures have been tested to ensure consistent practices and have undergone rigorous quality assurance processes to ensure reproducibility. Offers assay services for qPCR, O ink Q100, Biorad Bioplex 200, Meso QuickPlex SQ120 Imager and Microscope Axio Observer." . + +SCR:024613 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2527" ; + rdfs:label "Tulane University TNPRC Confocal Microscopy and Molecular Pathology Core Facility" ; + NIFRID:synonym "TNPRC Confocal Microscopy and Molecular Pathology Core", + "Tulane University TNPRC Confocal Microscopy and Molecular Pathology Core" ; + NIFRID:abbrev "CMMPC" ; + definition: "Core provides research support and training with molecular pathology skills, confocal microscopy, image analysis, and multicolor immunohistochemistry and in-situ hybridization techniques for internal and affiliate scientists. Services include assistance with experimental design, antibody selection, molecular probe selection, fixation and staining protocols, operating fluorescent and confocal microscopes, acquiring and storing imaging data, interpretation of results, and generation of publication-quality images. Image analysis services include assistance with capturing images for evaluation and with use of various image analysis software." . + +SCR:024614 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2524" ; + rdfs:label "Tulane University TNPRC Pathogen Detection and Quantification Core Facility" ; + NIFRID:synonym "TNPRC Pathogen Detection and Quantification Core", + "Tulane University TNPRC Pathogen Detection and Quantification Core" ; + NIFRID:abbrev "PDQC" ; + definition: "Core provides services for maintaining Specific Pathogen Free status in macaque breeding colonies. Services include antibody detection in serum or plasma by Luminex-based assays and /or ELISA for SPF-agents like SIV, SRV, STLV, B virus, SFV. CMV, RRV, SVV, SV40, and LCV, and non-SPF infectious agents like measles, Burkholderia pseudomallei, Tripanosoma cruzi, Mycobacterium tuberculosis, and SARS-CoV-2. Offers services of cytokines quantification, and molecular assays for detection of SRV, CMV, SFV, and RRV.Performs nucleic acid purification from blood and tissue samples as well as qPRC for SIV viral load in plasma, cells, or tissue." . + +SCR:024615 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2529" ; + rdfs:label "Tulane University TNRPC Genetics and Genome Banking Core Facility" ; + NIFRID:synonym "TNRPC Genetics and Genome Banking", + "Tulane University TNRPC Genetics and Genome Banking" ; + definition: "Core assists in design of breeding groups and monitors genetic diversity among colony breeding animals. Core is responsible for maintaining genome bank including DNA and cryopreserved primary fibroblast cell lines, including cell lines and DNA samples representing nearly 9,000 animals. Genotype data using NPRC standardized SNP array is available and whole genome sequence is available for over 520 animals. Genomic data is available via mGAP and can be integrated with physical resource and records by contacting the core. Targeted genotyping for new model development and specialized breeding is also available." . + +SCR:024626 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PRECISE Traumatic Brain Injury Model Catalog" ; + NIFRID:synonym "PRE Clinical Interagency reSearch resourcE Traumatic Brain Injury Model Catalog", + "PRECISE catalog", + "PRECISE TBI Model Catalog", + "PRECISE-TBI", + "PRECISE-TBI Model Catalog" ; + definition: "Platform for preclinical Traumatic Brain Injury model literature metadata. Model catalog to enhance reproducibility of preclinical TBI research by increasing ability to find and access preclinical TBI model papers." . + +SCR:024627 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "WebProtege" ; + NIFRID:synonym "WebProtégé" ; + definition: "Web based platform for editing biomedical ontologies. Web application for editing OWL 2 ontologies. Open source, lightweight, web based ontology editor implemented in Java and JavaScript using OWL API and Google Web Toolkit. For users who do not wish to host their ontologies on Stanford servers, WebProtégé is available as Web app that can be run locally using Servlet container such as Tomcat." . + +SCR:024628 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Brain Injury Knowledge Ontology" ; + NIFRID:synonym "BIKO TBI", + "BIKO Traumatic Brain Injury", + "BIKO-TBI", + "Brain Injury Knowledge Ontology Traumatic Brain Injury" ; + NIFRID:abbrev "BIKO" ; + definition: "Application ontology to formalize concepts and methods used in translational traumatic brain injury research. Multi species translational traumatic brain injury ontology to assist in formalizing concepts and methods used in traumatic brain injury research." . + +SCR:024629 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RDFLib" ; + NIFRID:synonym "Resource Description Framework Library" ; + definition: "Software Python library for working with Resource Description Framework. Used for working with RDF which is standard model for data interchange on the Web." . + +SCR:024630 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MMV Im2Im" ; + NIFRID:synonym "MMV_Im2Im" ; + definition: "Software Python package for image to image transformation in bioimaging applications. Can be used for semantic segmentation, instance segmentation, image restoration, image generation, and more." . + +SCR:024631 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Dementias Platform UK" ; + NIFRID:abbrev "DPUK" ; + definition: "Public-private partnership of universities, charities, and pharmaceutical and technology companies with core funding from Medical Research Council. Based at Oxford University, in the Department of Psychiatry, and have project sites at Swansea University and Cambridge University, we bring together expertise to enable breakthroughs in dementia research." . + +SCR:024632 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_465" ; + rdfs:label "Mayo Clinic Medical Genome Core Facility" ; + NIFRID:synonym "Mayo Clinic Medical Genome Facility", + "Medical Genome Facility" ; + definition: "Medical Genome Facility includes Cytogenetics Core, Genome Analysis Core and Proteomics Core. Available services include Sanger DNA sequencing, genotyping, gene expression and cytogenetic analysis, biospecimens accessioning and processing, tissue and cell molecular analysis, RNA interference, and oligonucleotide synthesis. Provides Illumina HiSeq2000 platforms and Pacific Biosciences RS single molecule real-time sequencer.Offers applied research services for development of innovative, personalized tests and treatments, especially with regard to biomarkers." . + +SCR:024633 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2534" ; + rdfs:label "State University of Campinas Institute of Chemistry Microscopy Core Facility" ; + NIFRID:synonym "UNICAMP - Institute of Chemistry - Microscopy Core Facility", + "UNICAMP Institute of Chemistry Microscopy Core Facility" ; + definition: "Core offers services in advancing scientific research in the field of chemistry. Provides Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), Confocal Laser Scanning Microscopy (CLSM), and Optical Microscopy. Offers sample preparation techniques, including ultramicrotome, ultracryomicrotome, and sputter coating,training and technical support." . + +SCR:024637 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Partnership for Interdisciplinary Studies of Coastal Oceans" ; + NIFRID:synonym "Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)" ; + NIFRID:abbrev "PISCO" ; + definition: "Academic consortium that conducts research to advance understanding of the coastal ocean within the California Current Large Marine Ecosystem and inform management and policy." . + +SCR:024638 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SDSC Center for Applied Internet Data Analysis" ; + NIFRID:synonym "San Diego Supercomputer Center CAIDA" ; + NIFRID:abbrev "SDSC CAIDA" ; + definition: "Center aimes at promoting greater cooperation in engineering and maintenance of global Internet infrastructure, better manage ever increasing volume of digitally based information including security and network data analysis. Provides open access data and tools. " . + +SCR:024639 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Center for Effective Global Action" ; + NIFRID:abbrev "CEGA" ; + definition: "Network of world class researchers and innovators to improve lives of people living in poverty by generating insights and tools for decision makers backed by rigorous, inclusive, and transparent research. Hub for research, training and innovation headquartered at University of California, Berkeley." . + +SCR:024640 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Triton Shared Computing Cluster" ; + NIFRID:abbrev "TSCC" ; + definition: "Provides advanced computing resources and services to support needs of UC San Diego research community. In addition, researchers from other academic institutions and industries can also participate in this research computing program. TSCC operates on two different computing models – Condo (a system purchase model) and Hotel (a pay-as-you-go model) to support broad range of research computing workloads including traditional HPC, HTC, and emerging big data pipelines." . + +SCR:024641 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Project Production Systems Laboratory" ; + NIFRID:synonym "The Project Production Systems Laboratory", + "UC Berkeley Project Production Systems Laboratory" ; + NIFRID:abbrev "P2SL" ; + definition: "Research institute dedicated to developing and deploying knowledge and tools for project management. Projects are temporary production systems. Dedicated to developing and deploying knowledge and tools for management of project production systems and the management of organizations that produce and deliver goods and services through such systems." . + +SCR:024642 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UC Berkeley Research IT" ; + definition: "Provides research data and computing technologies, consulting, and community for the UC Berkeley campus to advance research through IT innovation. " . + +SCR:024643 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UC Davis eScholarship" ; + definition: "Provides scholarly publishing and repository services that enable departments, research units, publishing programs, and individual scholars associated with University of California to have direct control over creation and dissemination of the full range of their scholarship." . + +SCR:024644 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UC Davis Social Science Data Service" ; + NIFRID:synonym "UC Davis Social Science Data Resources" ; + definition: "Portal provides information about social science data." . + +SCR:024645 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UC Medical Humanities Consortium" ; + NIFRID:synonym "University of California Medical Humanities Consortium" ; + definition: "Faculty directors from UC Berkeley, UC Davis, UC Irvine, and UCSF support collaborative student research projects, publications, and resources with the aim to have substantial record of achievement and innovation pursued through allocated research funding to support humanism in medicine and health science education." . + +SCR:024646 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UC Natural Reserve System" ; + NIFRID:abbrev "UCNRS" ; + definition: "Library of ecosystems throughout California. Most of the state’s major habitat types are represented, from coastal tidepools to inland deserts, and lush wetlands to redwood forests." . + +SCR:024647 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "University of California Press" ; + NIFRID:synonym "UC Press" ; + definition: "Publishing house associated with University of California that engages in academic publishing. UC Press Foundation raises funds to uphold vital role as independent, nonprofit publisher, and receives philanthropic support." . + +SCR:024648 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UCSC Library" ; + NIFRID:synonym "University of California Santa Cruz Library" ; + definition: "Library shares with other academic libraries commitment to intellectual freedom and access to information. This commitment is reflected in open stacks, active interlibrary loan service, online catalog, and Web site linked efficiently to other sites and databases. Has partnerships with libraries at other University of California campuses, local California State Universities, community colleges, and public libraries. Has active participation in California Digital Library." . + +SCR:024649 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Coastal Data Information Program" ; + NIFRID:synonym "UCSD CDIP" ; + NIFRID:abbrev "CDIP" ; + definition: "Network for monitoring waves and beaches and prediction of waves and shoreline change along coastlines of United States. Since 1975 program has produced database of publicly accessible environmental data for use by coastal engineers and planners, scientists, mariners, and marine enthusiasts. Forefront of coastal monitoring, developing numerous innovations in instrumentation, system control and management, computer hardware and software, field equipment, and installation techniques. Operated by Ocean Engineering Research Group, part of Integrative Oceanography Division at Scripps Institution of Oceanography. CDIP measures, analyzes, archives and disseminates coastal environment data for use by coastal engineers, planners and managers, as well as scientists and mariners." . + +SCR:024650 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UCSD WIFIRE" ; + NIFRID:synonym "UCSD WIFIRE Lab", + "WIFIRE Lab" ; + definition: "Consortium of UC San Diego organizations and number of partnerships including university collaborators, industry partners, fire departments, utilities, State’s CalOES and CPUC. Develops science driven technologies with fire management community using collaborative workflows integrating science and AI. Provides real time fire modeling and predictions for firefighters. Harnesses emerging AI techniques to offer novel way to approach spatial heterogeneity and upgrading of data." . + +SCR:024651 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "UC Davis Library" ; + NIFRID:synonym "University of California Davis Library" ; + definition: "Collections include print and ebooks, newspapers, maps, photographs, art, historical archives, and other materials in physical and digital formats. Provides campuswide subscriptions to wide range of licensed resources, from journals and library databases to streaming media, clinical apps, and lab experiment videos. Offers access to UC collection as part of University of California." . + +SCR:024652 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2535" ; + rdfs:label "New York Institute of Technology NYIT Visualization Center Core Facility" ; + NIFRID:synonym "New York Institute of Technology NYIT Visualization Center", + "NYIT Visualization Center" ; + definition: "Core provides instruments including micro-computed tomography scanner, non-contact 3D optical profiler , and high powered workstations." . + +SCR:024653 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2536" ; + rdfs:label "Broad Institute Imaging Platform Core Facility" ; + NIFRID:synonym "Broad Institute Broad Institute Imaging Platform", + "Broad Institute Imaging Platform" ; + definition: "Core to help users turn images into answers by offering assistance and training with open source image analysis tools, creating custom image analysis workflows, and creating custom software for image analysis when needed." . + +SCR:024654 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PyEGA" ; + NIFRID:synonym "Python European Genome-phenome Archive" ; + definition: "Software Python tool for viewing and downloading files from authorized European Genome-phenome Archive datasets. Python based EGA download client." . + +SCR:024655 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2537" ; + rdfs:label "University of Connecticut Health Center for Cell Analysis and Modeling Microscopy Core Facility" ; + NIFRID:synonym "CCAM Microscopy Facility", + "CCAM-Microscopy", + "UConn Health CCAM Microscopy Facility", + "University of Connecticut Health Center CCAM-Microscopy" ; + definition: "CCAM Microscopy Facility provides access to equipment for quantitative fluorescence imaging applications. Instruments include laser scanning confocal microscopes equipped with 34 channel highefficiency QUASAR detectors. One of these microscopes supports nonlinear optical excitation, fluorescence correlation spectroscopy, and fluorescence lifetime imaging microscopy. Additionally, there is a light sheet microscope available for micro/mesoscale 3D imaging. The Zeiss Elyra 7 microscope is capable of total internal reflection fluorescence microscopy and supports several super resolution techniques such as lattice structured illumination microscopy, stochastic optical reconstruction microscopy, 3D photoactivated localization microscopy, and DNA points accumulation for imaging in nanoscale topography." . + +SCR:024656 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ATAC Pipeline" ; + NIFRID:synonym "ATAC", + "atac", + "atac pipeline" ; + definition: "Software pipeline developed in collaboration with the BRAIN Initiative Cell Census Network, BRAIN Initiative Cell Atlas Network, and SCORCH. Supports processing of 10x single-nucleus data generated with 10x Multiome ATAC-seq (Assay for Transposase-Accessible Chromatin) assay." . + +SCR:024657 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_LMD7" ; + rdfs:label "Leica LMD7 Laser Microdissection microscope" ; + NIFRID:synonym "Leica LMD7" ; + definition: "Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. LMD7 provides higher laser power. Suited to dissect any kind of tissue independent of its size or shape." . + +SCR:024658 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_LMD6" ; + rdfs:label "Leica LMD6 Laser Microdissection microscope" ; + NIFRID:synonym "Leica LMD6" ; + definition: "Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. Leica LMD6 is for standard tissue dissection. Used for standard applications dissecting soft tissues such as brain, liver, or kidney." . + +SCR:024659 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_STELLARIS 8 DIVE" ; + rdfs:label "Leica STELLARIS 8 DIVE multiphoton microscope" ; + NIFRID:synonym "Leica STELLARIS 8 DIVE" ; + definition: "Multiphoton microscope provides flexible multicolor imaging beyond 1 mm in depth with spectrally tunable non-descanned detector to define up to four detection bands simultaneously or unlimited number when imaged sequentially. Possible fluorophore combinations to study complex processes, such as neuronal connectivity, organ structure, dynamic interactions, or spatial relationships of cells and proteins in much more detail." . + +SCR:024660 a "Microscope, functional imaging, investigate cellular physiology,dynamics in living cells, video rate lifetime imaging acquisition,", + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_ STELLARIS 8 FALCON FLIM" ; + rdfs:label "Leica STELLARIS 8 FALCON FLIM microscope" ; + NIFRID:synonym "STELLARIS 8 FALCON FLIM Microscope", + "STELLARIS 8 FAst Lifetime CONtrast Fluorescence Lifetime Imaging Microscope" ; + definition: "Microscope for functional imaging. Used to investigate cellular physiology and to explore dynamics in living cells. Enables video rate lifetime imaging acquisition for rapid kinetic studies in live cells. Adds new dimension of contrast to imaging for biosensing and tracking of interactions between proteins." . + +SCR:024661 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_STELLARIS 8 CRS" ; + rdfs:label "Leica STELLARIS 8 CRS microscope" ; + NIFRID:synonym "Leica STELLARIS 8 CRS Coherent Raman Scattering microscope", + "STELLARIS 8 CRS Coherent Raman Scattering microscope" ; + definition: "Microscope enables to implement label free chemical imaging. Used to study structures that cannot be visualized with traditional fluorescent microscopy methods." . + +SCR:024662 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_STELLARIS 8 STED" ; + rdfs:label "Leica STELLARIS 8 STED microscope" ; + NIFRID:synonym "Leica STELLARIS 8 Stimulated Emission Depletion microscope" ; + definition: "Microscope for imaging beyond the diffraction limit to obtain 2D and 3D nanoscopy results in no time with astounding image quality and resolution, while protecting sample. STED super resolution allows you to study multiple dynamic events simultaneously." . + +SCR:024663 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_STELLARIS 5" ; + rdfs:label "Leica STELLARIS 5 microscope" ; + definition: "STELLARIS 5 microscope has core system with integrated WLL, combined with proprietary Acousto-Optical Beam Splitter and Power HyD S detectors. Together with the TauSense technology, STELLARIS 5 sets a new standard for the quality of images and quantity of information generated. Imaging with user interface, ImageCompass." . + +SCR:024664 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_STELLARIS 8" ; + rdfs:label "Leica STELLARIS 8 microscope" ; + definition: "STELLARIS 8 microscope with core system addition of spectrum WLL and specialized detector options of Power HyD family to expand range of confocal applications. Can be combined with all Leica Microsystems modalities, including FAst Lifetime CONtrast (FALCON), Deep In Vivo Explorer (DIVE), STED, Digital Light Sheet (DLS) and CARS. STELLARIS 8 new features maximize the potential of these modalities." . + +SCR:024665 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Noraxon myoMuscle" ; + NIFRID:synonym "myoMuscle", + "Noraxon myoMuscle software" ; + definition: "Software tool for analyzing kinesiological data obtained from Noraxon Ultium EMG system, as well as older Noraxon legacy electromyography systems. Enables detailed insight for performance enhancement, injury prevention, and neuromuscular biofeedback." . + +SCR:024666 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Artinis Medical Systems Oxysoft" ; + definition: "Software application used to collect, store, view, and analyse all necessary data from the Brite Family devices, PortaMon, PortaLite, OctaMon and OxyMon developed by Artinis Medical Systems and highly customisable to individual requirements." . + +SCR:024667 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Wattbike Expert" ; + definition: "Software to scientifically analyse Wattbike sessions on Windows PC or Laptop, while Power Cycling is perfect for group training in health clubs and gyms." . + +SCR:024668 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Multitron Incubation Shaker" ; + NIFRID:synonym "Multitron Standard Incubation Shaker" ; + definition: "Shaker for cultivation of microorganisms and cell cultures provides homogeneous conditions for cultivation up to 63 liters or 23 000 batches in parallel in less than square meter of space." . + +SCR:024669 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Climate engine" ; + definition: "Climate Engine App is no-code solution for on-demand cloud computing and visualization of climate and satellite Earth Observation data. Provides rainfall, maximum and minimum temperature daily data." . + +SCR:024670 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Franklin" ; + definition: "Connectivity hub across medical genetics domain. Network of genomic information. Supports all vendors and workflows and thus enables any genetic professional to deliver more accurate, more actionable data insights." . + +SCR:024671 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_STELLARIS 5 Cryo" ; + rdfs:label "Leica STELLARIS 5 Cryo Confocal Light Microscope" ; + NIFRID:synonym "STELLARIS 5 Cryo", + "STELLARIS 5 Cryo Confocal Light Microscope" ; + definition: "Confocal light microscope system to target area of interest for cryo-electron tomography." . + +SCR:024672 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MapMyCells" ; + NIFRID:synonym "Allen MapMyCells" ; + definition: "MapMyCells maps single cell and spatial transcriptomics data sets to massive, high-quality, and high-resolution cell type taxonomies. It enables speeding up the creation of brain reference atlases by facilitating the integration of datasets from the scientific community with a shared reference. MapMyCells is part of the growing Brain Knowledge Platform. Its key advantage is scale: researchers can provide up to 327 million cell-gene pairs from their own data, a huge leap forward for working with whole-brain datasets. Allen Institute and its collaborators continue to add new reference taxonomies and algorithms to MapMyCells." . + +SCR:024673 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Instant Clue" ; + definition: "Software suite for interactive data visualization and analysis. Python based desktop application using PyQt6 library for data visualization and analysis." . + +SCR:024674 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SlicerMorph" ; + definition: "Open and extensible platform to retrieve, visualize and analyse 3D morphology.Extension to import microCT data and conduct 3D morphometrics in Slicer. Used for data import, visualization, measurement, annotation, and geometric morphometric analysis on 3D data, including volumetric scans (CTs and MRs) and 3D surface scans, all within the 3D Slicer application." . + +SCR:024675 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "scCustomize" ; + definition: "Software R package for custom visualizations and functions for streamlined analyses of single cell sequencing." . + +SCR:024676 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NovoExpress" ; + NIFRID:synonym "Agilent NovoExpress", + "NovoExpress flow cytometry software", + "NovoExpress version 1.6.2" ; + definition: "NovoExpress software enables sample acquisition and analysis. User hands-on time is minimized with the walk-away autosampler functionality as well as batch analysis, statistics, and reporting." . + +SCR:024677 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2540" ; + rdfs:label "University of Massachusetts Lowell Microscopy Core Facility" ; + NIFRID:synonym "UML - Microscopy Core Lab", + "University of Massachusetts Lowell UML - Microscopy Core Lab" ; + NIFRID:abbrev "MCL" ; + definition: "Core offers micro-imaging and micro-analysis solutions by providing access to several photon-, scanned probe-, ion beam-, and electron beam-based imaging and analytical instruments, services, and technical expertise for characterization of materials including nano-engineered materials, microelectronics, photonics, biomaterials, and others with applications in life sciences, drug discovery, environmental and energy research. Consultative services are also available." . + +SCR:024678 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2541" ; + rdfs:label "Seattle Children's Research Institute Micro Computed Tomography Imaging and Visualization Lab Core Facility" ; + NIFRID:synonym "SCRI Micro Computed Tomography Imaging and Visualization Lab" ; + definition: "Shared instrument facility that has Bruker Skyscan 1272 ex-vivo microCT that is capable of X-ray imaging at sub-microb resolution. Core provides visualization and image analysis support for researchers, using open-source 3D Slicer biomedical imaging suite." . + +SCR:024679 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2543" ; + rdfs:label "Tulane University TNPRC Virus Characterization, Isolation, Production and Sequencing Core Facility" ; + NIFRID:synonym "Isolation", + "Production and Sequencing Core", + "TNPRC Virus Characterization", + "Tulane University TNPRC Virus Characterization" ; + definition: "Core is divided into virus characterization, isolation, and production part and next generation sequencing part. Virus Characterization, Isolation and Production component provides virus expansion and characterization, viral titer by plaque and TCID50 assays, live virus neutralization and inhibition assays at both BSL-2 and -3 level including SARS-CoV-2. Next Generation Sequencing component provides expertise in next generation sequencing and genomic services including whole genome, epigenetics, targeted amplicons, and 16S metagenomics." . + +SCR:024680 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2542" ; + rdfs:label "Tulane University TNPRC Vector Borne Infectious Disease and Diagnostic Parasitology Core Facility" ; + NIFRID:synonym "TNPRC Vector-Borne Infectious Disease and Diagnostic Parasitology Core", + "Tulane University TNPRC Vector Borne Infectious Disease and Diagnostic Parasitology Core", + "Tulane University TNPRC Vector-Borne Infectious Disease and Diagnostic Parasitology Core", + "Tulane University Tulane National Primate Research Center Vector Borne Infectious Disease and Diagnostic Parasitology Core", + "Vector-Borne Infectious Disease and Diagnostic Parasitology" ; + NIFRID:abbrev "VIDDP" ; + definition: "Vector Borne Infectious Disease core produces tick vectors for research on Lyme disease and other tick borne diseases. Diagnostic Parasitology component provides diagnostic services to clinical veterinarians and core and affiliate investigators when parasitic diseases are suspected in resident nonhuman primates. Services for affiliate investigators include blood parasite detection via microscopic examination of prepared blood smears and quantitative buffy-coat analysis, and intestinal parasite detection via microscopic examination of direct wet mounts, zinc sulfate flotation prepared slides, or parasite specific assays." . + +SCR:024681 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PyPOLAR" ; + definition: "Software Python based app for analyzing polarization resolved microscopy data to measure molecular orientation and order in biological samples." . + +SCR:024682 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PERFect" ; + NIFRID:synonym "Permutation Filtering Package in R" ; + definition: "Software R package as filtering test for microbiome data. Permutation filtering approach to address two unsolved problems in microbiome data processing: (i) define and quantify loss due to filtering by implementing thresholds and (ii) introduce and evaluate a permutation test for filtering loss to provide a measure of excessive filtering." . + +SCR:024683 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "corrplot" ; + definition: "Software R package as visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.Used for graphical display of correlation matrix, confidence interval. Contains some algorithms to do matrix reordering. Good at details, including choosing color, text labels, color labels, layout, etc." . + +SCR:024684 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BICAN Specimen Portal" ; + definition: "Web application that tracks the status of the BICAN consortium tissue samples and related data." . + +SCR:024685 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NCI SEER Cancer Statistics Review" ; + NIFRID:synonym "and End Results Cancer Statistics Review", + "Epidemiology", + "National Cancer Institute SEER Cancer Statistics Review", + "NIH NCI SEER Cancer Statistics Review", + "NIH NCI Surveillance", + "SEER Cancer Statistics Review" ; + definition: "Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States." . + +SCR:024686 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NCI Lymphoid Neoplasm Recode 2020 Revision Definition" ; + NIFRID:synonym "Lymphoid Neoplasm Recode 2020 Revision Definition", + "National Cancer Institute Lymphoid Neoplasm Recode 2020 Revision Definition", + "NIH NCI Lymphoid Neoplasm Recode 2020 Revision Definition" ; + definition: "Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry." . + +SCR:024687 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NCI Site Recode ICD-O-3/WHO 2008 Definition" ; + NIFRID:synonym "National Cancer Institute Site Recode ICD-O-3/WHO 2008 Definition" ; + definition: "Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry." . + +SCR:024688 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MEBOCOST" ; + definition: "Software Python package to predict metabolite mediated cell-cell communications by single-cell RNA-seq data. Used for inferring metabolite, such as lipid, mediated cell-cell communication events using single-cell RNA-seq data." . + +SCR:024689 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Planet Labs PBC API" ; + NIFRID:synonym "PLANET APIS" ; + definition: "Portal provides everything needed to start using Planet services. Planet Application Program Interface to retrieve Planet Labs PBC's satellite images and products." . + +SCR:024690 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DeepGOPlus " ; + definition: "Software application for predicting protein functions from protein sequences using deep neural networks combined with sequence similarity based predictions." . + +SCR:024691 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "getorf" ; + NIFRID:synonym "EMBOSS getorf" ; + definition: "Web application to find and extract open reading frames (ORFs). Used to find and output sequences of open reading frames in one or more nucleotide sequences." . + +SCR:024692 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "dbEMT 2" ; + NIFRID:synonym "dbEMT2.0", + "Epithelial Mesenchymal Transition Gene database" ; + definition: "Database to establish comprehnsive gene resource for epithelial-mesenchymal transition." . + +SCR:024693 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SimpleITK" ; + NIFRID:synonym "Simple Insight Segmentation and Registration Toolkit" ; + definition: "Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms." . + +SCR:024694 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "qmazda" ; + definition: "Software package for digital image analysis. Used to search for optimal methods for image classification and segmentation. Computes shape, color and texture descriptors of arbitrary regions of interest. Color analysis includes RGB, CMY, HSY, YIQ, YUV, CIELab and CIEXYZ models. Texture feature extraction algorithms include co-occurrence matrix, run-length matrix, autoregression model, brightness distribution statistics, local binary patterns, histogram of oriented gradients, Haar and Gabor transforms. Enables calculation of morphological features such as moments of inertia, Feret diameters, ratios of Danielson, Blair-Bliss or Malinowska, and many others. Implements algorithms of discriminant analysis and data classification such as linear discriminant analysis, mutual information, convex decision boundary and support vector machines." . + +SCR:024695 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Noldus Erasmus Ladder" ; + NIFRID:synonym "Erasmus Ladder" ; + definition: "System consists of hardware and software for assessment of motor performance and motor learning in mice. Hardware includes two goal boxes with horizontal ladder in between. Touch sensitive rungs of the ladder make it possible to measure step durations and step types. ErasmusLadder software controls experiments by sending protocol and start command to apparatus. Sessions are performed automatically, and afterwards, data is sent back to software for storage and analysis." . + +SCR:024696 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Noldus PhenoTyper" ; + NIFRID:synonym "PhenoTyper" ; + definition: """System designed to facilitate behavioral observations in home cage environment. Instrumented observation cage to measure and test behavior of laboratory rodents. +Device comes with PhenoTyper top unit which included lighting and camera, both powered by EthoVision XT, and range of optional sensors and stimuli.""" . + +SCR:024697 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Focinator" ; + NIFRID:synonym "Focinator V2" ; + definition: "Open source software tool providing automated analysis of foci images including foci counting and colocalization of foci. Focinator v2-0 is able to perform multi channel analysis of four channels and evaluation of protein-protein colocalization by comparison of up to three foci channels. This enables for example the quantification of foci in cells of specific cell cycle phase." . + +SCR:024698 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Pyradigm" ; + definition: "Software Python package to arbitrarily combine and subset datasets, while ensuring dataset integrity and automatically updating their description and other provenance for neuroscience and neuroimaging applications where each sample needs to be uniquely identified . Container data structure to encapsulate machine learning dataset with all the key info necessary." . + +SCR:024699 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "microbiome" ; + definition: "Software R package for use in microbiome analysis. Used to provide comprehensive collection of tools and tutorials, with particular focus on amplicon sequencing data." . + +SCR:024700 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "Center for Sudden Unexpected Death in Epilepsy Research", + "Center for SUDEP Research" ; + definition: "NIH funded center to provide system for sharing multimodal epilepsy data for Sudden Unexpected Death in Epilepsy. Modality Epilepsy Data Capture and Integration System (MEDCIS) is cross cohort query interface for SUDEP (Sudden Unexpected Death in EPilepsy) research." . + +SCR:024701 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "rpy2" ; + definition: "Software interface to use R from Python." . + +SCR:024702 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "httk" ; + NIFRID:abbrev "high throughput toxicokinetics" ; + definition: "Software R package for high-throughput toxicokinetics. Pre-made models that can be rapidly tailored to various chemicals and species using chemical specific in vitro data and physiological information. Used for prediction toxicokinetics (chemical absorption, distribution, metabolism, and excretion by the body)." . + +SCR:024703 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Expasy Translate " ; + NIFRID:synonym "Translate" ; + definition: "Web tool for translation of nucleotide sequence to protein sequence." . + +SCR:024704 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Ensembl Covid-19" ; + definition: "Ensembl SARS-Cov2 data portal." . + +SCR:024705 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Stereo Investigator" ; + NIFRID:synonym "MBF Bioscience Stereo Investigator", + "Stereo Investigator system" ; + definition: "System provides means to make quantification of number, length, area, and volume of cells, subcellular and macro structures in tissue specimens. Used to make discoveries in numerous areas of neuroscience, including neurodegenerative diseases, addiction, autism, neuropathy, memory, and behavior, as well as other research fields including pulmonary and kidney research, and toxicology." . + +SCR:024706 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Zeiss Axio Imager M2" ; + NIFRID:synonym "Axio Imager M2" ; + definition: "Upright microscope platform for Life Science Research. System platform tailored to materials analysis tasks. System features include Universal stand transmitted-light; Motorized: luminous field stop; Light manager;Contrast manager; Motorized z-drive with 25nm step size; Reflected-light beam path; ACR for objectives; Apotome 3; 2- und 3-plate scanning stages; 2 TV tube motorized; Automatic image acquisition and analysis; 3D Imaging; Medium sample throughput; Multi-user environment." . + +SCR:024707 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Narishige IM-300 Microinjector " ; + NIFRID:synonym "IM-300 Microinjector" ; + definition: "Multi-functional, motor-driven injector for precise control of small volumes. " . + +SCR:024708 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Leica Angle Two Computer Assisted Stereotaxic System" ; + NIFRID:synonym "Angle Two™ system", + "Leica Angle Two™ Computer-Assisted Stereotaxic System" ; + definition: "System used for stereotaxic surgery on small animals (mice and rats)." . + +SCR:024709 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_CM120" ; + rdfs:label "Philips/FEI CM120 BioTwin Transmission Electron Microscope" ; + NIFRID:synonym "FEI CM120 Biotwin", + "FEI/PHILIPS CM120 TEM", + "Philips CM120 Biotwin Lens", + "Philips/FEI CM120 Bio Twin Transmission Electron Microscope" ; + definition: "Transmission electron microscope with maximum acceleration voltage of 120 kv.Microscope primarily used for sample screening." . + +SCR:024710 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Branson Digital Sonifier " ; + definition: "Digital sonifier to disrupt cells, bacteria, spores, or tissue. Ideal for initiating and accelerating chemical, biochemical, and physical reactions, and for degassing liquids. Used to prepare emulsion to 0.01 micron, homogenize immiscible liquids, polymerize some materials, and depolymerize others." . + +SCR:024711 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2545" ; + rdfs:label "University of Nebraska Lincoln Flow Cytometry Core Facility" ; + NIFRID:synonym "Flow Cytometry Core Facility" ; + definition: "Provides flow cytometry services. Instruments include Beckman Coulter CytoFLEX SRT sorter and CytoFLEX LX, as well as NanoAnalyzer from NanoFCM. Facility staff are able to assist with everything from experimental design, instrument training, sample collection, and data analysis." . + +SCR:024712 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Sample specific miRNA regulation" ; + NIFRID:synonym "Sample-specific miRNA regulation (Scan)" ; + NIFRID:abbrev "Scan" ; + definition: "Software application for scanning sample specific miRNA regulation from bulk and single cell RNA sequencing data." . + +SCR:024713 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "microbeMASST" ; + definition: "Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns." . + +SCR:024715 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SwinT-fairSIM" ; + definition: "This repository contain the source code for the denoising of SR-SIM images." . + +SCR:024716 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Machine Learning Cumulative Performance Score for Classification Problems" ; + NIFRID:synonym "MLcps: Machine Learning Cumulative Performance Score for Classification Problems" ; + NIFRID:abbrev "MLcps" ; + definition: "Machine Learning Cumulative Performance Score (MLcps), a novel evaluation metric for classification problems. MLcps integrates several pre-computed evaluation metrics into a unified score, enabling a comprehensive assessment of the trained model's strengths and weaknesses. We tested MLcps on four publicly available datasets, and the results demonstrate that MLcps provides a holistic evaluation of the model's robustness, ensuring a thorough understanding of its overall performance." . + +SCR:024718 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ToxCodAn-Genome" ; + definition: "ToxCodAn-Genome is a computational tool designed to annotate toxin genes in genomes of venomous lineages." . + +SCR:024719 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "X-omics ACTION demonstrator multi-omics analysis workflow" ; + definition: "Software application as multi-omics data analysis workflow. Comprises genome-wide DNA methylation, targeted metabolomics and behaviour data pre-processing, and integrative analysis methods. Individuals of a cohort are clustered using Similarity Network Fusion (SNF), latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) and Multiple Correspondence Analysis (MCA), and correlations between -omics and phenotype dimensions are determined in downstream analyses including results visualisation." . + +SCR:024720 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Vulture" ; + definition: "Software scalable cloud based pipeline that performs microbial calling for single cell RNA sequencing data, enabling meta analysis of the single cell host microbial studies from AWS Open Data and other public domain." . + +SCR:024721 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Pep2TCR" ; + definition: "Web tool for CD4 TCR specificity prediction and biology applications. Used for accurate prediction of CD4 T cell receptor binding specificity through transfer learning and ensemble approach. Repository comprises codes of Pep2TCR, providing comprehensive guidance for researchers interested in Pep2TCR." . + +SCR:024722 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "TheBehaviourForum.org" ; + definition: "Portal for discussion of scientific matters relating to use of home cages to behavioural research in laboratory animals, including experimental procedures, use of equipment, problem solving, ethical considerations, job offers and advertisement of community events." . + +SCR:024723 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2553" ; + rdfs:label "University of Chicago MRI Research Center Core Facility" ; + NIFRID:synonym "University of Chicago MRI Research Center" ; + definition: "MRI Research Center houses magnetic resonance scanners and highly qualified experienced staff for support of research projects with MR imaging component." . + +SCR:024724 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DSCompare" ; + definition: "Software tool that analyzes, compares and validates analysis and reanalysis datasets with observed dataset using statistical tests such as Mann Whitney (U-test), t-test, F-test, Root Mean Square Error (RMSE), correlation coefficient, BIAS, normalized BIAS, trend, scatter index and maximum anomalies." . + +SCR:024725 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Early Postnatal Developmental Mouse Brain Atlas" ; + NIFRID:abbrev "epDevAtlas" ; + definition: "Suite of open access resources including 3D atlases of early postnatally developing mouse brain and mapped cell type density growth charts, which can be used as standalone resources or to implement data integration. Web platform can be utilized to analyze and visualize the spatiotemporal growth of GABAergic, microglial, and cortical layer-specific cell type densities in 3D. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system with an isotropic resolution of 20 μm (XYZ in coronal plane). Average transformations were conducted at 20 μm voxel resolution by interpolating high resolution serial two photon tomography images from primarily Vip-IRES-Cre;Ai14 mice at postnatal (P) ages P4, P6, P8, P10, P12, and P14. For all ages, anatomical labels from the P56 Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) were iteratively down registered to each early postnatal time point in a non-linear manner, aided by manual parcellations of landmarks in 3D, consistent with the Allen Mouse Reference Atlas Ontology." . + +SCR:024726 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "MTS 2/4 digital microtiter shaker" . + +SCR:024727 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "American Community Survey" ; + NIFRID:abbrev "ACS" ; + definition: "American Community Survey is annual demographics survey program conducted by the U.S. Census Bureau. American Community Survey releases new data every year through variety of data tables. Provides information about other special datasets, such as the ACS Experimental Data, ACS Summary File, and ACS Public Use Microdata Sample files." . + +SCR:024728 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Hematological Malignancy Research Network" ; + NIFRID:abbrev "HMRN" ; + definition: "Network provides information about leukaemias, lymphomas, myelomas, and related blood disorders. The statistics are based on data from the UK, and use the World Health Organization’s Classification for Oncology (ICD-O-3) which currently recognises over 100 different haematological malignancy subtypes." . + +SCR:024729 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "dynamic Functional Connectivity" ; + NIFRID:abbrev "dFC", + "pydfc" ; + definition: "Open source Python toolbox that facilitates the implementation of multi analysis dynamic Functional Connectivity assessment using MRI data." . + +SCR:024730 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Boise State University; Idaho; USA" ; + definition: "Public research university in Boise, Idaho. Founded in 1932 by the Episcopal Church, it became independent junior college in 1934 and has been awarding baccalaureate and masters degrees since 1965. It became public institution in 1969." . + +SCR:024731 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Tractor" ; + NIFRID:synonym "Tractor - Local Ancestry Aware GWAS" ; + definition: "Software tool to enhance Genome Wide Association Studies for diverse cohorts by addressing challenges associated with analyzing admixed populations. Admixed populations are often excluded from genomic studies due to concerns about how to properly account for their complex ancestry.Tractor facilitates the inclusion of admixed individuals in association studies by leveraging local ancestry, allowing for finer resolution in controlling for ancestry in GWAS, and empowering identification of ancestry-specific loci." . + +SCR:024732 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Rare and Atypical Diabetes Network" ; + NIFRID:synonym "Rare and Atypical DIAbetes NeTwork" ; + NIFRID:abbrev "RADIANT" ; + definition: "Portal dedicated to characterizing, discovering and defining rare and atypical forms of diabetes. Network of universities, hospitals and clinics across the United States dedicated to better understanding atypical diabetes. Team of academic institutions and scientists collaborates with physicians and healthcare groups to identify those with atypical diabetes and learn more about their health." . + +SCR:024733 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2547" ; + rdfs:label "Boise State University Fabrication, Characterization, and Testing Core Facility" ; + NIFRID:synonym "Boise State University BSU FaCT Core", + "BSU FaCT Core" ; + NIFRID:abbrev "FaCT" ; + definition: "Core contains instrumentation and expertise for fabrication, characterization, and testing of biomedical devices, sensors, and systems. Core administratively combines 4 existing engineering cores: the Idaho Microfabrication Laboratory (IML); Boise State Center for Materials Characterization (BSCMC); Research Machining and Engineering (RME) center; and Biomechanics and Mechanobiology (BMMB) facility.Offers variety of instruments including 3D printers, deposition and photolithography tools, profilometers, SEM, TEM, light microscopy, confocal microscopy, cell culture. Offers services including design, machining, imaging, etc." . + +SCR:024734 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2548" ; + rdfs:label "University of Massachusetts Lowell Nanofabrication Lab Core Facility" ; + NIFRID:synonym "UML - Nanofabrication Lab", + "University of Massachusetts Lowell UML - Nanofabrication Lab" ; + definition: "Core features 4,200 ft2 Class 100 clean room equipped with over 40 pieces of process and analytical instrumentation for complex research projects that require micro and nano scale fabrication." . + +SCR:024735 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2549" ; + rdfs:label "University of Pennsylvania Bollinger Digital Fabrication Laboratory Core Facility" ; + NIFRID:synonym "Bollinger Digital Fabrication Lab", + "University of Pennsylvania UPenn-Bollinger Digital Fabrication Laboratory", + "UPenn-Bollinger Digital Fabrication Laboratory" ; + definition: "Provides fabrication services and consultations contributing to innovation in teaching, learning, research, and clinical care at the University of Pennsylvania." . + +SCR:024736 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Stanford Cryo-Electron Microscopy Center Core Facility" ; + NIFRID:synonym "Stanford Cryo-Electron Microscopy Center", + "Stanford Cryo-Electron Microscopy Center (cEMc)" ; + NIFRID:abbrev "cEMc" ; + definition: "Core enables macromolecular structure determination, mechanistic investigations, and drug discovery through cryo-electron microscopy. Services include High-resolution data collection for single-particle analysis (SPA), soft-matter research, and tomography; High-throughput cryo sample screening and collection of diagnostic small data sets; Screening negatively stained samples; Training and various levels of assistance for diverse experimental designs, including sample preparation, negative stain screening, and equipment operation; Full-service option for screening and data collection." . + +SCR:024737 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NuAire Laminar Flow Hood" ; + NIFRID:synonym "Laminar Flow Hood" ; + definition: """Laminar Flow Hood offer ISO Class 5 clean air product protection for USP 797 sterile non-hazardous drug compounding applications in pharmacy, microbiology labs, and agricultural research. Hood can be used where clean airflow per ISO 14644-1 is required to prepare injectable drugs, IV solutions, tissue culture, optics, microelectronics, and more. +All workstations use ultra high efficiency motor to provide robust 90 FPM (0,46 m/s) laminar flow of HEPA filtered air to work zone composed of stainless steel walls and work surface made of stainless steel on PVC core.""" . + +SCR:024739 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "org.Hs.eg.db" ; + definition: "Software R package as object for simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to all possible GenBank accession numbers." . + +SCR:024740 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Orthology.eg.db" ; + definition: "Software R package to provide orthology mappings between species, based on NCBI Gene IDs and NCBI orthology mappings." . + +SCR:024741 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "LinearSVC" ; + NIFRID:synonym "Linear Support Vector Classification" ; + definition: "Software application for linear support vector classification. Used in classification problems." . + +SCR:024742 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SingleCellNet" ; + definition: "Software tool to classify single cell RNA-Seq data across platforms and across species." . + +SCR:024743 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SciBet" ; + definition: "Software tool as supervised cell type identifier that accurately predicts cell identity for newly sequenced single cells." . + +SCR:024744 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Parsnip" ; + definition: "Software R package to create and manipulate functions commonly used during modeling e.g. fitting the model, making predictions, etc." . + +SCR:024745 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "IFNepitope" ; + definition: "Web server for predicting and designing interferon gamma inducing epitopes. Users are allowed to paste or upload file with multiple peptide sequences and each sequence would be predicted according to model selected. Used to predict IFN-gamma inducing peptide/epitope in set of peptides or peptide library." . + +SCR:024746 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "IL-10Pred" ; + definition: "Web server to predict IL-10 inducing peptides, where users are allowed to paste or upload file with multiple peptide sequences and each sequence would be predicted according to model selected. Used to design, discover and mapping of peptides that may induce IL-10." . + +SCR:024747 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Deep Learning Toolbox" ; + definition: "Software application provides simple MATLAB commands for creating and interconnecting layers of deep neural network." . + +SCR:024748 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2554" ; + rdfs:label "University of Calgary Live Cell Imaging Laboratory Core Facility" ; + NIFRID:synonym "Snyder Institute- Live Cell Imaging Laboratory", + "University of Calgary Snyder Institute- Live Cell Imaging Laboratory" ; + NIFRID:abbrev "LCI" ; + definition: "Offers advanced imaging technology, as well as training and support personalized to their imaging goals and experience. Provides Technology access and training; Assisted imaging and coaching at every step of the imaging workflow, from sample preparation to data analysis; Pilot experiments and feasibility testing; Developing custom image analysis pipelines; Image analysis consultation and training; Developing and testing new instruments and devices; Full scientific and technological collaborations and partnerships; Offsite coaching, assistance and consulting ; Collaborative projects in academic, health and allied industrial sectors;" . + +SCR:024749 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2550" ; + rdfs:label "University of Maryland School of Medicine Translational Genomics Laboratory Core Facility" ; + NIFRID:synonym "UMSOM-Translational Genomics Laboratory (TGL)", + "University of Maryland Medical Center Midtown Campus Translational Genomics Laboratory", + "University of Maryland Medical Center Midtown Campus Translational Genomics Laboratory Core Facility", + "University of Maryland Medical Center Midtown Campus UMSOM-Translational Genomics Laboratory (TGL)", + "University of Maryland Medical Center Translational Genomics Laboratory" ; + NIFRID:abbrev "TGL" ; + definition: "Core provides range of genomics technologies to support basic, translational, and clinical research.Services support basic research. Clinical assays offered are similar to those offered to support basic research, except that these assays are validated under CLIA, enabling them to be used in clinical decision making process in research protocols and for routine patient care." . + +SCR:024750 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Minerva" ; + NIFRID:synonym "Minerva Author", + "Minerva Story" ; + definition: "Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases." . + +SCR:024751 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "scimap" ; + definition: "Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells." . + +SCR:024752 a NLX:63400, + owl:NamedIndividual ; + definition: "Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events." . + +SCR:024753 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Nutil To Useable" ; + NIFRID:abbrev "N2U" ; + definition: "Web application to transform Nutil outputs and plots it on mouse anatomical heatmap." . + +SCR:024754 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2562" ; + rdfs:label "NCI Center for Cancer Research Genomics Core Facility" ; + NIFRID:synonym "National Cancer Institute Center for Cancer Research Genomics Core", + "NCI CCR Genomics Core", + "NCI Center for Cancer Research Genomics Core" ; + definition: "Core provides access to genomic technologies and Next-Generation Sequencing. Provides DNA and RNA quality control services, user accessible instrumentation, training, consultation services, bioinformatics support, and secure data delivery management." . + +SCR:024755 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "jMORP" ; + definition: "Japanese multi omics reference panel. Provides multidimensional approach to diversity of Japanese population. Public database for plasma metabolome and proteome analyses. Updated to metabolome, genome, transcriptome, metagenome, number of samples, analysis methods of each dataset, expanding links between each layer and links between hierarchies." . + +SCR:024756 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "JOSA" ; + NIFRID:synonym "JOint Spherical registration and Atlas building" ; + definition: "Software tool for joint surface based registration and atlas construction of brain geometry and function.Cortical registration framework that jointly models mismatch between geometry and function while simultaneously learning unbiased population specific atlas." . + +SCR:024757 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FindPlantNLRs" ; + definition: "Software pipeline for annotating predicted Nucleotide binding and leucine rich repeat genes from non-masked genome fasta file input." . + +SCR:024758 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PEPATAC" ; + definition: "Software standardized pipeline for ATAC-seq data analysis with serial alignments. Leverages unique features of ATAC-seq data to optimize for speed and accuracy, and provides several unique analytical approaches. Downstream analysis is simplified by standard definition format, modularity of components, and metadata APIs in R and Python. Restartable, fault-tolerant, and can be run on local hardware, using any cluster resource manager, or in provided Linux containers. We also emphasize the advantage of aligning to the mitochondrial genome serially, which improves alignment and quality control metrics. Includes quality control plots, summary statistics, and variety of data formats." . + +SCR:024759 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "scNAT" ; + definition: "Software application to integrate scRNA-seq and scTCR-seq data to allow for more comprehensive analysis that leverages the strengths of both data types.Repository contains code and information of data used in the paper “scNAT: A deep learning method for integrating paired single cell RNA and T cell receptor sequencing profiles”. Source code for scNAT are in the scNAT folder, the tutorial is in the tutorials folder." . + +SCR:024760 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2563" ; + rdfs:label "American Museum of Natural History Microscopy and Imaging Core Facility" ; + NIFRID:synonym "American Museum of Natural History Microscopy and Imaging Facility" ; + definition: "Shared instrumentation facility at the American Museum of Natural History with tools for X-ray tomography, electron microscopy, confocal microscopy, light microscopy and image analysis. Provides expert assistance in the use of all lab equipment." . + +SCR:024761 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2564" ; + rdfs:label "University of Manchester Mass Spectrometry and Separations Core Facility" ; + NIFRID:synonym "Mass Spectrometry and Separations", + "MS and Sep Facility" ; + definition: "Core is part of the University of Manchester Faculty of Science and Engineering. Facility offers support and services in chemistry, biology and materials. Mass spectrometers including Orbitraps, Ion Mobility, MALDI, DESI, hyphenated LC-MS and GC-MS apparatuses. Other instruments are HPLC systems, UHPLC systems and GC systems." . + +SCR:024762 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2558" ; + rdfs:label "Van Andel Institute VAI Bioinformatics and Biostatistics Core Facility" ; + NIFRID:synonym "VAI Bioinformatics and Biostatistics Core", + "Van Andel Institute VAI Bioinformatics and Biostatistics Core" ; + definition: "Core provides bioinformatics and statistics expertise. Core develops and maintains automated and customizable workflows for processing and analyzing many types of genomic data; supports design of experiments and proposals; assists in preparation of manuscripts, grants and presentations; and provides education and training in use of software and analysis methods.Core can contribute to many types of bioinformatics or statistical projects." . + +SCR:024763 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2565" ; + rdfs:label "University of Chicago PaleoCT Core Facility" ; + NIFRID:synonym "UChicago PaleoCT", + "University of Chicago PaleoCT Lab" ; + definition: "Core utilizes dual tube micro X-ray computed tomography scanner for imaging specimens in fields of paleontology, comparative anatomy, evolution and development, basic biomedical studies, and research in geology and material sciences.It is equipped with 180 kV nano-focus and high power 240 kV micro-focus CT tube. This setup allows to scan very small specimens with high resolution using nano tube or dense fossils using high power tube." . + +SCR:024764 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Opencast" ; + definition: "Open source platform to support management of educational audio and video content. Institutions can use Opencast to produce lecture recordings, manage existing video, serve designated distribution channels, and provide user interfaces to engage students with educational videos." . + +SCR:024765 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MSIsensor-pro" ; + definition: "Software tool for microsatellite instability detection using high throughput sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region sequencing data as input. Introduces multinomial distribution model to quantify polymerase slippages for each tumor sample and discriminative sites selection method to enable MSI detection without matched normal samples." . + +SCR:024766 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MRDetect" ; + definition: "Software application to estimate presence of MRD in plasma cfDNA WGS through evaluation of matched tumour-derived mutations (SNVs or CNVs)." . + +SCR:024767 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FusionAnnotator" ; + definition: "Software tool for annotating fusion transcripts, incorporated into Trinity Cancer Transcriptome Analysis Toolkit utilities, and leveraging databases including CTAT Human Fusion Lib." . + +SCR:024768 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ichorCNA" ; + definition: "Software tool that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. Used to simultaneously segment genome, predict large scale copy number alterations, and estimate tumor fraction of ultra low pass whole genome sequencing sample." . + +SCR:024769 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2560" ; + rdfs:label "LCSB Metabolomics and Lipidomics Platform Core Facility" ; + NIFRID:synonym "LCSB Metabolomics Platform", + "Luxembourg Centre for Systems Biomedicine Metabolomics and Lipidomics Platform" ; + definition: "Metabolomics and Lipidomics Platform facilitates metabolism related research, serving researchers from academia to industry in Luxembourg and beyond. Specializes in analysis of small molecules within complex biological matrices. Analytical infrastructure and broad method portfolio accelerate scientific discoveries in the areas of biology and biomedicine." . + +SCR:024771 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CalculiX" ; + definition: "Software finite element analysis package. Used to solve field problems." . + +SCR:024772 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Feature-specific Information Transfer scripts" ; + definition: "Software application as MATLAB scripts to compute measures of Feature-specific Information Transfer (FIT) and conditional FIT (cFIT). FIT quantifies direction and magnitude of information flow about specific feature S (such as feature of sensory stimulus) between simultaneously recorded brain regions X and Y. cFIT quantifies amount of directed feature information transmitted between regions X and Y that cannot be potentially routed through region Z." . + +SCR:024773 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "LemkeCelottoEtAl_codes_repo" ; + definition: "Software code package associated to the paper: Lemke et al. Information flow between motor cortex and striatum reverses during skill learning. 2023. Quantifies information theoretic quantities used in the associated study." . + +SCR:024774 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bioinformatics platform" ; + definition: "Web service for online data drawing and analysis, personalized data analysis, scientific research mapping, online page/database development and hosting. Used for high throughput sequencing data analysis including eccDNA-seq, MeRIP-seq, circRNA-seq, miRNA-seq, mRNA-seq, LncRNA-seq, piRNA-seq, ChIP-seq, etc." . + +SCR:024775 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2566" ; + rdfs:label "Louisiana State University in Shreveport Research Core Facility" ; + NIFRID:synonym "Research Core Facility" ; + NIFRID:abbrev "RCF" ; + definition: "Core provides access to research services, educational and training opportunities, and technologies including cellular metabolism, flow cytometry, fluorescence, confocal, super resolution confocal microscopy, next generation sequencing, and real-time PCR. Provides assistance with all aspects of these technologies, including experimental design, protocol optimization, instrument operation, and data analysis." . + +SCR:024776 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2568" ; + rdfs:label "Louisiana State University in Shreveport Animal Models and Histology Core Facility" ; + NIFRID:synonym "Animal Models and Histology Core", + "Louisiana State University in Shreveport Animal Models and Histology Core" ; + definition: "Core provides services for mouse genotyping and tissue histology, access to tools for analyzing cardiovascular function, data analysis, expertise and training. Services include genotyping using PCR or RT PCR, histology services with tissue processing, paraffin-embedding and sectioning, along with several cardiovascular relevant histological stains such as Picrosirius Red and Masson Trichrome." . + +SCR:024777 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2567" ; + rdfs:label "Louisiana State University in Shreveport Small Animal Imaging Core Facility" ; + NIFRID:synonym "Louisiana State University in Shreveport Small Animal Imaging Facility", + "Small Animal Imaging Facility" ; + NIFRID:abbrev "SAIF" ; + definition: "Core provides imaging support to investigators who use small animal models in their research. Offers bioluminescence and fluorescence imaging, X-ray imaging, computed tomography, and positron emission tomography. Core provides imaging support services for investigators, including assistance in experimental design, conducting animal studies including anesthetization and imaging acquisition, and processing and interpreting imaging data." . + +SCR:024778 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2569" ; + rdfs:label "Louisiana State University in Shreveport Redox Molecular Signaling Core Facility" ; + NIFRID:synonym "CoBRE Redox Molecular Signaling Core", + "Redox Molecular Signaling Core" ; + definition: "Facility includes Analytic Redox Biology and Molecular Signaling Sub-Cores. Provided services include measurements of reactive oxygen species, reactive nitrogen species, reactive sulfide species, protein, peptides, metabolites, and lipids in cell culture and tissue samples. High-performance liquid chromatography systems, coupled with UV-vis and fluorescence detectors to quantify cellular and mitochondrial superoxide production, hydrogen sulfide pools (free sulfide, sulfide bound to transitional metals, and sulfane sulfur), and thiols (glutathione, GSH/GSSG, cysteine, cystine, homocysteine, persulfides, and glutathionylation).Instruments include Sievers NO Analyzer (NOA 280i, GE), Agilent 8890 GC and 8335 sulfur chemiluminescence detector ,Thermo Scientific Orbitrap Exploris 480 and SCIEX Triple Quad 7500 mass spectrometer. Molecular Signaling Sub-Core offers services for molecular cloning and site-directed mutagenesis, design and production of vectors for CRISPR/Cas9 modification of vascular cells, services for endothelial, smooth muscle, and cardiac myocyte cell isolation, for generation of vascular cell lines, and for lentivirus production for transient or stable modification of cardiovascular cells, access to equipment and expertise for studying cellular effects of hypoxia/reoxygenation injury (Coy Hypoxic Chamber, CLARIOstar Spectrofluorometer), for automated capillary Western blot analysis (ProteinSimple Jess Simple Western), and for high-resolution fluo-respirometry to study mitochondrial function (Oroboros O2k modular system)." . + +SCR:024779 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2571" ; + rdfs:label "Louisiana State University in Shreveport CAIPP Bioinformatics and Modeling Core Facility" ; + NIFRID:synonym "CAIPP Bioinformatics and Modeling Core" ; + definition: "Core supports data analysis, network modeling, and data science research. Provides training and education opportunities." . + +SCR:024780 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2572" ; + rdfs:label "Cincinnati Children's Hospital Bionutrition Research Core Facility" ; + NIFRID:synonym "Bionutrition Research Facility", + "Cincinnati Children's Hospital Bionutrition Research Facility" ; + definition: "Facility works with investigators to obtain and analyze high-quality nutrition and body composition data from study participants. Staff and facilities are located in the Schubert Research Clinic at Cincinnati Childrens Hospital. Core provides diet assessment services." . + +SCR:024781 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2570" ; + rdfs:label "Louisiana State University in Shreveport CAIPP Immunophenotyping Core Facility" ; + NIFRID:synonym "CAIPP Immunophenotyping Core" ; + definition: "Immunophenotyping core provides services for isolation of cellular populations from tissues, automated quantification of cell numbers, quantification of GFP, DAPI, RFP, Cy5 or Cy7 positive populations, automated quantification of cytokine concentration in supernatants and biological samples, and flow cytometric and microscopic assay development and execution.Provides training and education opportunities." . + +SCR:024782 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Evident" ; + NIFRID:synonym "Evident Scientific", + "Olympus Scientific Solutions" ; + definition: "Company for development, manufacture, sale and provision of solutions for biological microscopes, industrial microscopes, industrial endoscopes, non-destructive inspection equipment, X-ray analyzers, etc." . + +SCR:024783 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_VS200" ; + rdfs:label "Olympus VS200 Slide Scanner" ; + NIFRID:synonym "SLIDEVIEW VS200 research slide scanner", + "VS200 Slide Scanner" ; + NIFRID:abbrev "VS200" ; + definition: "Flexible system that supports various slide sizes, different objectives, SILA optical sectioning device, oil dispenser, cameras, loaders, and LED/laser light sources with multiple filter sets. VS200 supports brightfield, darkfield, polarization, phase contrast, and fluorescence, with possibility to scan sample using multiple techniques at the same time. VS200 software supports offline analysis, deep learning, 3D deconvolution, and batch conversion to standard file formats. It also supports the NIS-SQL database for data management and the DICOM format for easy integration into lab information management system." . + +SCR:024784 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2589" ; + rdfs:label "University of Manchester Services and Equipment Core Facility" ; + NIFRID:synonym "UoMaH Services and Equipment" ; + definition: "Core to build partnerships with government, National Facilities, industrial and academic stakeholders at Harwell and beyond, to jointly address challenges set by UK’s Industrial Strategy through research and to discover and develop innovative techniques and technologies to enhance facility science, data analytics and workplace safety." . + +SCR:024785 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2590" ; + rdfs:label "University of Manchester X-ray Diffraction Platform Core Facility" ; + NIFRID:synonym "University of Manchester X-ray Diffraction Platform" ; + definition: "Core to bring together community of knowledge and best practise from three Faculty of Science and Engineering Departments: Chemistry, EES and Materials. Provided equipment is housed across numerous parts of campus with bulk being operated from Engineering Building A and Chemistry. Offers technical expertise in techniques such as residual stress analysis, texture analysis, phase identification in crystalline and semi crystalline powders and solid materials, single crystal and small angle scattering. Machines are available for examination of both small specimens and large components, and for wide range of materials." . + +SCR:024786 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2591" ; + rdfs:label "University of Manchester Magnetic Resonance and Related Technology Platform Core Facility" ; + NIFRID:synonym "University of Manchester Magnetic Resonance and Related Technology Platform" ; + definition: "Core is equipped with instrumentation supporting areas of NMR, EPR and related techniques." . + +SCR:024787 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2592" ; + rdfs:label "University of Manchester Corrosion and Materials for Demanding Environments Core Facility" ; + NIFRID:synonym "Corrosion and Materials for Demanding Environments" ; + definition: "Core includes facilities and techniques, supporting exploration of this unique research space. Provides expertise and services for advanced materials and interdisciplinary research activity." . + +SCR:024788 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2593" ; + rdfs:label "University of Manchester Biochemical and Biophysical Sciences Technology Platform Core Facility" ; + NIFRID:synonym "University of Manchester Biochemical and Biophysical Sciences Technology Platform" ; + definition: "Core includes range of facilities that support all biological related activity in Faculty of Science and Engineering. We work at the interface of physical sciences, engineering and biology and provide major link to facilities in Faculty of Biology, Medicine and Health. Supports research activities in areas that include physical understanding of biological systems, engineering biomolecules and biological processes, biomaterials and environmental sciences." . + +SCR:024789 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2594" ; + rdfs:label "University of Manchester Surface Characterisation Core Facility" ; + definition: "Core includes range of surface analysis techniques and supportive instruments across three research institutes: Henry Royce Institute, Photon Science Institute, and National Graphene Institute." . + +SCR:024790 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2595" ; + rdfs:label "University of Manchester Advanced Manufacturing Platform Core Facility" ; + definition: "Core offers services, teaching and collaboration between Laser Processing Research Laboratory, Manufacturing Technology Research Laboratory and Bioenergy laboratory." . + +SCR:024791 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Recentrifuge" ; + definition: "Software application for robust comparative analysis and contamination removal for metagenomics. Implements robust method for removal of negative control and crossover taxa from the rest of samples. Analyzes results from taxonomic classifiers using interactive charts with emphasis on confidence level of classifications. In addition to contamination subtracted samples, provides shared and exclusive taxa per sample, thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics." . + +SCR:024792 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MCFLIRT" ; + NIFRID:synonym "MC FMRIB's Linear Image Registration Tool", + "Motion Correction FMRIB's Linear Image Registration Tool" ; + definition: "Software intra-modal motion correction tool designed for use on fMRI time series for linear (affine) inter- and inter-modal brain image registration." . + +SCR:024793 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2596" ; + rdfs:label "University of Nevada Reno School of Medicine High Spatial and Temporal Resolution Imaging Core Facility" ; + NIFRID:synonym "University of Nevada High Spatial and Temporal Resolution Imaging Core" ; + NIFRID:abbrev "HSTRI Core" ; + definition: "Core provides high spatial and temporal resolution imaging methodologies and instrumentation for studying cellular structure, signaling pathways, and function in health and disease. Offers education, training and expertise in advising investigators in the use of the new technologies." . + +SCR:024794 a NLX:152328, + owl:NamedIndividual ; + oboInOwl:hasDbXref "GRID grid.266826.e", + "ISNI 0000 0000 9216 5478", + "Wikidata Q8215036" ; + rdfs:label "University of New England; Biddeford; USA" ; + definition: "Private research university in Maine with campuses in Portland and Biddeford, as well as study abroad campus in Tangier, Morocco. " . + +SCR:024795 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_FB11201" ; + rdfs:label "Fisherbrand 112xx Series Advanced Ultrasonic Cleaner" ; + NIFRID:synonym "Fisher Advanced Ultrasonic Cleaners" ; + definition: "Dual frequency sonicating water bath with temperature control." . + +SCR:024796 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Benchmark Scientific Orbi-Shaker MP4 orbital shaker" ; + NIFRID:synonym "Orbi-Shaker MP4", + "Orbi-shaker MP microplate shaker with 4 position platform" ; + definition: "Orbital shaker for up to 4 microplates with digital speed control.Designed with 3mm mixing orbit, optimized for thorough mixing of microplates and/or PCR plates. Up to four plates can be placed on the included platform." . + +SCR:024797 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2588" ; + rdfs:label "University of Wisconsin Madison Biotechnology Center Animal Models Core Facility" ; + NIFRID:synonym "University of Wisconsin Madison Biotechnology Center Animal Models Core", + "UW Biotechnology Center-Animal Models Core" ; + definition: "Core provides support for generation of novel animals including mice, rats and swine models using CRISPR or transgenic technology, cryopreservation, rederivation, and IVF recovery of rodent animal models." . + +SCR:024798 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "bulkGAN" ; + definition: "Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework." . + +SCR:024799 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "HDOCK server" ; + NIFRID:synonym "HDOCK" ; + definition: "Web server for protein-protein and protein-DNA/RNA docking based on hybrid strategy. With input information for receptor and ligand molecules either amino acid sequences or Protein Data Bank structures, the server automatically predicts their interaction through hybrid algorithm of template-based and template-free docking." . + +SCR:024800 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2576" ; + rdfs:label "University of Manchester National X-ray Computed Tomography Core Facility" ; + NIFRID:synonym "University of Manchester UoM-FSE-Section of The National X-ray Computed Tomography Facility", + "UoM-FSE-Section of The National X-ray Computed Tomography Facility" ; + NIFRID:abbrev "NXCT" ; + definition: "Provides access and expert support to run cutting-edge 3D and 3D time-lapse imaging experiments.Provides access to X-ray instruments, technical support for new and existing users, expertise to design complex experiments, infrastructure and resources to analyse 3D and 4D data.Funded by the Engineering and Physical Sciences Research Council (EPSRC)." . + +SCR:024801 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2584" ; + rdfs:label "University of Manchester Design, Fabrication and Testing Core Facility" ; + NIFRID:synonym "Fabrication & Testing", + "University of Manchester UoM-FSE-Platform of Design", + "UoM-FSE-Platform of Design" ; + definition: "Core supports areas of research from Heavy Structures and Concrete design, fabrication and testing to Non-Destructive Testing, development and construction of novel fibre, polymers and composite materials." . + +SCR:024802 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "XSwap" ; + definition: "Software Python library (C++ backend) for degree preserving network randomization." . + +SCR:024803 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SGAE" ; + NIFRID:synonym "Siamese Graph Autoencoder" ; + definition: "Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics." . + +SCR:024804 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SAIBR" ; + NIFRID:synonym "Spectral Autofluorescence Image Correction By Regression" ; + definition: "Software application as platform independent protocol and FIJI plug-in to correct for autofluorescence using standard filter sets and illumination conditions. Spectral autofluorescence correction method based on simple 2- or 3-Channel images implemented in Python and Fiji. Used for performing spectral autofluorescence correction on biological images." . + +SCR:024805 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Enformer" ; + definition: "Software package provides implementation of the Enformer model and examples on running the model." . + +SCR:024806 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ChromBPNet " ; + definition: "Software application as bias factorized, base-resolution deep learning models of chromatin accessibility." . + +SCR:024807 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "pyBigWig" ; + definition: "Software application as Python extension for quick access to bigWig and bigBed files." . + +SCR:024808 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "cisTarget" ; + definition: "Web application to download database for motif enrichment, motif annotations,cluster-buster implementation, precomputed regions for creating gene-based databases and to download lists of transcription factors for human, mouse and fly, chip-seq tracks annotations." . + +SCR:024809 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Tomtom" ; + definition: "Software motif comparison tool. Compares one or more motifs against database of known motifs, ranks motifs in database and produces alignment for each significant match." . + +SCR:024810 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Cluster-Buster" ; + definition: "Software application for detection of sequences that regulate gene transcription, such as enhancers and silencers, but other types of biological regulation may be mediated by motif clusters too." . + +SCR:024811 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "TF-Modisco " ; + NIFRID:synonym "TF MOtif Discovery from Importance SCOres", + "Transcription-Factor Motif Discovery from Importance Scores" ; + definition: "Software application as algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data." . + +SCR:024812 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "h5py " ; + definition: "Software package provides interface to HDF5 library from Python. The low-level interface is intended to be complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts." . + +SCR:024813 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ipykernel" ; + definition: "Software package provides IPython kernel for Jupyter." . + +SCR:024814 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "EazyDraw" ; + definition: "Software vector based drawing application for desk top publishing with Apple's macOS operating system. Illustration or drawing software application that offers vector-based graphics editing and creation capabilities for creating simple not-photographic drawings, technical diagrams and illustrations such as logos, icons, buttons and stylized art." . + +SCR:024815 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "AutoTube" ; + definition: "Software that quantifies vascular morphometry parameters like area covered by vessels, vessel width, skeleton length and branching or crossing points of vascular networks in tissues and in vitro assays." . + +SCR:024816 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2597" ; + rdfs:label "Creighton University Innovative Genomics and Bioinformatics Core Facility" ; + NIFRID:synonym "Creighton University Innovative Genomics and Bioinformatics Core", + "Innovative Genomics and Bioinformatics Core" ; + NIFRID:abbrev "IGBC" ; + definition: "Provides services for genomics research that range from sequencing to data analysis. Instruments available include Illumina NextSeq 2000, 10x Genomics Chromium iX Controller, Agilent TapeStation 4200, and Qubit Flex Fluorometer." . + +SCR:024817 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2600" ; + rdfs:label "Creighton University Drug Discovery and Delivery Core Facility" ; + NIFRID:synonym "Creighton University CU-DDD Core - Drug Design", + "CU-DDD Core - Drug Design", + "Synthesis and Validation Subcore" ; + NIFRID:abbrev "DDDC" ; + definition: "Core subcores include Drug Design, Synthesis and Validation Laboratory, ADMETox Laboratory,Zebrafish Laboratory. Offers experts and technologies to provide services tailored to drug development needs. Can assist with drug screening and design from small molecules to peptides, development and applying methodologies to synthesize drug candidate, and validate its chemical structure and purity. Offers services to detect and quantify drugs in biological samples. Follow-up studies can be conducted using services of ADMETox subcore to characterize drug candidate toxicity, efficacy, and pharmacokinetic and pharmacodynamic profiles, and assist in developing appropriate formulation and delivery approaches." . + +SCR:024818 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2599" ; + rdfs:label "Beth Israel Deaconess Medical Center Glycomics Core Facility" ; + NIFRID:synonym "Beth Israel Deaconess Medical Center Glycomics Core", + "Glycomics Core" ; + definition: "Glycomics Core provides services, instrumentation and expertise in glycomics. Services include Glycan Microarrays,Glycan analysis by Mass Spectrometry, Distribution of specific reagents,Trainings." . + +SCR:024819 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2598" ; + rdfs:label "Beth Israel Deaconess Medical Center Precision RNA Medicine Detection Unit Core Facility," ; + NIFRID:synonym "Beth Israel Deaconess Medical Center Detection Unit Precision RNA Medicine Core", + "BIDMC Detection Unit Precision RNA Medicine Core", + "Detection Unit Precision RNA Medicine Core" ; + definition: "Detection Unit of ncRNA Core can perform highly sensitive microRNA detection platform for diverse biospecimens.Technology is based on qPCR and uses single plate panel for simultaneous detection of 384 miRNAs using MIRXES technology. Services offered by unit include Detection of miRNA, Analysis of dysregulated miRNA,Consultation and support for non-coding RNA biology and research." . + +SCR:024820 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ExperimentHub" ; + definition: "Software R package provides central location where curated data from experiments, publications or training courses can be accessed." . + +SCR:024821 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Drugmonizome" ; + definition: "Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis." . + +SCR:024822 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GREP" ; + NIFRID:synonym "Genome for REPositioning drugs", + "GREP: Genome for REPositioning drugs" ; + definition: "Standalone Python software to quantify enrichment of user-defined set of genes in target of clinical indication categories and to capture potentially repositionable drugs targeting gene set." . + +SCR:024824 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ggbreak" ; + definition: "Software package provides several scale functions to break down ‘gg’ plot into pieces and align them together with gap plot or without (wrap plot or cut plot) ignoring subplots. Package was first designed to set breakpoints for truncating plot to shrink outlier long branch of phylogenetic tree. Set Axis Break for ggplot2." . + +SCR:024825 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ggrastr" ; + definition: "Software R package to Rasterize Layers for ggplot2." . + +SCR:024826 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "patchwork" ; + definition: "Software R package to combine separate ggplots into same graphic. Composer of Plots." . + +SCR:024827 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Colorectal cancer detection" ; + NIFRID:synonym "ColoPola: Colorectal cancer polarimetric image", + "Polarimetric imaging" ; + definition: "Software application to classify colorectal cancer using ColoPola dataset." . + +SCR:024828 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "spatiAlign" ; + definition: "Software tool as unsupervised contrastive learning model that employs expression of all measured genes and spatial location of cells, to integrate multiple tissue sections. Enables joint downstream analysis of multiple datasets in low-dimensional embeddings and also in reconstructed full expression space. Used for integrative analysis of time-series brain sections, including spatial clustering, differential expression analysis, and particularly trajectory inference that requires corrected gene expression matrix." . + +SCR:024829 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Anton Paar NHT3 Nanoindentation Tester" ; + NIFRID:synonym "NHT³ Nanoindentation Tester" ; + definition: "Used for testing hardness, elastic modulus, creep and other surface properties at nanometer to micrometer scale. Its range is from 0.1 mN to 500mN with no need to wait to reach thermal stable state, and instrument indentation test can be performed immediately after startup." . + +SCR:024830 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_FACSymphony_A1" ; + rdfs:label "BD FACSymphony A1 Cell Analyzer" ; + NIFRID:synonym "BD FACSymphony A1" ; + definition: """Analyzer applies BD FACSymphony instrument technology to reduce background noise and increase detection sensitivity. Features low-noise electronics, high-powered lasers and tight beam spot to support immunophenotyping up to 16 colors. Enables independent analysis of large and small particles on single instrument. Optional small particle detector enables detection of small particles such as extracellular vesicles, viral particle and more. +Compatible with broad portfolio of catalog and custom BD Horizon Brilliant Reagents and BD FACSDiva Software. Permits easy placement on standard lab bench with its compact format.""" . + +SCR:024831 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SpikeHunter" ; + definition: "Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins." . + +SCR:024832 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_BioFlux_1000z" ; + rdfs:label "Fluxion Biosciences BioFlux 1000z" ; + NIFRID:synonym "BIOFLUX 1000Z", + "BioFlux 1000z" ; + definition: "Gives ability to introduce flow to research and drug discovery experiments with in vivo conditions. Microfluidic well plate format opens up multitude of experiments. Customizable BioFlux solutionon for ultimate imaging flexibility. Additional Standard Features to those in BioFlux 200 include Custom automated microscope configuration, User defined camera and Fully integrated control and analysis software." . + +SCR:024833 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_TS420" ; + rdfs:label "Transonic TS420 Perivascular Flow Module" ; + NIFRID:synonym "TS420 Perivascular Flow Module" ; + definition: "TS420 Perivascular Flow Module with Flowprobes to fit every vessel in research models from mice to sheep and even giraffes, provides high resolution blood flow wave forms and arterial/venous flow measurements in mL/min or L/min. Gold Standard for blood flow measurement in cardiovascular research with outputs analog signals compatible with most data acquisition systems. Features plug and play set up routines to calibrate/scale/test and measure. Fit into 400-Series Instrumentation Consoles and compatible to mix and match with other 400-Series Modules. Perivascular Flowprobes are available for small and large vessel sizes, and for acute use and chronic implantation." . + +SCR:024834 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "3D HISTECH PANNORAMIC MIDI II scanner" ; + NIFRID:synonym "3D HISTECH PANNORAMIC MIDI II", + "PANNORAMIC MIDI II" ; + definition: "Automatic digital slide scanner with 12 slide capacity in one run, fluorescence scanning, 9 physical filter cubes and 45 logical fluorescence channels. Powered by PANNORAMIC Scanner Software. Supports Carl Zeiss objectives, achieving up to 43x or 86x magnification and 0.087 µm/pixel resolution within the same instrument, along with advanced FISH scanning technique." . + +SCR:024835 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_ECLIPSE_Ni-U" ; + rdfs:label "Nikon ECLIPSE Ni-U Microscope" ; + definition: "Manual model using halogen light source, manual focus, motorized nosepiece and motorized fluorescence cube turret. Standard model suitable for brightfield observation of pathological specimens and digital imaging." . + +SCR:024836 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2606" ; + rdfs:label "University of Washington I-LABS MEG Brain Imaging Center Core Facility" ; + NIFRID:synonym "I-LABS MEG Brain Imaging Center", + "Institute for Learning and Brain Sciences (I-LABS) MEG Brain Imaging Center", + "MagnetoEncephaloGraphy Brain Imaging", + "MEG Brain Imaging" ; + definition: "Magnetoencephalography facility focusing on children. Equipped with MEGIN TRIUX Neo system with helium recycler, MAGSTIM EEG data acquisition system, Tucker-Davis Technologies RZ6 for stimulus generation, Epson Home Cinema 3200 for video projection, custom video recording system with 4 cameras, Eyelink eyetracker, and Polhemus 3D digitizer." . + +SCR:024837 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "GenomeSpy" ; + definition: "Software visualization grammar and GPU-accelerated toolkit for genomic data. Visualization grammar and GPU-accelerated rendering engine for genomic data. Grammar based toolkit for authoring tailored, interactive visualizations for genomic data analysis." . + +SCR:024838 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "NAVIP" ; + NIFRID:synonym "Neighborhood-Aware Variant Impact Predictor", + "Neighborhood-Aware Variant Impact Predictor (NAVIP)" ; + definition: "Software tool for functional impact prediction for sequence variants. Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the functional consequences." . + +SCR:024839 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "National Primate Research Center Consortium" ; + NIFRID:synonym "NPRC Consortium", + "The National Primate Research Center (NPRC) Consortium", + "The National Primate Research Center Consortium" ; + definition: "NPRC Consortium is collaboration across seven Centers to increase access and promote sharing of NonHuman Primate related resources among biomedical researchers. NPRCs advance missions of NIH Institutes, Centers, and Offices by providing animals, facilities, expertise, and resources required by investigators in disease specific areas. Each Center provides expertise on the use of various NHP species as models of human disease to address specific research projects in major research fields such as infectious diseases, aging, cardiovascular disease, diabetes and metabolic disorders, neuroscience, pediatrics, regenerative medicine, reproductive health, and women’s health. ORIP supports Specific Pathogen Free rhesus macaque colonies at the California,Oregon, Southwest, Yerkes, and Tulane NPRCs and the Caribbean Primate Research Center in Puerto Rico. Additionally, SPF pigtail macaque colonies are maintained at the Washington NPRC and at the Johns Hopkins University School of Medicine." . + +SCR:024840 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "DeepDraw" ; + definition: "Software application for creating scalable muscle spindles dataset based on kinematic data and define action recognition task as benchmark. Training and analysis of hierarchical neural networks to solve recognition task from muscle spindle inputs." . + +SCR:024841 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "World Health Organization Health Action International project on medicine prices and availability" ; + NIFRID:synonym "WHO/Health Action International project on medicine prices and availability" ; + definition: "Project on Medicine Prices and Availability collaborative partnership between WHO and international non-governmental organization Health Action International. Through project, standardized survey methodology for measuring medicine prices, availability, affordability and price components was developed." . + +SCR:024842 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Statistics Sweden" ; + definition: "Organization responsible for official statistics and for other government statistics. Used to develop, produce and disseminate statistics, coordinate system for official statistics in Sweden, conduct long term cooperation projects with statistical offices in developing countries, which are financed by Sida." . + +SCR:024843 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "StatFin database" ; + NIFRID:synonym "StatFin" ; + definition: "Finland's statistical database contains collection of statistical tables on Finnish society and population of Finland including economy, housing, transport, tourism, consumption, prices, wages and salaries, energy, enterprises and other topics." . + +SCR:024844 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "National Prostate Cancer Register of Sweden" ; + NIFRID:synonym "National Prostate Cancer Register (NPCR) of Sweden" ; + NIFRID:abbrev "NPCR of Sweden" ; + definition: "National Prostate Cancer Register of Sweden database." . + +SCR:024845 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RATTEN" ; + NIFRID:synonym "Interactive On Line Report from National Prostate Cancer Register (NPCR) of Sweden" ; + definition: "Online report from NPCR that contains data on prostate cancer care from all healthcare providers in Sweden. Source of knowledge about Swedish prostate cancer healthcare for all stakeholders, patients, healthcare professionals, researchers, administrators and decision makers." . + +SCR:024846 a NLX:63400, + owl:NamedIndividual . + +SCR:024847 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_DNBSEQ-T7" ; + rdfs:label "MGI DNBSEQ-T7 Genetic Sequencer" ; + NIFRID:synonym "DNBSEQ-T7 Sequencer" ; + definition: "Instrument features include High Speed: 22 hrs to 24 hrs for PE150 sequencing; High Flexibility: 4 Flow Cells, PE150, and PE100 at the same time; Ultra-high Throughput: 7 Tb per day; high quality data around the clock." . + +SCR:024848 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "BGI Genomics" ; + definition: "Provider of precision medicine serving customers in more than 100 countries, involving over 2,300 medical institutions. Relying on sequencing and bioinformatics technology, provides clinical molecular diagnostic solutions and high-throughput sequencing research services." . + +SCR:024849 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Innomics Inc." ; + definition: "Provides expertise in multi-omics (Genomics, Transcriptomics, Epigenomics, Proteomics and Metabolomics), offering end-to-end next-generation sequencing and mass spectrometry solutions to researchers and healthcare professionals." . + +SCR:024850 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MoticEasyScan One-FS" ; + NIFRID:synonym "MoticEasyScan One-FS scanning system" ; + definition: "Compact scanner for any digital slide application. Scanning system with FS-Live software suite, optimized for frozen section, cytology, ROSE, and FNA adequacy evaluation, places control into hands of remote pathologist to pilot the system and provide diagnosis without travel time." . + +SCR:024851 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MoticEasyScan Pro 6-FS" ; + NIFRID:synonym "MoticEasyScan Pro 6-FS Scanner System" ; + definition: "MoticEasyScan Pro scanner system scans up to 6 slides in one click and uploads digital slides to your slide management server. Ideal for any application that requires glass slide digitization." . + +SCR:024852 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MoticEasyScan Infinity 102" ; + NIFRID:synonym "MoticEasyScan Infinity 102 Scanning System" ; + definition: "Scanning solution for high volume scanning. Scanner system scans up to 60 slides in one click, providing scanning at 20X and40X magnifications. With Infinity Scanning design, slides can be added to the system without interrupting the scanning process." . + +SCR:024853 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MoticEasyScan Infinity 60" ; + NIFRID:synonym "MoticEasyScan Infinity 60 Scanning System" ; + definition: "Scanning solution for high volume scanning. Scanner system scans up to 60 slides in just one click, providing scanning at 20X and40X magnifications with Infinity Scanning design, slides can be added to the system at any time, without interrupting the scanning process." . + +SCR:024854 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MoticEasyScan Pro 6" ; + NIFRID:synonym "MoticEasyScan Pro 6 Scanning System" ; + definition: "Scanner system scans up to 6 slides in just one click. It scans and uploads high-quality digital slides to your slide management server. Multipurpose scanner for any application that requires glass slide digitization." . + +SCR:024855 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "MoticEasyScan One" ; + NIFRID:synonym "MoticEasyScan One Scanner" ; + definition: "Compact scanner for any digital slide application. This scanning system with FS-Live software suite, optimized for frozen section, cytology, ROSE, and FNA adequacy evaluation, for remote pathologist to pilot the system and provide diagnosis without travel time." . + +SCR:024856 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "Motic" ; + definition: "Company provides innovative microscope and microscopy solutions designed for education, medical, clinical, and industrial needs. Motic Microscopes specializes in designing and manufacturing conventional and digital microscopy solutions. Motic Digital Pathology drives adoption of digital medicine by making whole slide imaging, AI, and software technologies approachable for hospitals and labs everywhere.Motic Electric designs, develops and manufactures High Voltage insulation components for transmission and distribution systems in the electric power industry.Motic Energy strives to lead in smart energy technology through our next-gen management platform, using big data, AI, and cloud technology to create networked energy ecosystem for the world." . + +SCR:024857 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_DM6_B" ; + rdfs:label "Leica DM6 B Upright Microscope" ; + NIFRID:synonym "Leica DM6 B Automated Upright Microscope System" ; + definition: "Leica DM6 B Upright Microscope includes the Leica DFC7000 T Camera and LAS X Software." . + +SCR:024858 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_DM4_B" ; + rdfs:label "Leica DM4 B Upright Microscope" ; + NIFRID:synonym "Leica DM4 B Automated Upright Microscope System" ; + definition: "Leica DM4 B Upright Microscopes are designed specifically for use in clinical and life science research applications. These microscopes simplify your workflow with automated functions and easy-to-use software. The DM4 features 19-mm sCMOS camera imaging port to capture publication quality images and LAS X Navigator Software. Variety of optional accessories are available." . + +SCR:024859 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "cell2location " ; + definition: "Software tool that can resolve fine grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Used for comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics." . + +SCR:024860 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RcisTarget" ; + definition: "Software R package to identify transcription factor binding motifs over represented on gene list. RcisTarget selects DNA motifs that are significantly over represented in surroundings of transcription start site of genes in gene-set, then annotates to TFs and those that have high Normalized Enrichment Score are retained and than candidate target genes are predicted. Used to identify transcription factor binding motifs enriched on list of genes or genomic regions." . + +SCR:024861 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "StrataQuest" ; + NIFRID:synonym "StrataQuest tissue flow cytometry quantitative analysis system" ; + definition: "Tissue flow cytometry quantitative analysis platform integrates precise quantitative analysis solution at single cell level in tissue provided by HistoQuest/TissueQuest software. Software is compatible with multiple types of tissue and cell samples, enabling quantitative analysis in different biological research fields." . + +SCR:024862 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2603" ; + rdfs:label "Beth Israel Deaconess Medical Center Precision RNA Medicine Delivery Unit Core Facility" ; + NIFRID:synonym "Beth Israel Deaconess Medical Center Precision RNA Medicine Core - Delivery Unit", + "Precision RNA Medicine Core - Delivery Unit" ; + definition: "Delivery Unit offers training and services on the NanoAssemblr Spark, NanoAssemblr Ignite+, and Malvern Zetasizer for the purpose of synthesis and characterisation of Lipid Nanoparticles (LNPs). The Zetasizer is able to read zeta potential and size of particles, including exosomes, liposomes, and LNPs." . + +SCR:024863 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CLASTR" ; + NIFRID:synonym "Cellosaurus Short Tandem Repeat search tool" ; + definition: "Web tool to seach for similarity between cell line Short Tandem Repeat markers and those stored in Cellosaurus knowledge resource.Cellosaurus STR similarity search tool for cell line authentication." . + +SCR:024864 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "HFOApp" ; + NIFRID:synonym "High Frequency Oscillation App" ; + definition: "Software for detecting and identifying high frequency oscillations observed in EEG recordings. MATLAB based graphical user interface for High Frequency Oscillation marking." . + +SCR:024865 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SciLifeLab Data Platform" ; + definition: "Platform collates tools, databases, information, and other resources that can be useful to researchers and data producing facilities working in the area of data driven life science. Hub for data driven life science research in Sweden." . + +SCR:024866 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Swedish Pathogens Portal" ; + definition: "Portal provides information, guidelines, data, services, and other resources aimed at supporting Swedish research community to share data related to pathogens and pandemic preparedness." . + +SCR:024867 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "neuTube" ; + definition: "Software for reconstructing neurons from fluorescence microscope images. Used to generate neuron structure from 3D image with user interaction, which mainly consists of mouse clicks. It can also load SWC files from any other source for visualization or further editing." . + +SCR:024868 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Neuropactor" ; + definition: "Electromagnetic instrument to mount on stereotaxic device, that delivers accurate reproducible contact with small laboratory animals for preclinical research." . + +SCR:024869 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Stereotaxic Impactor" ; + definition: "Precise spinal impactor used for reproducible impact on laboratory animals to generate neurotrauma injury for preclinical research." . + +SCR:024870 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Fluid Percussion Device" ; + definition: "Device creates controlled and measurable fluid percussion in small to medium sized animals for preclinical research." . + +SCR:024871 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_HPD-1700" ; + rdfs:label "Fluid Percussion Device" ; + definition: "FP device consisting of falling pendulum that generates reproducible, hydraulic pulses to replicate closed TBI for neurological research." . + +SCR:024872 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Weight Drop TBI Model apparatus for Mice and Rats" ; + definition: "Weight drop device that allows for angled impact to the head of free-roaming laboratory animal for preclinical research." . + +SCR:024873 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_AMS 201" ; + rdfs:label "Pneumatic Cortical Impact Device" ; + definition: "Pneumatic impact device designed to reproduce controlled cortical impact to laboratory animals for preclinical research." . + +SCR:024874 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_TBI-0310" ; + rdfs:label "Head Impactor" ; + definition: "Computer controlled device with accurate and reproducible detection of cortical surface prior to initiating injury sequence, designed for preclinical research." . + +SCR:024875 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Fluid Percussion Injury Device" ; + definition: "Fluid percussion device to be used on laboratory animals for neurologic research." . + +SCR:024877 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2604" ; + rdfs:label "Beth Israel Deaconess Medical Center Functional Genomics and Bioinformatics Core Facility" ; + NIFRID:synonym "Functional Genomics and Bioinformatics Core" ; + definition: "Core provides consultative, laboratory, and bioinformatic services for next generation sequencing based applications.Core services include Pre- and post-experimental consultation to determine proper experimental approach, design, and interpretation; Standalone RNA preparation, RNA and DNA Bioanalyzer analyses, chromatin shearing/shear checks; Sample quality assessment of DNA and RNA using the BioAnalyzer and Qubit assays; Library preparation, sequencing, and analysis of transcriptomes (RNA-seq), cistromes (ChIP-seq), chromatin accessibility (ATAC-seq); Standalone sequencing on NextSeq500; Multiplexed 10x Single Cell/Nucleus Library RNA-seq Droplet generation, Library Preparation; Basic data analysis: quality assessment and normalization, genomic alignment, differential expression/enrichment, functional enrichment analysis (overrepresentation and GSEA), sample clustering, and motif enrichment; Bespoke data analysis, including integration of complex ChIP-seq and RNA-seq data sets, single-cell sequencing analyses.Core is located on the 7th floor of the Center for Life Sciences building in the Longwood Medical area (3 Blackfan Circle, CLS-728)." . + +SCR:024878 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "RZ5P Fiber Photometry Processor" ; + definition: "Optimized processor for fiber photometry.RZ5P is intended for use with TDT’s Synapse software." . + +SCR:024879 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Wireless Running Wheel" ; + definition: "Allows monitoring of wireless wheel running activity without running wires." . + +SCR:024880 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "Model_Number_DIG-807" ; + rdfs:label "Wireless Running Wheel Hub" ; + definition: "Device connects wireless running wheels to data acquisition computer via a USB cable.All wheels must be set to the same address as the hub with which they communicate.Hub relays data to Wheel Manager Software." . + +SCR:024881 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Julearn" ; + definition: "Software library of easy testing ML models directly from pandas DataFrames, while keeping the flexibility of using scikit-learn’s models." . + +SCR:024882 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "San Diego Instruments Rotor Rod System" ; + NIFRID:synonym "Rotor Rod", + "Rotor Rod System", + "ROTOR-ROD System" ; + definition: "System to study motor coordination using natural fear of falling response with reliability and accuracy. System measures motor function, motor learning, coordination, and equilibrium in both rats and mice." . + +SCR:024883 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Qt Creator" ; + definition: "Cross-platform, complete Integrated Development Environment for application developers to create applications for multiple desktop, embedded, and mobile device platforms, such as Android and iOS. It is available for Linux, macOS and Windows operating systems. In addition, you can use the experimental WebAssembly plugin to build applications in web format and run them in web browsers." . + +SCR:024884 a NLX:63400, + owl:NamedIndividual ; + NIFRID:synonym "Arduino IDE 1.x", + "Arduino IDE 2.0", + "Arduino IDE 2.2.", + "Arduino IDE 2.x", + "Arduino Integrated Development Environment" . + +SCR:024885 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "3DHISTECH SlideViewer" ; + NIFRID:synonym "SlideViewer" ; + definition: "Software tool for working with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software used in clinical pathology and research." . + +SCR:024887 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Adobe Fresco" ; + definition: "Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support." . + +SCR:024888 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ggfortify" ; + definition: """Software tool as unified interface to visualize statistical results of popular R packages. +Provides unified interface that enables users to use one line of code to visualize statistical results of many R packages using ggplot2 idioms. Allows ggplot2 to handle some popular R packages.""" . + +SCR:024889 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "tidybayes" ; + definition: "Software R package to integrate popular Bayesian modeling methods into tidy data plus ggplot workflow." . + +SCR:024890 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Octopus" ; + definition: "Software tool as mapping based variant caller that implements several calling models within unified haplotype aware framework. Variant caller that uses polymorphic Bayesian genotyping model capable of modeling sequencing data from range of experimental designs within unified haplotype aware framework. Bayesian haplotype based mutation calling." . + +SCR:024891 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SomaticSeq" ; + definition: "Software accurate somatic mutation detection pipeline implementing stochastic boosting algorithm to produce somatic mutation calls for both single nucleotide variants and small insertions and deletions. NGS variant calling and classification." . + +SCR:024892 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PEPhub" ; + NIFRID:synonym "Portable Encapsulated Projects hub" ; + definition: "Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end." . + +SCR:024893 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CellTypist" ; + definition: "Web application for automated cell type annotation for scRNA-seq datasets. Allows for cell prediction using either built-in or custom models, in order to assist in accurate classification of different cell types and subtypes." . + +SCR:024894 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "CZ CELLxGENE Discover" ; + NIFRID:synonym "Chan Zuckerberg CELL by GENE Discover" ; + definition: "Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer." . + +SCR:024895 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Epi-Retro-Seq" ; + NIFRID:synonym "Epi-Retro-Seq web application" ; + definition: "Web application to link single-cell epigenomes and cell types." . + +SCR:024896 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "United States Cancer Statistics Public Information Data" ; + definition: "United States Cancer Statistics public information data provided by Centers for Disease Control and Prevention." . + +SCR:024897 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "score-assemblies" ; + definition: "Software Snakemake workflow for scoring and comparing multiple bacterial genome assemblies from Illumina and Nanopore to reference genomes." . + +SCR:024898 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ont-assembly-snake" ; + definition: "Software Snakemake workflow for bacterial genome assembly plus polishing for Oxford Nanopore sequencing using multiple tools." . + +SCR:024899 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "lifelines" ; + definition: "Software survival analysis library written in Python." . + +SCR:024900 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "table1" ; + definition: "Software R package to create HTML tables of descriptive statistics, as one would expect to see as the first table in medical epidemiological journal article. Used for generating tables of descriptive statistics in HTML." . + +SCR:024901 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "ANCOM-BC2" ; + NIFRID:synonym "Analysis of Compositions of Microbiomes with Bias Correction 2" ; + definition: "Software R package for differential abundance of microbiome. Used for performing differential abundance analysis of microbiome count data. Microbiome differential abudance and correlation analyses with bias correction." . + +SCR:024902 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2607" ; + rdfs:label "Donald Danforth Plant Science Center Plant Growth Core Facility" ; + NIFRID:synonym "DDPSC Plant Growth Facility", + "Donald Danforth Plant Science Center DDPSC Plant Growth Facility" ; + definition: "Core offers scientists variety of advanced plant growth spaces and expert horticultural services.This includes Greenhouse Complex,Growth Chamber facility and Headhouse space. Greenhouses are designed for cultivation and containment of research crops, including regulated and protected plant materials.All greenhouses are environmentally controlled for temperature, humidity and light levels, and have automated irrigation and nutrient delivery capability using Argus Control Systems. Many houses have 14 to 20 ft sidewalls for growing taller crops, as well as in-floor heating, height-adjustable light canopies and automated irrigation capabilities. Over 95% of the greenhouse complex utilizes high intensity, energy-efficient horticultural LED lighting. Plant Growth Facility has multiple special-use work spaces including potting areas, seed processing, seed storage coolers, plant dry-down and soil handling rooms, autoclave, fertigation/utility rooms, as well as general storage space.Core is also responsible for managing Seed Storage coolers housing Danforth Center Institutional Seed Collection." . + +SCR:024903 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2610" ; + rdfs:label "Van Andel Institute Mass Spectrometry Core Facility" ; + NIFRID:synonym "Mass Spectrometry Core", + "VAI Mass Spectrometry Core", + "VAI Mass Spectrometry Core (MSC)", + "Van Andel Institute Mass Spectrometry Core" ; + definition: "Core is committed to developing scientific partnerships with research labs to develop and deploy LC/MS and GC/MS methods specifically tailored to meet the needs of every project. Provides suite of technologies, experimental design support and staff expertise to deliver metabolomics, lipidomics, and proteomics capabilities to VARI scientists and collaborators. Analytical capabilities are combined with custom informatics and statistics solutions.Specific capabilities include: Metabolomics and Lipidomics liquid chromatography mass spectrometry (LC/MS) systems (Thermo Orbitrap ID-X, Thermo Orbitrap Exploris 240, and Agilent 6470 QQQ) and gas chromatography (GC)/MS systems (Agilent 5977b (2), Thermo 7610 ISQ) dedicated to small molecule analysis;Proteomics nano LC/MS systems (Orbitrap Eclipse and Orbitrap Exploris 480) for protein analysis; Bioinformatics for developing and maintaining informatics pipelines for mass spectrometry data analysis and visualization.Major equipment in the facility includes Thermo Scientific Orbitrap ID-X LC/MS,Thermo Scientific Orbitrap Exploris 240 LC/MS,Thermo Scientific Orbitrap Eclipse nanoLC/MS,Thermo Scientific Orbitrap Exploris 4800 LC/MS,Agilent 6470 Triple Quadrupole LC/MS ,Agilent Infinity 1290II UPLC,Agilent 5977B GC/MS,Thermo Scientific ISQ7610 EI/CI enabled GC/M." . + +SCR:024904 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2609" ; + rdfs:label "University of Victoria Genome BC Proteomics Centre Core Facility" ; + NIFRID:synonym "University of Victoria Genome BC Proteomics Centre", + "University of Victoria Proteomics Centre" ; + definition: "Core for proteomics technology development and service. Provides mass spectrometry analytical services to academic, industrial, and government laboratories." . + +SCR:024905 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2608" ; + rdfs:label "Beth Israel Deaconess Medical Center Spatial Technologies Unit Core Facility" ; + NIFRID:synonym "Spatial Technologies Unit" ; + definition: "Core for spatial and single cell technologies provides expertise, training, education and equipment. Supports projects, starting from consultation with matching right technologies to project needs, budget, and timeline. Provided services include single cell and spatial assays, tissue preparations, staining, sequencing, bioinformatic analyses.Equipment include 10x Genomics Visium,10x Genomics Xenium,Akoya PhenoImager HT whole slide scanner, Akoya Phenocycler Fusion,Bruker Vutara VXL,Nanostring GeoMX DSP, Vizgen MERSCOPE, Epredia TMA Grandmaster and more." . + +SCR:024906 a owl:NamedIndividual ; + rdfs:label "Roboinject" ; + NIFRID:synonym "Resource" ; + definition: "Fully automated robot for compound injection into oocytes, eggs, and embryos. Uses industry standard 96, 384, as well as custom well plates." . + +SCR:024907 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Roboocyte2" ; + NIFRID:synonym "Roboocyte" ; + definition: "Roboocyte provides automated cDNA/mRNA injection and subsequent TEVC recording on Xenopus oocytes in 96-well microtiter plates. Roboocyte2 was designed not only for Xenopus oocyte expression system, but to also for drug discovery. Provides sequential two electrode voltage clamp recording in oocytes and classical perfusion of compounds." . + +SCR:024908 a NLX:152328, + owl:NamedIndividual ; + rdfs:label "SolidWorks" ; + definition: "Brand within Dassault Systèmes that develops and markets solid modeling computer-aided design, computer-aided engineering, 3D CAD design and collaboration, analysis, and product data management software." . + +SCR:024909 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Single Cell Pathway Analysis" ; + NIFRID:synonym "Single Cell Pathway Analysis (SCPA)" ; + NIFRID:abbrev "SCPA" ; + definition: "Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes." . + +SCR:024910 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Synaptic Vesicles Detection" ; + definition: "Software tool as Python based synaptic vesicle classifier algorithm to identify neurotransmitter vesicles in electron microscopy images using Pytorch." . + +SCR:024911 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Tulane University TNPRC Animal Resources Core Facility" ; + NIFRID:synonym "nter Animal Resources Core Facility", + "Tulane University Tulane National Primate Research Ce" ; + definition: "Core is part of Tulane National Primate Research Center. Provides services including routine husbandry care for animal colonies, reporting of animals abnormal clinical signs or activities to veterinary medical staff and faculty. Animal Care Technicians provide support during diagnostic and therapeutic procedures and administration of preventive medicine program. Core coordinates its activities with research personnel to provide assistance, equipment and support for their work. After hours care includes administration of treatments, collection of biologic samples for research activities and observation of animals. TNPRC facilities are accredited by Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC)." . + +SCR:024912 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "PS:Power and Sample Size Calculation" ; + NIFRID:abbrev "PS" ; + definition: "Software application as interactive program for performing power and sample size calculations. Can determine the sample size needed to detect specified alternative hypothesis with required power, the power with which specific alternative hypothesis can be detected with given sample size, or the specific alternative hypotheses that can be detected with given power and sample size." . + +SCR:024913 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Daphnia Atlas" ; + definition: "Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia." . + +SCR:024914 a NLX:63400, + owl:NamedIndividual ; + oboInOwl:hasDbXref "ABRF_2614" ; + rdfs:label "University of California Los Angeles Broad Stem Cell Research Center Microscopy Core Facility" ; + NIFRID:synonym "Los Angeles UCLA-Broad Stem Cell Research Center Microscopy Core", + "UCLA-Broad Stem Cell Research Center Microscopy Core", + "University of California" ; + definition: "Microscopy Core is collaboration of Broad Stem Cell Research Center and Department of Molecular, Cell and Developmental Biology at UCLA. Provides high resolution technologies for imaging and analyzing molecular and structural organization of cells and tissue as well as bioengineered materials. Services include confocal, wide field fluorescence and live cell imaging, as well as image analysis software." . + +SCR:024915 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FMRI Expert Analysis Tool" ; + NIFRID:abbrev "FEAT" ; + definition: "Software tool for high quality model based FMRI data analysis. Used for preprocessing and statistical analysis of FMRI data." . + +SCR:024916 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "Multivariate Exploratory Linear Optimized Decomposition into Independent Components" ; + NIFRID:synonym "MELODIC:Multivariate Exploratory Linear Optimized Decomposition into Independent Components" ; + NIFRID:abbrev "MELODIC" ; + definition: "Software tool to use at both the subject and group level to decompose FMRI data into time courses and spatial maps using Independent Component Analysis. Used to decompose single or multiple 4D data sets into different spatial and temporal components." . + +SCR:024917 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FABBER" ; + definition: "Software command-line tool for approximate Bayesian inference using generative signal models." . + +SCR:024918 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "BASIL" ; + NIFRID:synonym "BASIL:Bayesian Inference for Arterial Spin Labeling MRI", + "Bayesian Inference for Arterial Spin Labeling MRI" ; + definition: "Software toolbox for kinetic model inversion to the data using Bayesian algorithm. Performs kinetic model inversion on ASL label control difference data." . + +SCR:024919 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "VERBENA" ; + NIFRID:synonym "VERBENA:Vascular Model Based Perfusion Quantification for DSC-MRI" ; + definition: "Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain." . + +SCR:024920 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FMRIB's Automated Segmentation Tool" ; + NIFRID:synonym "FAST:FMRIB's Automated Segmentation Tool", + "Functional Magnetic Resonance Imaging of the Brain's Automated Segmentation Tool" ; + NIFRID:abbrev "FAST" ; + definition: "Software tool to segment 3D image of brain into different tissue types like Grey Matter, White Matter, CSF, etc., whilst also correcting for spatial intensity variations also known as bias field or RF inhomogeneities. Used to perform tissue type segmentation and bias field correction." . + +SCR:024921 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FMRIB’s Integrated Registration and Segmentation Tool" ; + NIFRID:synonym "Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool" ; + NIFRID:abbrev "FIRST" ; + definition: "Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences." . + +SCR:024922 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FMRIB's Linear Image Registration Tool" ; + NIFRID:abbrev "FLIRT" ; + definition: "Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration." . + +SCR:024923 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FNIRT" ; + definition: "Software tool to perform linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another." . + +SCR:024924 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "FSLVBM" ; + NIFRID:synonym "FSL Voxel Based Morphometry" ; + definition: "Software tool to analyse structural data. Voxel based morphometry style analysis carried out with FSL tools." . + +SCR:024925 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SIENA " ; + definition: "Software package for both single-time-point and two-time-point analysis of brain change. Used to estimate percentage brain volume change between two input images, taken of the same subject, at different points in time." . + +SCR:024926 a NLX:63400, + owl:NamedIndividual ; + rdfs:label "SIENAX" ; + definition: "Software tool to estimate total brain tissue volume, from single image, normalized for skull size." . + +SCR:024927 a owl:NamedIndividual ; + rdfs:label "Multimodal Image Segmentation Tool" ; + NIFRID:abbrev "MIST" ; + definition: "Software flexible tool for subcortical segmentation. It differs from FIRST in that it can use complementary information in different MRI modalities and is less reliant on manual segmentations." . + +### Serialized using the ttlser deterministic serializer v1.2.2 diff --git a/ttl/generated/chebi-dead.ttl b/ttl/generated/chebi-dead.ttl index 16aae260..5ee1c57b 100644 --- a/ttl/generated/chebi-dead.ttl +++ b/ttl/generated/chebi-dead.ttl @@ -10,8 +10,8 @@ a owl:Ontology ; rdfs:label "NIF ChEBI deprecated" ; skos:altLabel "chebidead" ; - owl:versionInfo "2023-07-26" ; - prov:wasGeneratedBy . + owl:versionInfo "2024-01-26" ; + prov:wasGeneratedBy . ### Annotations @@ -427,4 +427,4 @@ CHEBI:50895 rdfs:label "cefalotin"^^xsd:string ; CHEBI:50911 rdfs:label "neurotoxin"^^xsd:string ; rdfs:subClassOf owl:DeprecatedClass . -### Serialized using the ttlser deterministic serializer v1.2.1 +### Serialized using the ttlser deterministic serializer v1.2.2 diff --git a/ttl/generated/chebislim.ttl b/ttl/generated/chebislim.ttl index 69f4726e..f2f04668 100644 --- a/ttl/generated/chebislim.ttl +++ b/ttl/generated/chebislim.ttl @@ -21,19 +21,19 @@ a owl:Ontology ; rdfs:label "NIF ChEBI slim" ; skos:altLabel "chebislim" ; - owl:versionInfo "2023-07-26" ; - prov:wasDerivedFrom , - ; + owl:versionInfo "2024-01-26" ; + prov:wasDerivedFrom , + ; prov:qualifiedDerivation [ a prov:Derivation ; - prov:entity ; + prov:entity ; prov:hadActivity [ a prov:Activity ; - prov:startedAtTime "2023-07-27T04:35:47Z" ; - prov:used ; + prov:startedAtTime "2024-01-26T19:47:23Z" ; + prov:used ; prov:wasAssociatedWith [ a prov:SoftwareAgent ; ilxtr:implementationOf ; - ilxtr:versionString "3.10.12 (af44d0b8114cb82c40a07bb9ee9c1ca8a1b3688c, Jul 22 2023, 08:19:47) [PyPy 7.3.12 with GCC 12.3.1 20230526]" ] ] ] ; - oboInOwl:date "26:07:2023 23:21"^^xsd:string ; - prov:wasGeneratedBy . + ilxtr:versionString "3.10.13 (fc59e61cfbff, Jan 24 2024, 00:15:15) [PyPy 7.3.15 with GCC 12.3.1 20230825]" ] ] ] ; + oboInOwl:date "26:01:2024 00:30"^^xsd:string ; + prov:wasGeneratedBy . ### Object Properties @@ -1581,7 +1581,6 @@ CHEBI:2877 a owl:Class ; "HMDB:HMDB0001894"^^xsd:string, "KEGG:C11045"^^xsd:string, "KEGG:D02381"^^xsd:string, - "MetaCyc:CPD-5583"^^xsd:string, "Patent:US3492131"^^xsd:string, "PDBeChem:PME"^^xsd:string, "PMID:1771173"^^xsd:string, @@ -1622,6 +1621,10 @@ CHEBI:2877 a owl:Class ; "PMID:27728881"^^xsd:string, "PMID:27840415"^^xsd:string, "PMID:27845306"^^xsd:string, + "PMID:30000570"^^xsd:string, + "PMID:37291632"^^xsd:string, + "PMID:37297402"^^xsd:string, + "PMID:37454665"^^xsd:string, "Reaxys:2223850"^^xsd:string, "Wikipedia:Aspartame"^^xsd:string ; rdfs:label "aspartame"^^xsd:string ; @@ -1635,6 +1638,9 @@ CHEBI:2877 a owl:Class ; [ a owl:Restriction ; owl:onProperty chebi2:has_functional_parent ; owl:someValuesFrom CHEBI:49339 ], + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:195544 ], [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:27027 ], @@ -6560,7 +6566,10 @@ CHEBI:5115 a owl:Class ; "Wikipedia:Fluorobenzene"^^xsd:string ; rdfs:label "monofluorobenzene"^^xsd:string ; definition: "The simplest member of the class of monofluorobenzenes that is benzene carrying a single fluoro substituent."^^xsd:string ; - rdfs:subClassOf CHEBI:83575 ; + rdfs:subClassOf CHEBI:83575, + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "C6H5F"^^xsd:string ; chebi:inchi "InChI=1S/C6H5F/c7-6-4-2-1-3-5-6/h1-5H"^^xsd:string ; @@ -17199,13 +17208,17 @@ CHEBI:10033 a owl:Class ; oboInOwl:hasDbXref "Beilstein:1293536"^^xsd:string, "CAS:81-81-2"^^xsd:string, "DrugBank:DB00682"^^xsd:string, + "FooDB:FDB022750"^^xsd:string, "HMDB:HMDB0001935"^^xsd:string, "KEGG:C01541"^^xsd:string, "KEGG:D08682"^^xsd:string, + "LINCS:LSM-1405"^^xsd:string, "Patent:US2427578"^^xsd:string, "Patent:US2765321"^^xsd:string, "Patent:US2777859"^^xsd:string, "Patent:US3239529"^^xsd:string, + "Pesticides:warfarin"^^xsd:string, + "PMCID:PMC10207235"^^xsd:string, "PMID:13358873"^^xsd:string, "PMID:15578879"^^xsd:string, "PMID:18294321"^^xsd:string, @@ -17232,6 +17245,10 @@ CHEBI:10033 a owl:Class ; "PMID:26142525"^^xsd:string, "PMID:26203765"^^xsd:string, "PMID:26238769"^^xsd:string, + "PMID:37359384"^^xsd:string, + "PMID:37648560"^^xsd:string, + "PMID:37755126"^^xsd:string, + "PPDB:681"^^xsd:string, "Reaxys:1293536"^^xsd:string, "Wikipedia:Warfarin"^^xsd:string ; rdfs:label "warfarin"^^xsd:string ; @@ -17258,25 +17275,33 @@ CHEBI:10033 a owl:Class ; [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:55347 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C19H16O4"^^xsd:string ; + chebi:mass "308.333"^^xsd:string ; + chebi:monoisotopicmass "308.10486"^^xsd:string ; oboInOwl:hasExactSynonym "rac-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "1-(4'-Hydroxy-3'-coumarinyl)-1-phenyl-3-butanone"^^xsd:string, - "2H-1-Benzopyran-2-one, 4-hydroxy-3-(3-oxo-1-phenylbutyl)-"^^xsd:string, - "3-(1'-Phenyl-2'-acetylethyl)-4-hydroxycoumarin"^^xsd:string, - "3-(Acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, - "3-(Alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, - "3-(alpha-Phenyl-beta-acetylaethyl)-4-hydroxycumarin"^^xsd:string, - "3-(alpha-Phenyl-beta-acetylethyl)-4-hydroxycoumarin"^^xsd:string, - "4-Hydroxy-3-(3-oxo-1-phenyl-butyl)-cumarin"^^xsd:string, - "4-Hydroxy-3-(3-oxo-1-phenylbutyl)coumarin"^^xsd:string, - "(+/-)-Warfarin"^^xsd:string, - "(Phenyl-1 acetyl-2 ethyl) 3-hydroxy-4 coumarine"^^xsd:string, - "(RS)-Warfarin"^^xsd:string, + oboInOwl:hasRelatedSynonym "4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one"^^xsd:string, + "4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]-2H-chromen-2-one"^^xsd:string, + "4-hydroxy-3-[(1RS)-3-oxo-1-phenylbutyl]coumarin"^^xsd:string, + "(+-)-warfarin"^^xsd:string, + "(RS)-warfarin"^^xsd:string, + "Brumolin"^^xsd:string, "Coumafene"^^xsd:string, "DL-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, "DL-warfarin"^^xsd:string, + "Kumadu"^^xsd:string, + "Kumatox"^^xsd:string, + "rac-1-(4'-hydroxy-3'-coumarinyl)-1-phenyl-3-butanone"^^xsd:string, + "rac-3-(1'-phenyl-2'-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "rac-3-(acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "rac-3-(alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "rac-3-(alpha-phenyl-beta-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "rac-4-hydroxy-3-(3-oxo-1-phenylbutyl)coumarin"^^xsd:string, "rac-warfarin"^^xsd:string, "racemic warfarin"^^xsd:string, + "Ratron"^^xsd:string, + "Rodafarin"^^xsd:string, "Warf 10"^^xsd:string, "warfarin"^^xsd:string, "warfarina"^^xsd:string, @@ -21323,7 +21348,10 @@ CHEBI:16134 a owl:Class ; owl:someValuesFrom CHEBI:77941 ], [ a owl:Restriction ; owl:onProperty hasRole: ; - owl:someValuesFrom CHEBI:78433 ] ; + owl:someValuesFrom CHEBI:78433 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "H3N"^^xsd:string ; chebi:inchi "InChI=1S/H3N/h1H3"^^xsd:string ; @@ -27304,7 +27332,7 @@ CHEBI:17135 a owl:Class ; "PMID:22436224"^^xsd:string, "PMID:22444994"^^xsd:string ; rdfs:label "long-chain fatty alcohol"^^xsd:string ; - definition: "A fatty alcohol with a chain length ranging from C13-C23."^^xsd:string ; + definition: "A fatty alcohol with a chain length ranging from C13 to C22."^^xsd:string ; rdfs:subClassOf CHEBI:24026 ; chebi:charge "0"^^xsd:string ; chebi:formula "HOR"^^xsd:string ; @@ -31006,8 +31034,7 @@ CHEBI:17824 a owl:Class ; "YMDB:YMDB01718"^^xsd:string ; rdfs:label "propan-2-ol"^^xsd:string ; definition: "A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group."^^xsd:string ; - rdfs:subClassOf CHEBI:35681, - CHEBI:167095, + rdfs:subClassOf CHEBI:167095, [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:48356 ] ; @@ -32064,15 +32091,14 @@ CHEBI:18140 a owl:Class ; chebi:formula "HX"^^xsd:string ; chebi:mass "1.008"^^xsd:string ; chebi:monoisotopicmass "1.00783"^^xsd:string ; - chebi:smiles "[F,Cl,Br,I]"^^xsd:string ; + chebi:smiles "*[H]"^^xsd:string ; oboInOwl:hasAlternativeId "CHEBI:5599"^^xsd:string, "CHEBI:13368"^^xsd:string, "CHEBI:37140"^^xsd:string ; oboInOwl:hasExactSynonym "hydrogen halide"^^xsd:string, "hydrogen halides"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "HX"^^xsd:string, - "hydrogen halides"^^xsd:string ; + oboInOwl:hasRelatedSynonym "hydrogen halides"^^xsd:string ; oboInOwl:id "CHEBI:18140"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . @@ -35674,7 +35700,8 @@ CHEBI:24026 a owl:Class ; chebi:smiles "O[*]"^^xsd:string ; oboInOwl:hasExactSynonym "fatty alcohol"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "alcool gras"^^xsd:string, + oboInOwl:hasRelatedSynonym "a fatty alcohol"^^xsd:string, + "alcool gras"^^xsd:string, "fatty alcohols"^^xsd:string, "Fettalkohol"^^xsd:string, "Fettalkohole"^^xsd:string ; @@ -38547,7 +38574,10 @@ CHEBI:26078 a owl:Class ; owl:someValuesFrom CHEBI:77746 ], [ a owl:Restriction ; owl:onProperty hasRole: ; - owl:someValuesFrom CHEBI:84735 ] ; + owl:someValuesFrom CHEBI:84735 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "H3O4P"^^xsd:string ; chebi:inchi "InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)"^^xsd:string ; @@ -42136,6 +42166,9 @@ CHEBI:27870 a owl:Class ; [ a owl:Restriction ; owl:onProperty chebi2:has_functional_parent ; owl:someValuesFrom CHEBI:15956 ], + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:195545 ], [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:75771 ] ; @@ -46500,6 +46533,9 @@ CHEBI:29073 a owl:Class ; [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:77962 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:78006 ], [ a owl:Restriction ; owl:onProperty hasRole: ; owl:someValuesFrom CHEBI:85046 ], @@ -52477,6 +52513,9 @@ CHEBI:32550 a owl:Class ; [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; owl:someValuesFrom CHEBI:18019 ], + [ a owl:Restriction ; + owl:onProperty chebi2:is_conjugate_base_of ; + owl:someValuesFrom CHEBI:133538 ], [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; owl:someValuesFrom CHEBI:194466 ], @@ -53412,7 +53451,7 @@ CHEBI:32644 a owl:Class ; CHEBI:32646 a owl:Class ; oboInOwl:hasDbXref "Gmelin:326567"^^xsd:string ; rdfs:label "methioninium"^^xsd:string ; - definition: "A sulfur-containing amino-acid anion that is the conjugate acid of methionine, arising from protonation of the amino group."^^xsd:string ; + definition: "A sulfur-containing amino-acid cation that is the conjugate acid of methionine, arising from protonation of the amino group."^^xsd:string ; rdfs:subClassOf CHEBI:33719, [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_acid_of ; @@ -57569,12 +57608,19 @@ CHEBI:33709 a owl:Class ; CHEBI:33710 a owl:Class ; rdfs:label "alpha-amino-acid residue"^^xsd:string ; + definition: "An amino-acid residue derived from an alpha-amino acid."^^xsd:string ; rdfs:subClassOf CHEBI:33708, [ a owl:Restriction ; owl:onProperty chebi2:is_substituent_group_from ; owl:someValuesFrom CHEBI:33704 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C2H2NOR"^^xsd:string ; + chebi:mass "56.043"^^xsd:string ; + chebi:monoisotopicmass "56.01364"^^xsd:string ; + chebi:smiles "*-NC([*])C(-*)=O"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; - oboInOwl:hasRelatedSynonym "alpha-amino-acid residues"^^xsd:string ; + oboInOwl:hasRelatedSynonym "alpha-amino-acid residues"^^xsd:string, + "an alpha-amino acid residue"^^xsd:string ; oboInOwl:id "CHEBI:33710"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . @@ -58508,7 +58554,10 @@ CHEBI:34856 a owl:Class ; CHEBI:38785, [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; - owl:someValuesFrom CHEBI:167868 ] ; + owl:someValuesFrom CHEBI:167868 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "C4H9NO"^^xsd:string ; chebi:inchi "InChI=1S/C4H9NO/c1-3-6-4-2-5-1/h5H,1-4H2"^^xsd:string ; @@ -63770,6 +63819,7 @@ CHEBI:36791 a owl:Class ; "PMID:24424469"^^xsd:string, "PMID:24469525"^^xsd:string, "PMID:24528284"^^xsd:string, + "PMID:34406668"^^xsd:string, "Wikipedia:Escitalopram"^^xsd:string ; rdfs:label "escitalopram"^^xsd:string ; definition: "A 1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile that has S-configuration at the chiral centre. It is the active enantiomer of citalopram."^^xsd:string ; @@ -63886,7 +63936,10 @@ CHEBI:36810 a owl:Class ; owl:someValuesFrom CHEBI:46787 ], [ a owl:Restriction ; owl:onProperty hasRole: ; - owl:someValuesFrom CHEBI:78298 ] ; + owl:someValuesFrom CHEBI:78298 ], + [ a owl:Restriction ; + owl:onProperty hasRole: ; + owl:someValuesFrom CHEBI:228364 ] ; chebi:charge "0"^^xsd:string ; chebi:formula "C7H5F3"^^xsd:string ; chebi:inchi "InChI=1S/C7H5F3/c8-7(9,10)6-4-2-1-3-5-6/h1-5H"^^xsd:string ; @@ -73324,7 +73377,8 @@ CHEBI:46766 a owl:Class ; CHEBI:46767 a owl:Class ; rdfs:label "pyrrolidinecarboxylic acid"^^xsd:string ; - rdfs:subClassOf CHEBI:38260 ; + rdfs:subClassOf CHEBI:33575, + CHEBI:38260 ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "pyrrolidinecarboxylic acids"^^xsd:string ; oboInOwl:id "CHEBI:46767"^^xsd:string ; @@ -96360,6 +96414,22 @@ CHEBI:78000 a owl:Class ; oboInOwl:id "CHEBI:78000"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . +CHEBI:78006 a owl:Class ; + oboInOwl:hasDbXref "Wikipedia:Colour_retention_agent"^^xsd:string ; + rdfs:label "food colour retention agent"^^xsd:string ; + definition: "A food additive that intensifies, retains or stabilises the colour of a food."^^xsd:string ; + rdfs:subClassOf CHEBI:64047 ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "color retention agent"^^xsd:string, + "color retention agents"^^xsd:string, + "colour retention agent"^^xsd:string, + "colour retention agents"^^xsd:string, + "food color retention agent"^^xsd:string, + "food color retention agents"^^xsd:string, + "food colour retention agents"^^xsd:string ; + oboInOwl:id "CHEBI:78006"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + CHEBI:78016 a owl:Class ; rdfs:label "food gelling agent"^^xsd:string ; definition: "A food additive that enhances the texture of a foodstuff by gel formation."^^xsd:string ; @@ -97515,8 +97585,7 @@ CHEBI:83813 a owl:Class ; oboInOwl:hasDbXref "Wikipedia:Proteinogenic_amino_acid"^^xsd:string ; rdfs:label "proteinogenic amino acid"^^xsd:string ; definition: "Any of the 23 alpha-amino acids that are precursors to proteins, and are incorporated into proteins during translation. The group includes the 20 amino acids encoded by the nuclear genes of eukaryotes together with selenocysteine, pyrrolysine, and N-formylmethionine. Apart from glycine, which is non-chiral, all have L configuration."^^xsd:string ; - rdfs:subClassOf CHEBI:33575, - CHEBI:35352 ; + rdfs:subClassOf CHEBI:33709 ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "canonical amino acid"^^xsd:string, "canonical amino acids"^^xsd:string, @@ -98567,11 +98636,10 @@ CHEBI:87635 a owl:Class ; oboInOwl:inSubset chebi3:_STAR . CHEBI:87732 a owl:Class ; - oboInOwl:hasDbXref "LINCS:LSM-1405"^^xsd:string, - "PPDB:681"^^xsd:string ; rdfs:label "4-hydroxy-3-(3-oxo-1-phenylbutyl)-1-benzopyran-2-one"^^xsd:string ; definition: "A member of the class of coumarins that is 4-hydroxycoumarin which is substituted at position 3 by a 1-phenyl-3-oxo-1-butyl group."^^xsd:string ; - rdfs:subClassOf CHEBI:37912, + rdfs:subClassOf CHEBI:22712, + CHEBI:37912, CHEBI:51867 ; chebi:charge "0"^^xsd:string ; chebi:formula "C19H16O4"^^xsd:string ; @@ -98580,13 +98648,25 @@ CHEBI:87732 a owl:Class ; chebi:mass "308.329"^^xsd:string ; chebi:monoisotopicmass "308.10486"^^xsd:string ; chebi:smiles "C1=CC=CC2=C1C(=C(C(O2)=O)C(CC(C)=O)C3=CC=CC=C3)O"^^xsd:string ; - oboInOwl:hasExactSynonym "4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string ; + oboInOwl:hasExactSynonym "4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-chromen-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "1-(4'-hydroxy-3'-coumarinyl)-1-phenyl-3-butanone"^^xsd:string, + "2H-1-Benzopyran-2-one, 4-hydroxy-3-(3-oxo-1-phenylbutyl)-"^^xsd:string, + "3-(1'-phenyl-2'-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "3-(acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "3-(alpha-acetonylbenzyl)-4-hydroxycoumarin"^^xsd:string, + "3-(alpha-phenyl-beta-acetylaethyl)-4-hydroxycumarin"^^xsd:string, + "3-(alpha-phenyl-beta-acetylethyl)-4-hydroxycoumarin"^^xsd:string, + "4-Hydroxy-3-(3-oxo-1-phenyl-butyl)-cumarin"^^xsd:string, + "4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string, + "4-hydroxy-3-(3-oxo-1-phenylbutyl)coumarin"^^xsd:string, + "(Phenyl-1 acetyl-2 ethyl) 3-hydroxy-4 coumarine"^^xsd:string ; oboInOwl:id "CHEBI:87732"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . CHEBI:87737 a owl:Class ; oboInOwl:hasDbXref "CAS:5543-58-8"^^xsd:string, + "DrugBank:DB08496"^^xsd:string, "PDBeChem:RWF"^^xsd:string, "PMID:7354137"^^xsd:string, "PMID:21949493"^^xsd:string, @@ -98594,6 +98674,11 @@ CHEBI:87737 a owl:Class ; "PMID:24962085"^^xsd:string, "PMID:26142522"^^xsd:string, "PMID:26161443"^^xsd:string, + "PMID:28735507"^^xsd:string, + "PMID:31608877"^^xsd:string, + "PMID:34579096"^^xsd:string, + "PMID:37122027"^^xsd:string, + "PMID:37598356"^^xsd:string, "Reaxys:4298023"^^xsd:string ; rdfs:label "(R)-warfarin"^^xsd:string ; definition: "A 4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one that has (R)-configuration (the racemate is warfarin, an anticoagulant drug and rodenticide)."^^xsd:string ; @@ -98615,15 +98700,21 @@ CHEBI:87737 a owl:Class ; oboInOwl:hasExactSynonym "4-hydroxy-3-[(1R)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "4-hydroxy-3-[(1R)-3-oxo-1-phenylbutyl]-2H-chromen-2-one"^^xsd:string, + "(+)-(R)-warfarin"^^xsd:string, "(+)-warfarin"^^xsd:string, - "(R)-4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, - "(R)-4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string, - "Dextrowarfarin"^^xsd:string ; + "(R)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, + "(R)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one"^^xsd:string, + "(R)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-chromen-2-one"^^xsd:string, + "(R)-(+)-warfarin"^^xsd:string, + "Dextrowarfarin"^^xsd:string, + "R-wafarin"^^xsd:string ; oboInOwl:id "CHEBI:87737"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . CHEBI:87738 a owl:Class ; oboInOwl:hasDbXref "CAS:5543-57-7"^^xsd:string, + "DrugBank:DB14055"^^xsd:string, + "KEGG:C20129"^^xsd:string, "LINCS:LSM-5404"^^xsd:string, "PDBeChem:SWF"^^xsd:string, "PMID:7354137"^^xsd:string, @@ -98632,6 +98723,17 @@ CHEBI:87738 a owl:Class ; "PMID:24962085"^^xsd:string, "PMID:26142522"^^xsd:string, "PMID:26161443"^^xsd:string, + "PMID:29433307"^^xsd:string, + "PMID:32601017"^^xsd:string, + "PMID:32680916"^^xsd:string, + "PMID:33341662"^^xsd:string, + "PMID:33754183"^^xsd:string, + "PMID:34579970"^^xsd:string, + "PMID:35426132"^^xsd:string, + "PMID:35699912"^^xsd:string, + "PMID:35798369"^^xsd:string, + "PMID:36914276"^^xsd:string, + "PMID:37598356"^^xsd:string, "Reaxys:4298024"^^xsd:string ; rdfs:label "(S)-warfarin"^^xsd:string ; definition: "A 4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-1-benzopyran-2-one that has (S)-configuration (the racemate is warfarin, an anticoagulant drug and rodenticide)."^^xsd:string ; @@ -98653,9 +98755,12 @@ CHEBI:87738 a owl:Class ; oboInOwl:hasExactSynonym "4-hydroxy-3-[(1S)-3-oxo-1-phenylbutyl]-2H-1-benzopyran-2-one"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "4-hydroxy-3-[(1S)-3-oxo-1-phenylbutyl]-2H-chromen-2-one"^^xsd:string, - "(-)-Warfarin"^^xsd:string, - "(S)-4-Hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, - "levrowarfarin"^^xsd:string ; + "(-)-warfarin"^^xsd:string, + "(S)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2-benzopyrone"^^xsd:string, + "(S)-4-hydroxy-3-(3-oxo-1-phenylbutyl)-2H-chromen-2-one"^^xsd:string, + "(S)-(-)-warfarin"^^xsd:string, + "levrowarfarin"^^xsd:string, + "S-warfarin"^^xsd:string ; oboInOwl:id "CHEBI:87738"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . @@ -99081,9 +99186,11 @@ CHEBI:90709 a owl:Class ; oboInOwl:inSubset chebi3:_STAR . CHEBI:90710 a owl:Class ; + oboInOwl:hasDbXref "Wikipedia:Receptor_modulator"^^xsd:string ; rdfs:label "receptor modulator"^^xsd:string ; definition: "A drug that acts as an antagonist, agonist, reverse agonist, or in some other fashion when interacting with cellular receptors."^^xsd:string ; rdfs:subClassOf CHEBI:23888 ; + oboInOwl:hasAlternativeId "CHEBI:189678"^^xsd:string ; oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; oboInOwl:hasRelatedSynonym "receptor modulators"^^xsd:string ; oboInOwl:id "CHEBI:90710"^^xsd:string ; @@ -100307,6 +100414,9 @@ CHEBI:133538 a owl:Class ; rdfs:label "L-lysine zwitterion"^^xsd:string ; definition: "An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of L-lysine; major species at pH 7.3."^^xsd:string ; rdfs:subClassOf CHEBI:59869, + [ a owl:Restriction ; + owl:onProperty chebi2:is_conjugate_acid_of ; + owl:someValuesFrom CHEBI:32550 ], [ a owl:Restriction ; owl:onProperty chebi2:is_conjugate_base_of ; owl:someValuesFrom CHEBI:32551 ], @@ -102620,7 +102730,8 @@ CHEBI:167055 a owl:Class ; CHEBI:167095 a owl:Class ; rdfs:label "secondary fatty alcohol"^^xsd:string ; definition: "A fatty alcohol consisting of a chain of 3 to greater than 27 carbon atoms in which a hydroxy group is attached to a saturated carbon atom different from the terminal carbons. Secondary fatty alcohols may be saturated or unsaturated and may be branched or unbranched."^^xsd:string ; - rdfs:subClassOf CHEBI:24026 ; + rdfs:subClassOf CHEBI:24026, + CHEBI:35681 ; chebi:charge "0"^^xsd:string ; chebi:formula "CH2OR2"^^xsd:string ; chebi:mass "30.026"^^xsd:string ; @@ -103750,6 +103861,64 @@ CHEBI:195233 a owl:Class ; oboInOwl:id "CHEBI:195233"^^xsd:string ; oboInOwl:inSubset chebi3:_STAR . +CHEBI:195544 a owl:Class ; + oboInOwl:hasDbXref "MetaCyc:CPD-5583"^^xsd:string ; + rdfs:label "aspartame zwitterion"^^xsd:string ; + definition: "A dipeptide zwitterion resulting from transfer of a proton from the carboxy to the amino group of aspartame; major species at pH 7.3."^^xsd:string ; + rdfs:subClassOf CHEBI:90799, + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:2877 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C14H18N2O5"^^xsd:string ; + chebi:inchi "InChI=1S/C14H18N2O5/c1-21-14(20)11(7-9-5-3-2-4-6-9)16-13(19)10(15)8-12(17)18/h2-6,10-11H,7-8,15H2,1H3,(H,16,19)(H,17,18)/t10-,11-/m0/s1"^^xsd:string ; + chebi:inchikey "IAOZJIPTCAWIRG-QWRGUYRKSA-N"^^xsd:string ; + chebi:mass "294.307"^^xsd:string ; + chebi:monoisotopicmass "294.12157"^^xsd:string ; + chebi:smiles "COC(=O)[C@H](CC1=CC=CC=C1)NC(=O)[C@@H]([NH3+])CC([O-])=O"^^xsd:string ; + oboInOwl:hasExactSynonym "(3S)-3-azaniumyl-4-{[(2S)-1-methoxy-1-oxo-3-phenylpropan-2-yl]amino}-4-oxobutanoate"^^xsd:string ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "aspartame"^^xsd:string ; + oboInOwl:id "CHEBI:195544"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + +CHEBI:195545 a owl:Class ; + oboInOwl:hasDbXref "MetaCyc:CPD-17700"^^xsd:string ; + rdfs:label "biocytin zwitterion"^^xsd:string ; + definition: "An L-alpha-amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of biocytin; major species at pH 7.3."^^xsd:string ; + rdfs:subClassOf CHEBI:59869, + [ a owl:Restriction ; + owl:onProperty chebi2:is_tautomer_of ; + owl:someValuesFrom CHEBI:27870 ] ; + chebi:charge "0"^^xsd:string ; + chebi:formula "C16H28N4O4S"^^xsd:string ; + chebi:inchi "InChI=1S/C16H28N4O4S/c17-10(15(22)23)5-3-4-8-18-13(21)7-2-1-6-12-14-11(9-25-12)19-16(24)20-14/h10-12,14H,1-9,17H2,(H,18,21)(H,22,23)(H2,19,20,24)/t10-,11-,12-,14-/m0/s1"^^xsd:string ; + chebi:inchikey "BAQMYDQNMFBZNA-MNXVOIDGSA-N"^^xsd:string ; + chebi:mass "372.480"^^xsd:string ; + chebi:monoisotopicmass "372.18313"^^xsd:string ; + chebi:smiles "[H][C@]12CS[C@@H](CCCCC(=O)NCCCC[C@H]([NH3+])C([O-])=O)[C@@]1([H])NC(=O)N2"^^xsd:string ; + oboInOwl:hasExactSynonym "(2S)-2-azaniumyl-6-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoate"^^xsd:string ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "biocytin"^^xsd:string ; + oboInOwl:id "CHEBI:195545"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + +CHEBI:228364 a owl:Class ; + rdfs:label "NMR chemical shift reference compound"^^xsd:string ; + definition: "Any compound that produces a peak used to reference an NMR spectrum during data pre-processing."^^xsd:string ; + rdfs:subClassOf CHEBI:33232, + CHEBI:51086 ; + oboInOwl:hasOBONamespace "chebi_ontology"^^xsd:string ; + oboInOwl:hasRelatedSynonym "NMR chemical shift reference compounds"^^xsd:string, + "NMR chemical shift standard"^^xsd:string, + "NMR chemical shift standards"^^xsd:string, + "NMR internal standard"^^xsd:string, + "NMR internal standards"^^xsd:string, + "NMR reference standard"^^xsd:string, + "NMR reference standards"^^xsd:string ; + oboInOwl:id "CHEBI:228364"^^xsd:string ; + oboInOwl:inSubset chebi3:_STAR . + CHEBI:237958 a owl:Class ; rdfs:label "({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(9H-purin-9-yl)oxolan-2-yl]methyl phosphonato}oxy)(phosphonatooxy)phosphinate"^^xsd:string ; rdfs:subClassOf CHEBI:37045, @@ -104265,4 +104434,4 @@ CHEBI:616459 a owl:Class ; oboInOwl:id "CHEBI:616459"^^xsd:string ; oboInOwl:inSubset chebi1:_STAR . -### Serialized using the ttlser deterministic serializer v1.2.1 +### Serialized using the ttlser deterministic serializer v1.2.2 diff --git a/ttl/generated/ncbigeneslim.ttl b/ttl/generated/ncbigeneslim.ttl index db72eb68..3b8008a1 100644 --- a/ttl/generated/ncbigeneslim.ttl +++ b/ttl/generated/ncbigeneslim.ttl @@ -12,7 +12,7 @@ rdfs:label "NIF NCBI Gene subset" ; skos:altLabel "ncbigeneslim" ; rdfs:comment "This subset is automatically generated from the NCBI Gene database on a subset of terms listed in /home/tom/git/pyontutils/nifstd/resources/gene-subset-ids.txt." ; - owl:versionInfo "2023-07-26" . + owl:versionInfo "2024-01-26" . ### Classes @@ -2609,6 +2609,7 @@ NCBIGene:13405 a owl:Class ; "dystrophin", "dystrophin delta-E40e", "dystrophin Dp71d(delta71,73-74)", + "dystrophin Dp71f-delta71,74", "dystrophin Dp427-E40e", "dystrophin E40e", "dystrophin E51b", @@ -4435,7 +4436,8 @@ NCBIGene:15242 a owl:Class ; "homeobox protein PRH", "mHex", "Prh", - "Prhx" ; + "Prhx", + "proline-rich homeodomain protein" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -6163,10 +6165,12 @@ NCBIGene:17476 a owl:Class ; skos:prefLabel "macrophage expressed gene 1" ; NIFRID:synonym "macrophage gene 1 protein", "macrophage-expressed gene 1 protein", + "mPFN2", "Mpg-1", "MPS1", "P-2", - "perforin-2" ; + "perforin-2", + "PFN2" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -7711,11 +7715,12 @@ NCBIGene:19141 a owl:Class ; NCBIGene:19142 a owl:Class ; rdfs:label "Prss12" ; - skos:prefLabel "protease, serine 12 neurotrypsin (motopsin)" ; + skos:prefLabel "serine protease 12 neurotrypsin (motopsin)" ; NIFRID:synonym "brain-specific serine protease 3", "Bssp-3", "motopsin", "neurotrypsin", + "protease, serine 12 neurotrypsin (motopsin)", "serine protease 12" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -8181,7 +8186,7 @@ NCBIGene:19701 a owl:Class ; NCBIGene:19704 a owl:Class ; rdfs:label "Upf1" ; - skos:prefLabel "UPF1 regulator of nonsense transcripts homolog (yeast)" ; + skos:prefLabel "UPF1 RNA helicase and ATPase" ; NIFRID:synonym "ATP-dependent helicase RENT1", "B430202H16Rik", "NORF1", @@ -8189,6 +8194,7 @@ NCBIGene:19704 a owl:Class ; "regulator of nonsense transcripts 1", "regulator of nonsense transcripts 1 (Nonsense mRNA reducing factor 1) (NORF1) (Up-frameshift suppressor 1 homolog)", "Rent1", + "UPF1 regulator of nonsense transcripts homolog", "Upflp" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -9098,7 +9104,11 @@ NCBIGene:20670 a owl:Class ; rdfs:label "Sox15" ; skos:prefLabel "SRY (sex determining region Y)-box 15" ; NIFRID:synonym "protein SOX-15", - "SRY-box containing gene 15" ; + "protein SOX-16", + "Sox16", + "SRY (sex determining region Y)-box 16", + "SRY-box containing gene 15", + "SRY-box containing gene 16" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -10032,8 +10042,9 @@ NCBIGene:22139 a owl:Class ; NCBIGene:22158 a owl:Class ; rdfs:label "Tulp3" ; - skos:prefLabel "tubby-like protein 3" ; + skos:prefLabel "TUB like protein 3" ; NIFRID:synonym "2310022L06Rik", + "tubby-like protein 3", "tubby-related protein 3" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -10552,12 +10563,12 @@ NCBIGene:23871 a owl:Class ; ilxtr:definedForTaxon NCBITaxon:10090 . NCBIGene:23880 a owl:Class ; - rdfs:label "Fyb" ; - skos:prefLabel "FYN binding protein" ; + rdfs:label "Fyb1" ; + skos:prefLabel "FYN binding protein 1" ; NIFRID:synonym "ADAP", "adhesion and degranulation promoting adaptor protein", "B630013F22Rik", - "Fyb1", + "Fyb", "FYB-120/130", "FYN binding protein FYB-130", "FYN-binding protein 1", @@ -13077,7 +13088,7 @@ NCBIGene:66700 a owl:Class ; NCBIGene:66713 a owl:Class ; rdfs:label "Actr2" ; - skos:prefLabel "ARP2 actin-related protein 2" ; + skos:prefLabel "actin related protein 2" ; NIFRID:synonym "4921510D23Rik", "actin-like protein 2", "actin-related protein 2", @@ -15533,7 +15544,7 @@ NCBIGene:104681 a owl:Class ; NCBIGene:104759 a owl:Class ; rdfs:label "Pld4" ; - skos:prefLabel "phospholipase D family, member 4" ; + skos:prefLabel "phospholipase D family member 4" ; NIFRID:synonym "5'-3' exonuclease PLD4", "choline phosphatase 4", "phosphatidylcholine-hydrolyzing phospholipase D4", @@ -15550,6 +15561,7 @@ NCBIGene:104776 a owl:Class ; "aldehyde dehydrogenase family 6 member A1", "malonate-semialdehyde dehydrogenase", "methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial", + "methylmalonate-semialdehyde/malonate-semialdehyde dehydrogenase [acylating], mitochondrial", "Mmsdh" ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . @@ -16862,7 +16874,7 @@ NCBIGene:214855 a owl:Class ; NCBIGene:215819 a owl:Class ; rdfs:label "Nhsl1" ; - skos:prefLabel "NHS-like 1" ; + skos:prefLabel "NHS like 1" ; NIFRID:synonym "5730409E15Rik", "A630035H13Rik", "A730096F01", @@ -17891,7 +17903,8 @@ NCBIGene:242202 a owl:Class ; NCBIGene:242274 a owl:Class ; rdfs:label "Lrrc7" ; skos:prefLabel "leucine rich repeat containing 7" ; - NIFRID:synonym "densin", + NIFRID:synonym "B230334C09Rik", + "densin", "densin 180", "leucine-rich repeat-containing protein 7", "mKIAA1365" ; @@ -18460,4 +18473,4 @@ NCBIGene:102632117 a owl:Class ; rdfs:subClassOf SO:0000110 ; ilxtr:definedForTaxon NCBITaxon:10090 . -### Serialized using the ttlser deterministic serializer v1.2.1 +### Serialized using the ttlser deterministic serializer v1.2.2