From f009134936b4583c2d2b1a4f2f003125a0905447 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 1 Feb 2024 01:29:26 +0000 Subject: [PATCH] Actions - slim updated --- external-dev/aopo-slim.owl | 15 ++- external-dev/bao-slim.owl | 2 +- external-dev/bfo-slim.owl | 2 +- external-dev/bto-slim.owl | 2 +- external-dev/ccont-slim.owl | 2 +- external-dev/chebi-slim.owl | 20 ++- external-dev/cheminf-slim.owl | 2 +- external-dev/chmo-slim.owl | 2 +- external-dev/clo-slim.owl | 22 ++-- external-dev/efo-slim.owl | 19 ++- external-dev/envo-slim.owl | 2 +- external-dev/fabio-slim.owl | 2 +- external-dev/go-slim.owl | 24 ++-- external-dev/iao-slim.owl | 2 +- external-dev/msio-slim.owl | 2 +- external-dev/ncit-slim.owl | 2 +- external-dev/npo-slim.owl | 2 +- external-dev/oae-slim.owl | 2 +- external-dev/obcs-slim.owl | 2 +- external-dev/obi-slim.owl | 45 +++++-- external-dev/pato-slim.owl | 2 +- external-dev/sio-slim.owl | 2 +- external-dev/uberon-slim.owl | 226 ++++++++++++++++++++++++++-------- external-dev/uo-slim.owl | 2 +- 24 files changed, 295 insertions(+), 110 deletions(-) diff --git a/external-dev/aopo-slim.owl b/external-dev/aopo-slim.owl index 977970b6..31f4c5a3 100644 --- a/external-dev/aopo-slim.owl +++ b/external-dev/aopo-slim.owl @@ -43,15 +43,15 @@ https://raw.githubusercontent.com/jmillanacosta/aop-ontology/patch-1/aopo.owl Slimmer - 07:12:2023 17:27 - 2024-01-01 01:36:43 + 04:01:2024 19:44 + 2024-02-01 01:22:53 chebi_ontology human_phenotype 1.2 has_part chebi Author: ChEBI curation team - ChEBI Release version 227 + ChEBI Release version 228 ChEBI subsumes and replaces the Chemical Ontology first Contact: Stephan Schurer @@ -98,7 +98,7 @@ Uma Vempati, Hande Küçük, Ubbo Visser, Saminda Abeyruwan, Kunie Sakurai, Vanc 2.8.6 2.8.8 2.8.9 - 2023-10-09 + 2024-01-16 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. @@ -186,6 +186,13 @@ Uma Vempati, Hande Küçük, Ubbo Visser, Saminda Abeyruwan, Kunie Sakurai, Vanc + + + + + + + diff --git a/external-dev/bao-slim.owl b/external-dev/bao-slim.owl index 3b40c78f..7ebb8230 100644 --- a/external-dev/bao-slim.owl +++ b/external-dev/bao-slim.owl @@ -24,7 +24,7 @@ http://bioassayontology.org/bao/bao_complete_merged.owl Slimmer - 2024-01-01 01:36:51 + 2024-02-01 01:23:02 Contact: Stephan Schurer stephan dot schurer at gmail dot com diff --git a/external-dev/bfo-slim.owl b/external-dev/bfo-slim.owl index 96beac3b..fa41f65c 100644 --- a/external-dev/bfo-slim.owl +++ b/external-dev/bfo-slim.owl @@ -45,7 +45,7 @@ http://purl.obolibrary.org/obo/bfo/classes-only.owl Slimmer - 2024-01-01 01:36:53 + 2024-02-01 01:23:03 The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO ("bfo_classes_only.owl") includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no object properties or logical axioms that use the object properties in bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl variant are limited to subclass and disjoint assertions they are much weaker than the logical axioms in bfo.owl. If you plan to use the relations that define BFO 2, you should import bfo.owl instead of bfo_classes_only.owl. To the extent that the relations are used without importing bfo.owl, be mindful that they should be used in a manner consistent with their use in bfo.owl. Otherwise if your ontology is imported by a another ontology that imports bfo.owl there may be inconsistencies. diff --git a/external-dev/bto-slim.owl b/external-dev/bto-slim.owl index fa54b399..524d16ec 100644 --- a/external-dev/bto-slim.owl +++ b/external-dev/bto-slim.owl @@ -20,7 +20,7 @@ http://purl.obolibrary.org/obo/bto.owl OBO-Edit 2.3.1 Slimmer - 2024-01-01 01:36:59 + 2024-02-01 01:23:08 23:10:2021 16:56 BrendaTissueOBO 1.2 diff --git a/external-dev/ccont-slim.owl b/external-dev/ccont-slim.owl index 5d43717e..2487c3bb 100644 --- a/external-dev/ccont-slim.owl +++ b/external-dev/ccont-slim.owl @@ -15,7 +15,7 @@ https://raw.githubusercontent.com/enanomapper/ontologies/master/internal/ccont-ext.owl Matthias Ganzinger, matthias.ganzinger@med.uni-heidelberg.de Slimmer - 2024-01-01 01:37:00 + 2024-02-01 01:23:09 cell culture ontology (CCONT) 1.1 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. diff --git a/external-dev/chebi-slim.owl b/external-dev/chebi-slim.owl index faefb615..82c95086 100644 --- a/external-dev/chebi-slim.owl +++ b/external-dev/chebi-slim.owl @@ -17,13 +17,13 @@ http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi_lite.obo Slimmer - 07:12:2023 17:27 - 2024-01-01 01:39:17 + 04:01:2024 19:44 + 2024-02-01 01:24:45 chebi_ontology 1.2 chebi Author: ChEBI curation team - ChEBI Release version 227 + ChEBI Release version 228 ChEBI subsumes and replaces the Chemical Ontology first For any queries contact chebi-help@ebi.ac.uk developed by Michael Ashburner & Pankaj Jaiswal. @@ -1314,6 +1314,20 @@ + + + + + + The compound producing the peak used to reference an NMR spectrum during data pre-processing + chebi_ontology + CHEBI:228364 + + NMR chemical shift reference compound + + + + diff --git a/external-dev/cheminf-slim.owl b/external-dev/cheminf-slim.owl index 216db7bf..69a458d3 100644 --- a/external-dev/cheminf-slim.owl +++ b/external-dev/cheminf-slim.owl @@ -79,7 +79,7 @@ http://creativecommons.org/publicdomain/zero/1.0/ http://semanticchemistry.github.io/semanticchemistry/ontology/cheminf.owl Slimmer - 2024-01-01 01:37:05 + 2024-02-01 01:23:12 An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO Document containing upporting external terms IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 diff --git a/external-dev/chmo-slim.owl b/external-dev/chmo-slim.owl index df92e584..d56787f6 100644 --- a/external-dev/chmo-slim.owl +++ b/external-dev/chmo-slim.owl @@ -19,7 +19,7 @@ http://purl.obolibrary.org/obo/chmo.owl Slimmer - 2024-01-01 01:39:23 + 2024-02-01 01:24:50 1.2 batchelorc This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. diff --git a/external-dev/clo-slim.owl b/external-dev/clo-slim.owl index 3b65c87f..7c028cb5 100644 --- a/external-dev/clo-slim.owl +++ b/external-dev/clo-slim.owl @@ -44,9 +44,9 @@ http://purl.obolibrary.org/obo/cl.owl Slimmer - 2024-01-01 01:39:35 + 2024-02-01 01:25:02 See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. - 2023-12-05 + 2024-01-04 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. @@ -342,6 +342,15 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( + + + + + + + + + @@ -978,15 +987,6 @@ WHERE { - - - - - - - - - diff --git a/external-dev/efo-slim.owl b/external-dev/efo-slim.owl index 655814ec..77311183 100644 --- a/external-dev/efo-slim.owl +++ b/external-dev/efo-slim.owl @@ -54,9 +54,9 @@ License. www.apache.org/licenses/LICENSE-2.0 http://www.ebi.ac.uk/efo/efo.owl Slimmer - 2024-01-01 01:40:41 - 2023-12-18 - 3.61.0 + 2024-02-01 01:25:43 + 2024-01-15 + 3.62.0 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. @@ -8491,6 +8491,19 @@ Established melanoma cell line from the Skin Cancer Unit at the German Cancer Re + + + + + + The age at which diverticulitis manifestations first appear. + age at onset of diverticulitis + age diverticulitis symptoms begin + age of onset of diverticulitis + + + + diff --git a/external-dev/envo-slim.owl b/external-dev/envo-slim.owl index 85be8e73..f22d5e9a 100644 --- a/external-dev/envo-slim.owl +++ b/external-dev/envo-slim.owl @@ -35,7 +35,7 @@ https://github.com/EnvironmentOntology/envo/ https://github.com/EnvironmentOntology/envo/issues/ Slimmer - 2024-01-01 01:40:48 + 2024-02-01 01:25:50 ENVO Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>) VersionIRI(<null>))) [Axioms: 679 Logical Axioms: 119] Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>) VersionIRI(<null>))) [Axioms: 206 Logical Axioms: 34] diff --git a/external-dev/fabio-slim.owl b/external-dev/fabio-slim.owl index 33d499cd..f0dc79d3 100644 --- a/external-dev/fabio-slim.owl +++ b/external-dev/fabio-slim.owl @@ -33,7 +33,7 @@ FaBiO classes are structured according to the FRBR schema of Works, Expressions, fabio http://purl.org/spar/fabio/ Slimmer - 2024-01-01 01:40:52 + 2024-02-01 01:25:54 FaBiO, the FRBR-aligned Bibliographic Ontology, is an ontology for recording and publishing on the Semantic Web bibliographic records of scholarly endeavours. It forms part of SPAR, a suite of Semantic Publishing and Referencing Ontologies. Other SPAR ontologies are described at http://purl.org/spar/. This ontology is available at http://purl.org/spar/fabio, and uses the namespace prefix fabio. diff --git a/external-dev/go-slim.owl b/external-dev/go-slim.owl index 27707391..5c4ea5a0 100644 --- a/external-dev/go-slim.owl +++ b/external-dev/go-slim.owl @@ -24,10 +24,10 @@ http://purl.obolibrary.org/obo/go.owl Slimmer - 2024-01-01 01:41:14 + 2024-02-01 01:26:16 gene_ontology 1.2 - 2023-11-15 + 2024-01-17 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. @@ -270,6 +270,16 @@ + + + + + GO subset for prokaryotes + + + + + @@ -297,16 +307,6 @@ - - - - - GO subset for prokaryotes - - - - - diff --git a/external-dev/iao-slim.owl b/external-dev/iao-slim.owl index b819e0b0..f3364039 100644 --- a/external-dev/iao-slim.owl +++ b/external-dev/iao-slim.owl @@ -57,7 +57,7 @@ http://purl.obolibrary.org/obo/iao.owl Slimmer - 2024-01-01 01:41:17 + 2024-02-01 01:26:18 An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 diff --git a/external-dev/msio-slim.owl b/external-dev/msio-slim.owl index 93809e4a..e22d4bc9 100644 --- a/external-dev/msio-slim.owl +++ b/external-dev/msio-slim.owl @@ -181,7 +181,7 @@ http://www.cosmos-fp7.eu/WP2 Slimmer Daniel Schober 2017-10-19T10:11:26Z - 2024-01-01 01:44:28 + 2024-02-01 01:29:11 Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif. The BSD license on the BFO project site refers to code used to build BFO. This version (1.1.0) uses the Basic Formal Ontology (BFO) as its top level ontology. We might at some point close the resulting semantic gap by using OBI and IAO as intermediate bridges. diff --git a/external-dev/ncit-slim.owl b/external-dev/ncit-slim.owl index 989564c5..5aa65968 100644 --- a/external-dev/ncit-slim.owl +++ b/external-dev/ncit-slim.owl @@ -21,7 +21,7 @@ NCI Thesaurus OBO Edition http://purl.obolibrary.org/obo/ncit.owl Slimmer - 2024-01-01 01:43:29 + 2024-02-01 01:28:21 NCI Thesaurus, a controlled vocabulary in support of NCI administrative and scientific activities. Produced by the Enterprise Vocabulary System (EVS), a project by the NCI Center for Biomedical Informatics and Information Technology. National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, U.S.A. 23.09d This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. diff --git a/external-dev/npo-slim.owl b/external-dev/npo-slim.owl index b2062840..b16ded67 100644 --- a/external-dev/npo-slim.owl +++ b/external-dev/npo-slim.owl @@ -17,7 +17,7 @@ http://purl.bioontology.org/ontology/npo https://raw.githubusercontent.com/enanomapper/npo/master/npo-inferred.owl Slimmer - 2024-01-01 01:43:33 + 2024-02-01 01:28:25 Inferred version created with Pellet reasoner in Protege editor (v. 4.1) The NPO was primarily developed by Dennis G. Thomas in collaboration with Nathan A. Baker and Rohit V. Pappu. This development was supported by the NIH through grants U54 CA119342 and U54 HG004028. 2013-05-31 (yyyy-mm-dd) diff --git a/external-dev/oae-slim.owl b/external-dev/oae-slim.owl index 29b419ef..f7698999 100644 --- a/external-dev/oae-slim.owl +++ b/external-dev/oae-slim.owl @@ -58,7 +58,7 @@ OAE: Ontology of Adverse Events http://purl.obolibrary.org/obo/oae.owl Slimmer - 2024-01-01 01:43:40 + 2024-02-01 01:28:31 1.2.47 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. diff --git a/external-dev/obcs-slim.owl b/external-dev/obcs-slim.owl index 2d14313f..1bf2a2ff 100644 --- a/external-dev/obcs-slim.owl +++ b/external-dev/obcs-slim.owl @@ -37,7 +37,7 @@ http://purl.obolibrary.org/obo/obcs.owl Slimmer - 2024-01-01 01:43:44 + 2024-02-01 01:28:34 2023-12-08 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. diff --git a/external-dev/obi-slim.owl b/external-dev/obi-slim.owl index 44cee41a..70a4d54a 100644 --- a/external-dev/obi-slim.owl +++ b/external-dev/obi-slim.owl @@ -82,9 +82,9 @@ Ontology for Biomedical Investigations http://purl.obolibrary.org/obo/obi.owl Slimmer - 2024-01-01 01:43:50 + 2024-02-01 01:28:39 Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. - 2023-09-20 + 2024-01-09 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. @@ -1036,13 +1036,6 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891 - - - - - - - @@ -21663,6 +21656,40 @@ https://www.doi.org/ + + + + + + + electron microscopy assay determining the 3D structure of a T cell epitope:MHC:TCR complex + + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR complex. + PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters + IEDB + 3D structure|electron microscopy + electron microscopy assay determining the 3D structure of a T cell epitope:MHC:TCR complex + + + + + + + + + + + electron microscopy assay determining the 3D structure of a MHC:ligand complex + + An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex. + PERSON:Randi Vita, Sebastian Duesing, Bjoern Peters + IEDB + 3D structure|electron microscopy + electron microscopy assay determining the 3D structure of a MHC:ligand complex + + + + diff --git a/external-dev/pato-slim.owl b/external-dev/pato-slim.owl index 7a9c8d8c..e524fe3d 100644 --- a/external-dev/pato-slim.owl +++ b/external-dev/pato-slim.owl @@ -39,7 +39,7 @@ http://purl.obolibrary.org/obo/pato.owl Slimmer - 2024-01-01 01:44:00 + 2024-02-01 01:28:48 quality 1.2 2023-05-18 diff --git a/external-dev/sio-slim.owl b/external-dev/sio-slim.owl index 6d8459a2..d83a1c95 100644 --- a/external-dev/sio-slim.owl +++ b/external-dev/sio-slim.owl @@ -80,7 +80,7 @@ mailing list: http://groups.google.com/group/sio-ontology role chains: 'has capability' o 'is realized in' -> 'is participant in' Slimmer - 2024-01-01 01:44:03 + 2024-02-01 01:28:51 http://sio.semanticscience.org 1.59 This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer. diff --git a/external-dev/uberon-slim.owl b/external-dev/uberon-slim.owl index 7319c36c..781a663f 100644 --- a/external-dev/uberon-slim.owl +++ b/external-dev/uberon-slim.owl @@ -22,6 +22,7 @@ xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:chebi="http://purl.obolibrary.org/obo/chebi/" xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#" + xmlns:sssom="https://w3id.org/sssom/" xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:terms="http://purl.org/dc/terms/" xmlns:vocab="https://w3id.org/semapv/vocab/" @@ -158,7 +159,7 @@ https://github.com/obophenotype/uberon/issues/ https://lists.sourceforge.net/lists/listinfo/obo-anatomy Slimmer - 2024-01-01 01:44:22 + 2024-02-01 01:29:07 uberon 1.2 AEO @@ -540,6 +541,29 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. + + + + + A synonym type for describing dubious synonyms + + + 2023-03-03 + dubious synonym + + + + + + + + + + + + + + @@ -565,6 +589,7 @@ Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary. 2023-10-12 latin term + @@ -1733,6 +1758,15 @@ WHERE { + + + + + + + + + @@ -1904,15 +1938,6 @@ WHERE { - - - - - - - - - @@ -2122,16 +2147,6 @@ WHERE { - - - - - dubious or contested synonym - - - - - @@ -2162,16 +2177,6 @@ WHERE { - - - - - latin term - - - - - @@ -3457,6 +3462,27 @@ WHERE { + + + + + + + + + + + + + + + + + + + + +