diff --git a/external-dev/aopo-slim.owl b/external-dev/aopo-slim.owl
index 0f1a75c6..afdb45f0 100644
--- a/external-dev/aopo-slim.owl
+++ b/external-dev/aopo-slim.owl
@@ -44,7 +44,7 @@
https://raw.githubusercontent.com/jmillanacosta/aop-ontology/patch-1/aopo.owl
Slimmer
- 2023-07-20 11:55:15
+ 2023-08-01 01:46:17
27:06:2023 19:06
chebi_ontology
human_phenotype
diff --git a/external-dev/bao-slim.owl b/external-dev/bao-slim.owl
index 3642d242..398f7270 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
- 2023-07-20 11:55:23
+ 2023-08-01 01:46:24
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 61658220..d456562c 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
- 2023-07-20 11:55:25
+ 2023-08-01 01:46:26
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 1cdc4565..0fac23f9 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
- 2023-07-20 11:55:29
+ 2023-08-01 01:46:31
23:10:2021 16:56
BrendaTissueOBO
1.2
diff --git a/external-dev/ccont-slim.owl b/external-dev/ccont-slim.owl
index 225d0370..99910f1d 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
- 2023-07-20 11:55:31
+ 2023-08-01 01:46:32
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 88d6aa52..4dce56c1 100644
--- a/external-dev/chebi-slim.owl
+++ b/external-dev/chebi-slim.owl
@@ -17,7 +17,7 @@
http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi_lite.obo
Slimmer
- 2023-07-20 11:57:10
+ 2023-08-01 01:48:13
27:06:2023 19:06
chebi_ontology
1.2
diff --git a/external-dev/cheminf-slim.owl b/external-dev/cheminf-slim.owl
index 75dd36e9..2ada2809 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
- 2023-07-20 11:55:34
+ 2023-08-01 01:46:35
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 629630a1..cd2c8ef2 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
- 2023-07-20 11:57:15
+ 2023-08-01 01:48:18
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 565a5aee..d320ee88 100644
--- a/external-dev/clo-slim.owl
+++ b/external-dev/clo-slim.owl
@@ -46,7 +46,7 @@
http://purl.obolibrary.org/obo/cl.owl
Slimmer
- 2023-07-20 11:57:30
+ 2023-08-01 01:48:33
See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo.
2023-07-20
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/efo-slim.owl b/external-dev/efo-slim.owl
index 182705ac..f3c84c62 100644
--- a/external-dev/efo-slim.owl
+++ b/external-dev/efo-slim.owl
@@ -54,7 +54,7 @@ License.
Sirarat Sarntivijai
Tomasz Adamusiak
Slimmer
- 2023-07-20 11:59:10
+ 2023-08-01 01:51:03
2023-07-17
3.56.0
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/envo-slim.owl b/external-dev/envo-slim.owl
index 6242beca..c7ef7205 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
- 2023-07-20 11:59:16
+ 2023-08-01 01:51:09
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 7bd67e90..d7b66b51 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
- 2023-07-20 11:59:21
+ 2023-08-01 01:51:14
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 8ff72f31..03ea4463 100644
--- a/external-dev/go-slim.owl
+++ b/external-dev/go-slim.owl
@@ -16,15 +16,18 @@
xmlns:terms2="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+
+
+
The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms.
Gene Ontology
http://purl.obolibrary.org/obo/go.owl
Slimmer
- 2023-07-20 11:59:49
+ 2023-08-01 01:51:42
gene_ontology
1.2
- 2023-06-11
+ 2023-07-27
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
@@ -87,6 +90,13 @@
+
+
+
+
+
+
+
@@ -736,6 +746,15 @@
results_in_maintenance_of
results in maintenance of
+
+ IAO:0000700
+ external
+ has_ontology_root_term
+ true
+ true
+ has_ontology_root_term
+ has ontology root term
+
RO:0000053
external
diff --git a/external-dev/iao-slim.owl b/external-dev/iao-slim.owl
index 30708e42..95ab7817 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
- 2023-07-20 11:59:51
+ 2023-08-01 01:51:45
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 48d91c83..6975a564 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
- 2023-07-20 12:03:28
+ 2023-08-01 01:55:17
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 df1eeeba..bd2822ba 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
- 2023-07-20 12:02:26
+ 2023-08-01 01:54:18
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.
22.07d
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 b49acda9..c21cec39 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
- 2023-07-20 12:02:29
+ 2023-08-01 01:54:23
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 b2428b68..ef0fe1da 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
- 2023-07-20 12:02:37
+ 2023-08-01 01:54:29
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 b8eaaa60..739c0cac 100644
--- a/external-dev/obcs-slim.owl
+++ b/external-dev/obcs-slim.owl
@@ -27,7 +27,7 @@
http://purl.obolibrary.org/obo/obcs.owl
Slimmer
- 2023-07-20 12:02:41
+ 2023-08-01 01:54:33
101
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 289f085d..e822d7c6 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
- 2023-07-20 12:02:46
+ 2023-08-01 01:54:38
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.
- 2023-03-10
+ 2023-07-25
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
@@ -1309,6 +1309,7 @@ https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891
+
A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series.
LC-MS-MS
@@ -1372,8 +1373,9 @@ Previous. An information content entity is a non-realizable information entity t
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
- A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
+ A planned process that has the objective to produce information about a material entity (the evaluant) by examining it.
12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
+ Discussion on OBI call 2023-05-01 resulted in an agreement to revise the textual definition of 'assay'. https://github.com/obi-ontology/obi/issues/1683.
PlanAndPlannedProcess Branch
measuring
scientific observation
@@ -12558,11 +12560,11 @@ Previous. An information content entity is a non-realizable information entity t
-
+
carboxyfluorescein succinimidyl ester staining assay
Measuring T cell proliferation based on the progressive halving of CFSE fluorescence within daughter cells following each cell division.
- a assay detecting a molecular label assay where the amount of carboxyfluorescein succinimidyl ester is measured using fluorescence detection.
+ An assay using carboxyfluorescein succinimidyl ester staining.
IEDB
CFSE assay
IEDB
@@ -13854,10 +13856,10 @@ https://www.doi.org/
- physical examination of individual
+ physical examination of an organism
- An assay that produces a description of the qualities of an entity that has not been transformed, through observation and physical, non-invasive techniques.
- physical examination of individual
+ An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques.
+ physical examination of an organism
@@ -16918,7 +16920,7 @@ https://www.doi.org/
coma severity assay
Examining a patient and grading their coma status on the Blantyre or Glasgow coma scale.
- A physical examination of individual that has the objective to determine the severity of coma in a patient.
+ A physical examination of an organism that has the objective to determine the severity of coma in a patient.
John Judkins
https://github.com/obi-ontology/obi/issues/1357
John Judkins
@@ -21391,6 +21393,117 @@ https://www.doi.org/
+
+
+
+
+
+ proximity ligation-assisted ChIP-seq
+
+ A chromosome conformation capture assay in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation. Immunopreciptation with an antibody that targets a transcription factor or histone modification allows for selection and enrichment of specific genomic regions for investigation of long-range chromosomal interactions.
+ Hector Guzman-Orozco
+ PLAC-seq
+ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5143423/
+ https://github.com/obi-ontology/obi/issues/1145
+ proximity ligation-assisted ChIP-seq
+
+
+
+
+
+
+
+
+
+ skin of body microbiology assay
+
+ An organism detection assay that detects microorganisms in a skin of body specimen.
+ John Judkins ORCID:0000-0001-6595-0902
+ VEuPathDB
+ https://github.com/obi-ontology/obi/issues/1680
+ skin of body microbiology assay
+
+
+
+
+
+
+
+
+
+ bone marrow microbiology assay
+
+ An organism detection assay that detects microorganisms in a bone marrow specimen.
+ John Judkins ORCID:0000-0001-6595-0902
+ VEuPathDB
+ https://github.com/obi-ontology/obi/issues/1680
+ bone marrow microbiology assay
+
+
+
+
+
+
+
+
+
+ nasal aspirate microbiology assay
+
+ An organism detection assay that detects microorganisms in a nasal aspirate specimen.
+ John Judkins ORCID:0000-0001-6595-0902
+ VEuPathDB
+ https://github.com/obi-ontology/obi/issues/1680
+ nasal aspirate microbiology assay
+
+
+
+
+
+
+
+
+
+
+ cell proliferation assay using carboxyfluorescein succinimidyl ester staining
+
+ A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division.
+ Sebastian Duesing
+ https://github.com/obi-ontology/obi/issues/1007
+ cell proliferation assay using carboxyfluorescein succinimidyl ester staining
+
+
+
+
+
+
+
+
+
+ cell viability assay
+
+ A cytometry assay which measures the number of living cells in a population.
+ Sebastian Duesing
+ https://github.com/obi-ontology/obi/issues/1007
+ cell viability assay
+
+
+
+
+
+
+
+
+
+ cell viability assay using Annexin V staining
+
+ A cell viability assay that uses Annexin V staining to detect apoptotic cells.
+ Sebastian Duesing
+ https://github.com/obi-ontology/obi/issues/1007
+ cell viability assay using Annexin V staining
+
+
+
+
diff --git a/external-dev/pato-slim.owl b/external-dev/pato-slim.owl
index 297be089..f96d779a 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
- 2023-07-20 12:02:57
+ 2023-08-01 01:54:48
quality
1.2
2023-05-18
diff --git a/external-dev/sio-slim.owl b/external-dev/sio-slim.owl
index 7bbb3da8..8462e924 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
- 2023-07-20 12:02:59
+ 2023-08-01 01:54:51
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 ed4fce7b..ba74bfec 100644
--- a/external-dev/uberon-slim.owl
+++ b/external-dev/uberon-slim.owl
@@ -24,11 +24,13 @@
xmlns:ncicp="http://ncicb.nci.nih.gov/xml/owl/EVS/ComplexProperties.xsd#"
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/"
xmlns:chebi2="http://purl.obolibrary.org/obo/chebi#"
xmlns:chebi3="http://purl.obolibrary.org/obo/chebi#1"
xmlns:chebi4="http://purl.obolibrary.org/obo/chebi#3"
xmlns:chebi5="http://purl.obolibrary.org/obo/chebi#2"
xmlns:terms6="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/"
+ xmlns:uberon="http://purl.obolibrary.org/obo/uberon#"
xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#"
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
@@ -157,7 +159,7 @@
https://github.com/obophenotype/uberon/issues/
https://lists.sourceforge.net/lists/listinfo/obo-anatomy
Slimmer
- 2023-07-20 12:03:23
+ 2023-08-01 01:55:12
uberon
1.2
AEO
@@ -199,10 +201,8 @@
ZFA part_of NCBITaxon:7954
ZFS part_of NCBITaxon:7954
Aurelie Comte, Bill Bug, Catherine Leroy, Duncan Davidson and Trish Whetzel are also contributors. However their ORCIDs were not found.
- Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/TEMP>) VersionIRI(<null>))) [Axioms: 437 Logical Axioms: 0]
Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon-bridge-to-bfo.owl>) VersionIRI(<null>))) [Axioms: 20 Logical Axioms: 9]
- Includes Ontology(OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/uberon/disjoint_union_over.owl>) VersionIRI(<null>))) [Axioms: 38 Logical Axioms: 38]
- 2023-06-27
+ 2023-07-25
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.
http://uberon.org
@@ -235,6 +235,13 @@
+
+
+
+
+
+
+
@@ -246,6 +253,11 @@
+ example of usage
+
+ A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
+ PERSON:Daniel Schober
+ GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
IAO:0000112
uberon
example_of_usage
@@ -269,6 +281,31 @@
+ definition
+
+ The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
+ 2012-04-05:
+Barry Smith
+
+The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
+
+Can you fix to something like:
+
+A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
+
+Alan Ruttenberg
+
+Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
+
+On the specifics of the proposed definition:
+
+We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
+
+Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
+
+We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
+ PERSON:Daniel Schober
+ GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition
definition
@@ -280,6 +317,11 @@
+ editor note
+
+ An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
+ PERSON:Daniel Schober
+ GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
IAO:0000116
uberon
editor_note
@@ -316,7 +358,13 @@
-
+
+ has obsolescence reason
+ Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
+ PERSON:Alan Ruttenberg
+ PERSON:Melanie Courtot
+ has obsolescence reason
+
@@ -324,6 +372,10 @@
+ curator note
+
+ An administrative note of use for a curator but of no use for a user
+ PERSON:Alan Ruttenberg
IAO:0000232
uberon
curator_notes
@@ -341,6 +393,12 @@
+ term tracker item
+ the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
+
+ An IRI or similar locator for a request or discussion of an ontology term.
+ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
+ Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
IAO:0000233
external
uberon
@@ -348,18 +406,13 @@
true
true
term_tracker_item
+ The 'tracker item' can associate a tracker with a specific ontology term.
+ term tracker item
term tracker item
-
-
-
-
-
-
-
@@ -371,6 +424,14 @@
+ expand assertion to
+ ObjectProperty: RO???
+Label: spatially disjoint from
+Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
+
+ A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom.
+ Chris Mungall
+ expand assertion to
expand assertion to
@@ -436,7 +497,12 @@
+ term replaced by
+ Use on obsolete terms, relating the term to another term that can be used as a substitute
+ Person:Alan Ruttenberg
+ Person:Alan Ruttenberg
+ Add as annotation triples in the granting ontology
term replaced by
term replaced by
@@ -663,7 +729,6 @@ WHERE {
- defined by inverse
@@ -1462,7 +1527,6 @@ WHERE {
- synonym typically used in the context of vertebrate anatomy
@@ -1987,12 +2051,20 @@ WHERE {
- eco subset
+
+
+
+
+
+
+
+
+
@@ -2542,6 +2614,13 @@ WHERE {
+
+
+
+
+
+
+
@@ -2876,7 +2955,12 @@ WHERE {
+ An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/18
+ has broad synonym
has_broad_synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/18
@@ -2894,7 +2978,12 @@ WHERE {
+ An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/20
+ has exact synonym
has_exact_synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/20
@@ -2903,7 +2992,12 @@ WHERE {
+ An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/19
+ has narrow synonym
has_narrow_synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/19
@@ -2928,7 +3022,12 @@ WHERE {
+ An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
+
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/21
+ has related synonym
has_related_synonym
+ https://github.com/information-artifact-ontology/ontology-metadata/issues/21
@@ -3376,6 +3475,13 @@ WHERE {
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ example to be eventually removed
+ example to be eventually removed
+
+
+
+
+
+
+
+
+ metadata complete
+ Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
+ metadata complete
+
+
+
+
+
+
+
+
+ organizational term
+ Term created to ease viewing/sort terms for development purpose, and will not be included in a release
+ organizational term
+
+
+
+
+
+
+
+
+ ready for release
+
+ Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
+ ready for release
+
+
+
+
+
+
+
+
+ metadata incomplete
+ Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
+ metadata incomplete
+
+
+
+
+
+
+
+
+ uncurated
+ Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
+ uncurated
+
+
+
+
+
+
+
+
+ pending final vetting
+
+ All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
+ pending final vetting
+
+
+
+
+
+
+
+
+ to be replaced with external ontology term
+ Terms with this status should eventually replaced with a term from another ontology.
+ Alan Ruttenberg
+ group:OBI
+ to be replaced with external ontology term
+
+
+
+
+
+
+
+
+ requires discussion
+
+ A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
+ Alan Ruttenberg
+ group:OBI
+ requires discussion
+
@@ -4194,11 +3981,15 @@ WHERE {
+ has ontology root term
+ Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root.
+ Nicolas Matentzoglu
IAO:0000700
uberon
has_ontology_root_term
true
has_ontology_root_term
+ has ontology root term
has ontology root term
preferred_root
@@ -4321,6 +4112,86 @@ WHERE {
foaf-homepage
homepage
+
+ researcher
+ Shawn Zheng Kai Tan
+
+
+
+
+ researcher
+
+
+
+
+
+ Shawn Zheng Kai Tan
+
+
+
+ data scientist
+ Anne Thessen
+
+
+
+
+ data scientist
+
+
+
+
+
+ Anne Thessen
+
+
+
+ bioinformatics researcher
+ Christopher J. Mungall
+
+
+
+
+ bioinformatics researcher
+
+
+
+
+
+ Christopher J. Mungall
+
+
+
+ researcher
+ David Osumi-Sutherland
+
+
+
+
+ researcher
+
+
+
+
+
+ David Osumi-Sutherland
+
+
+
+ researcher
+ James P. Balhoff
+
+
+
+
+ researcher
+
+
+
+
+
+ James P. Balhoff
+
+
diff --git a/external-dev/uo-slim.owl b/external-dev/uo-slim.owl
index 61eae7b6..3a8a0535 100644
--- a/external-dev/uo-slim.owl
+++ b/external-dev/uo-slim.owl
@@ -12,7 +12,7 @@
http://purl.obolibrary.org/obo/uo.owl
Slimmer
- 2023-07-20 12:03:25
+ 2023-08-01 01:55:14
2023-05-25
This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.