Skip to content

Commit

Permalink
Actions - slim updated
Browse files Browse the repository at this point in the history
  • Loading branch information
@actions-user
actions-user committed Nov 1, 2023
1 parent 525c9a5 commit eaae784
Show file tree
Hide file tree
Showing 24 changed files with 3,097 additions and 754 deletions.
21 changes: 16 additions & 5 deletions external-dev/aopo-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,10 @@
<dc:creator>Sebastian Köhler</dc:creator>
<dc:date>10 Nov 2022</dc:date>
<dc:date>29 June 2023</dc:date>
<dc:date>31 January 2023</dc:date>
<dc:date>8 Jul 2021</dc:date>
<dc:date>March 9, 2023</dc:date>
<dc:date>May 12, 2023</dc:date>
<dc:date>Oct 9, 2023</dc:date>
<dc:date>September 8, 2023</dc:date>
<dc:description>The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities and clinical features encountered in human disease.</dc:description>
<dc:license rdf:resource="https://creativecommons.org/licenses/by-sa/4.0/"/>
Expand All @@ -43,15 +43,15 @@
<terms:license rdf:resource="https://hpo.jax.org/app/license"/>
<pav:importedFrom>https://raw.githubusercontent.com/jmillanacosta/aop-ontology/patch-1/aopo.owl</pav:importedFrom>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:33:31</oboInOwl:date>
<oboInOwl:date>27:08:2023 19:12</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:23:34</oboInOwl:date>
<oboInOwl:date>27:09:2023 19:34</oboInOwl:date>
<oboInOwl:default-namespace>chebi_ontology</oboInOwl:default-namespace>
<oboInOwl:default-namespace>human_phenotype</oboInOwl:default-namespace>
<oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
<oboInOwl:logical-definition-view-relation>has_part</oboInOwl:logical-definition-view-relation>
<oboInOwl:saved-by>chebi</oboInOwl:saved-by>
<rdfs:comment>Author: ChEBI curation team</rdfs:comment>
<rdfs:comment>ChEBI Release version 225</rdfs:comment>
<rdfs:comment>ChEBI Release version 226</rdfs:comment>
<rdfs:comment>ChEBI subsumes and replaces the Chemical Ontology first</rdfs:comment>
<rdfs:comment>Contact:
Stephan Schurer
Expand All @@ -61,6 +61,9 @@ Stephan Schurer
schurer at med dot miami dot edu</rdfs:comment>
<rdfs:comment>Contact:
Stephan Schurer
sschurer at miami dot edu</rdfs:comment>
<rdfs:comment>Contact:
Stephan Schurer
stephan dot schurer at gmail dot com</rdfs:comment>
<rdfs:comment>Contact:
Stephan Schurer
Expand Down Expand Up @@ -94,7 +97,8 @@ Uma Vempati, Hande Küçük, Ubbo Visser, Saminda Abeyruwan, Kunie Sakurai, Vanc
<owl:versionInfo>2.8.2</owl:versionInfo>
<owl:versionInfo>2.8.6</owl:versionInfo>
<owl:versionInfo>2.8.8</owl:versionInfo>
<owl:versionInfo>2023-09-01</owl:versionInfo>
<owl:versionInfo>2.8.9</owl:versionInfo>
<owl:versionInfo>2023-10-09</owl:versionInfo>
<owl:versionInfo>This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.</owl:versionInfo>
</owl:Ontology>

Expand Down Expand Up @@ -429,6 +433,13 @@ Uma Vempati, Hande Küçük, Ubbo Visser, Saminda Abeyruwan, Kunie Sakurai, Vanc



<!-- http://purl.org/dc/terms/date -->


<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/date"/>



<!-- http://purl.org/dc/terms/license -->


Expand Down
2 changes: 1 addition & 1 deletion external-dev/bao-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@
<dc:license rdf:resource="https://creativecommons.org/licenses/by-sa/4.0/"/>
<pav:importedFrom>http://bioassayontology.org/bao/bao_complete_merged.owl</pav:importedFrom>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:33:38</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:23:43</oboInOwl:date>
<rdfs:comment>Contact:
Stephan Schurer
stephan dot schurer at gmail dot com</rdfs:comment>
Expand Down
2 changes: 1 addition & 1 deletion external-dev/bfo-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@
<dc:license rdf:resource="http://creativecommons.org/licenses/by/3.0/"/>
<pav:importedFrom>http://purl.obolibrary.org/obo/bfo/classes-only.owl</pav:importedFrom>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:33:41</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:23:45</oboInOwl:date>
<rdfs:comment xml:lang="en">The http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO (&quot;bfo_classes_only.owl&quot;) includes only the class hierarchy and annotations from the full OWL version of BFO 2: http://purl.obolibary.org/obo/bfo.owl (&quot;bfo.owl&quot;). 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.
Expand Down
2 changes: 1 addition & 1 deletion external-dev/bto-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
<pav:importedFrom>http://purl.obolibrary.org/obo/bto.owl</pav:importedFrom>
<oboInOwl:auto-generated-by>OBO-Edit 2.3.1</oboInOwl:auto-generated-by>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:33:48</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:23:49</oboInOwl:date>
<oboInOwl:date>23:10:2021 16:56</oboInOwl:date>
<oboInOwl:default-namespace>BrendaTissueOBO</oboInOwl:default-namespace>
<oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
Expand Down
2 changes: 1 addition & 1 deletion external-dev/ccont-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
<pav:importedFrom>https://raw.githubusercontent.com/enanomapper/ontologies/master/internal/ccont-ext.owl</pav:importedFrom>
<efo:creator>Matthias Ganzinger, [email protected]</efo:creator>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:33:50</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:23:50</oboInOwl:date>
<rdfs:label>cell culture ontology (CCONT)</rdfs:label>
<owl:versionInfo>1.1</owl:versionInfo>
<owl:versionInfo>This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.</owl:versionInfo>
Expand Down
6 changes: 3 additions & 3 deletions external-dev/chebi-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -17,13 +17,13 @@
<owl:Ontology rdf:about="http://purl.enanomapper.net/onto/external/chebi-slim.owl">
<pav:importedFrom>http://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi_lite.obo</pav:importedFrom>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:36:24</oboInOwl:date>
<oboInOwl:date>27:08:2023 19:12</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:24:26</oboInOwl:date>
<oboInOwl:date>27:09:2023 19:34</oboInOwl:date>
<oboInOwl:default-namespace>chebi_ontology</oboInOwl:default-namespace>
<oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
<oboInOwl:saved-by>chebi</oboInOwl:saved-by>
<rdfs:comment>Author: ChEBI curation team</rdfs:comment>
<rdfs:comment>ChEBI Release version 225</rdfs:comment>
<rdfs:comment>ChEBI Release version 226</rdfs:comment>
<rdfs:comment>ChEBI subsumes and replaces the Chemical Ontology first</rdfs:comment>
<rdfs:comment>For any queries contact [email protected]</rdfs:comment>
<rdfs:comment>developed by Michael Ashburner &amp; Pankaj Jaiswal.</rdfs:comment>
Expand Down
2 changes: 1 addition & 1 deletion external-dev/cheminf-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@
<terms:license>http://creativecommons.org/publicdomain/zero/1.0/</terms:license>
<pav:importedFrom>http://semanticchemistry.github.io/semanticchemistry/ontology/cheminf.owl</pav:importedFrom>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:33:54</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:23:53</oboInOwl:date>
<rdfs:comment xml:lang="en">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</rdfs:comment>
<rdfs:comment>Document containing upporting external terms</rdfs:comment>
<rdfs:comment>IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999</rdfs:comment>
Expand Down
2 changes: 1 addition & 1 deletion external-dev/chmo-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
<terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
<pav:importedFrom>http://purl.obolibrary.org/obo/chmo.owl</pav:importedFrom>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:36:30</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:24:30</oboInOwl:date>
<oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
<oboInOwl:saved-by>batchelorc</oboInOwl:saved-by>
<owl:versionInfo>This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.</owl:versionInfo>
Expand Down
136 changes: 18 additions & 118 deletions external-dev/clo-slim.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,8 @@
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:caro="http://purl.obolibrary.org/obo/caro#"
xmlns:cito="http://purl.org/spar/cito/"
xmlns:core="http://purl.obolibrary.org/obo/uberon/core#"
xmlns:fbbt="http://purl.obolibrary.org/obo/fbbt#"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:obo1="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/"
xmlns:pato="http://purl.obolibrary.org/obo/pato#"
Expand Down Expand Up @@ -46,9 +44,9 @@
<terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
<pav:importedFrom>http://purl.obolibrary.org/obo/cl.owl</pav:importedFrom>
<oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
<oboInOwl:date>2023-10-01 01:36:49</oboInOwl:date>
<oboInOwl:date>2023-11-01 01:24:41</oboInOwl:date>
<rdfs:comment>See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, [email protected], University at Buffalo.</rdfs:comment>
<owl:versionInfo>2023-09-21</owl:versionInfo>
<owl:versionInfo>2023-10-19</owl:versionInfo>
<owl:versionInfo>This SLIM file was generated automatically by the eNanoMapper Slimmer software library. For more information see http://github.com/enanomapper/slimmer.</owl:versionInfo>
</owl:Ontology>

Expand Down Expand Up @@ -122,7 +120,7 @@ We don&apos;t have definitions of &apos;meaning&apos; or &apos;expression&apos;

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. </obo:IAO_0000116>
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.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:&lt;http://purl.obolibrary.org/obo/obi&gt;</obo:IAO_0000119>
<rdfs:label xml:lang="en">definition</rdfs:label>
Expand Down Expand Up @@ -298,20 +296,6 @@ Annotations: IAO_0000424 &quot;http://purl.obolibrary.org/obo/BFO_0000051 some (



<!-- http://purl.obolibrary.org/obo/IAO_creation_date -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_creation_date"/>



<!-- http://purl.obolibrary.org/obo/IAO_scope -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_scope"/>



<!-- http://purl.obolibrary.org/obo/OMO_0002000 -->


Expand Down Expand Up @@ -343,6 +327,20 @@ Annotations: IAO_0000424 &quot;http://purl.obolibrary.org/obo/BFO_0000051 some (



<!-- http://purl.obolibrary.org/obo/OMO_0003000 -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0003000">
<obo:IAO_0000112>CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)</obo:IAO_0000112>
<obo:IAO_0000115>A synonym type for describing abbreviations or initalisms</obo:IAO_0000115>
<obo:IAO_0000233 rdf:resource="https://github.com/information-artifact-ontology/ontology-metadata/issues/122"/>
<terms:contributor rdf:resource="https://orcid.org/0000-0003-4423-4370"/>
<terms:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2023-03-03</terms:created>
<rdfs:label>abbreviation</rdfs:label>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/OMO_0003004 -->


Expand Down Expand Up @@ -743,24 +741,6 @@ WHERE {



<!-- http://purl.obolibrary.org/obo/caro#core -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/caro#core">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/caro#plus -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/caro#plus">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/cl#BDS_subset -->


Expand All @@ -770,18 +750,6 @@ WHERE {



<!-- http://purl.obolibrary.org/obo/cl#abbreviation -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/cl#abbreviation">
<dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-03-29T15:09:49Z</dc:date>
<terms:contributor rdf:resource="https://orcid.org/0000-0002-1773-2692"/>
<rdfs:label>abbreviation</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/cl#added_for_HCA -->


Expand Down Expand Up @@ -825,51 +793,6 @@ WHERE {



<!-- http://purl.obolibrary.org/obo/fbbt#FORMULA -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/fbbt#FORMULA">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/fbbt#IUPAC_NAME -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/fbbt#IUPAC_NAME">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/fbbt#InChI -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/fbbt#InChI">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/fbbt#InChIKey -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/fbbt#InChIKey">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/fbbt#SMILES -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/fbbt#SMILES">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate -->


Expand Down Expand Up @@ -1156,15 +1079,6 @@ WHERE {



<!-- http://purl.obolibrary.org/obo/pato#relational_slim -->


<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/pato#relational_slim">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/pato#scalar_slim -->


Expand Down Expand Up @@ -1692,13 +1606,6 @@ WHERE {



<!-- http://purl.org/dc/terms/title -->


<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/title"/>



<!-- http://purl.org/pav/importedFrom -->


Expand Down Expand Up @@ -2252,14 +2159,7 @@ WHERE {
<!-- http://xmlns.com/foaf/0.1/depicted_by -->


<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/depicted_by">
<oboInOwl:hasDbXref>http://xmlns.com/foaf/0.1/depicted_by</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>depicted_by</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>depicted_by</oboInOwl:shorthand>
<rdfs:label>depicted by</rdfs:label>
</owl:AnnotationProperty>
<owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/depicted_by"/>



Expand Down
Loading

0 comments on commit eaae784

Please sign in to comment.