4th batch adding terms for SbD4Nano

.github/workflows/build.yml

@@ -205,8 +205,10 @@ jobs:
       run: bash scripts/src/build-workflow/props.sh ro
   # Commit and push
     - name: Commit OWL files
-      if: ${{ github.event_name != 'pull_request' || github.event.action != 'closed' || github.event.pull_request.merged == false }} # do not try to commit if not ran in branch but on PR
       run: |
+        if [[ "${{ github.ref_name }}" == *"merge"* ]]; then
+          exit 0
+        fi
         git checkout "${{ github.ref_name }}"
         git pull
         git add external-dev/*.owl

config/go.iris

@@ -15,3 +15,4 @@
 +D(http://purl.obolibrary.org/obo/GO_0009987):http://purl.obolibrary.org/obo/GO_1902806 regulation of cell cycle G1/S phase transition
 +D(http://purl.obolibrary.org/obo/GO_0009987):http://purl.obolibrary.org/obo/GO_0051493 regulation of cytoskeleton organization
 +D(http://purl.obolibrary.org/obo/GO_0009987):http://purl.obolibrary.org/obo/GO_0141085 regulation of inflammasome-mediated signaling pathway
++(http://purl.obolibrary.org/obo/GO_0003824):http://purl.obolibrary.org/obo/GO_0016175 superoxide-generating NAD(P)H oxidase activity

config/pato.iris

@@ -20,4 +20,4 @@
 +(http://purl.obolibrary.org/obo/BFO_0000019):http://purl.obolibrary.org/obo/PATO_0000150 texture
 +(http://purl.obolibrary.org/obo/PATO_0000150):http://purl.obolibrary.org/obo/PATO_0002012 coating
 -:http://purl.org/spar/cito/citesAsAuthority
-+(http://purl.obolibrary.org/obo/BFO_0000019):http://purl.obolibrary.org/obo/PATO_0000014 color
++(http://semanticscience.org/resource/CHEMINF_000101):http://purl.obolibrary.org/obo/PATO_0001300 optical qualities (includes color)

config/sio.iris

@@ -4,3 +4,4 @@
 +D(http://purl.bioontology.org/ontology/npo#NPO_1793):http://semanticscience.org/resource/SIO_000769 uncertainty value
 +D(http://purl.obolibrary.org/obo/OBI_0100026):http://semanticscience.org/resource/SIO_010055 strain
 +D(http://purl.bioontology.org/ontology/npo#NPO_1597):http://semanticscience.org/resource/SIO_010471 protein part
++D(http://purl.obolibrary.org/obo/BFO_0000019):http://semanticscience.org/resource/SIO_000475 biological quality

enanomapper-dev.owl

@@ -55,6 +55,7 @@
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal-dev/wikidata.owl"/>
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal-dev/go-ext.owl"/>
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal-dev/efo-ext.owl"/>
+        <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal-dev/sio-ext.owl"/>
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal-dev/nmlco.owl"/> 
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/enanomapper-auto-dev.owl"/>
         <owl:versionInfo>11.0-SNAPSHOT</owl:versionInfo>

external-dev/aopo-slim.owl

@@ -44,7 +44,7 @@
         <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>2024-04-16 11:24:22</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:00:14</oboInOwl:date>
         <oboInOwl:date>28:03:2024 12:38</oboInOwl:date>
         <oboInOwl:default-namespace>chebi_ontology</oboInOwl:default-namespace>
         <oboInOwl:default-namespace>human_phenotype</oboInOwl:default-namespace>

external-dev/bao-slim.owl

@@ -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>2024-04-16 11:24:30</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:00:22</oboInOwl:date>
         <rdfs:comment>Contact:
 Stephan Schurer
 stephan dot schurer at gmail dot com</rdfs:comment>

external-dev/bfo-slim.owl

@@ -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>2024-04-16 11:24:32</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:00:24</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. 

external-dev/bto-slim.owl

@@ -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>2024-04-16 11:24:36</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:00:28</oboInOwl:date>
         <oboInOwl:date>23:10:2021 16:56</oboInOwl:date>
         <oboInOwl:default-namespace>BrendaTissueOBO</oboInOwl:default-namespace>
         <oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>

external-dev/ccont-slim.owl

@@ -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>2024-04-16 11:24:38</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:00:29</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>

external-dev/chebi-slim.owl

@@ -17,7 +17,7 @@
     <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>2024-04-16 11:26:17</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:02:06</oboInOwl:date>
         <oboInOwl:date>28:03:2024 12:38</oboInOwl:date>
         <oboInOwl:default-namespace>chebi_ontology</oboInOwl:default-namespace>
         <oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>

external-dev/cheminf-slim.owl

@@ -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>2024-04-16 11:24:40</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:00:32</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>

external-dev/chmo-slim.owl

@@ -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>2024-04-16 11:26:21</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:02:11</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>

external-dev/clo-slim.owl

@@ -38,7 +38,7 @@
         <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>2024-04-16 11:26:33</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:02:23</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>2024-04-05</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>

external-dev/efo-slim.owl

@@ -55,7 +55,7 @@ License. </dc:rights>
         <terms:license>www.apache.org/licenses/LICENSE-2.0</terms:license>
         <pav:importedFrom>http://www.ebi.ac.uk/efo/efo.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:27:39</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:03:47</oboInOwl:date>
         <rdfs:comment>2024-04-15</rdfs:comment>
         <owl:versionInfo>3.65.0</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>

external-dev/envo-slim.owl

@@ -35,7 +35,7 @@
         <doap:GitRepository rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/EnvironmentOntology/envo/</doap:GitRepository>
         <doap:bug-database rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/EnvironmentOntology/envo/issues/</doap:bug-database>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:27:46</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:03:54</oboInOwl:date>
         <oboInOwl:default-namespace>ENVO</oboInOwl:default-namespace>
         <rdfs:comment>Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 679 Logical Axioms: 119]</rdfs:comment>
         <rdfs:comment>Includes Ontology(OntologyID(OntologyIRI(&lt;http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl&gt;) VersionIRI(&lt;null&gt;))) [Axioms: 206 Logical Axioms: 34]</rdfs:comment>

external-dev/fabio-slim.owl

@@ -33,7 +33,7 @@ FaBiO classes are structured according to the FRBR schema of Works, Expressions,
         <vann:preferredNamespacePrefix>fabio</vann:preferredNamespacePrefix>
         <vann:preferredNamespaceUri rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://purl.org/spar/fabio/</vann:preferredNamespaceUri>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:27:51</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:03:58</oboInOwl:date>
         <rdfs:comment>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.</rdfs:comment>

external-dev/go-slim.owl

@@ -24,7 +24,7 @@
         <terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
         <pav:importedFrom>http://purl.obolibrary.org/obo/go.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:28:12</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:04:21</oboInOwl:date>
         <oboInOwl:default-namespace>gene_ontology</oboInOwl:default-namespace>
         <oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
         <owl:versionInfo>2024-03-28</owl:versionInfo>

external-dev/iao-slim.owl

@@ -57,7 +57,7 @@
         <terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
         <pav:importedFrom>http://purl.obolibrary.org/obo/iao.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:28:14</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:04:23</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>IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999</rdfs:comment>
         <rdfs:comment>IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999</rdfs:comment>

external-dev/msio-slim.owl

@@ -181,7 +181,7 @@ http://www.cosmos-fp7.eu/WP2</doap:maintainer>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
         <oboInOwl:created_by xml:lang="en">Daniel Schober</oboInOwl:created_by>
         <oboInOwl:creation_date xml:lang="en">2017-10-19T10:11:26Z</oboInOwl:creation_date>
-        <oboInOwl:date>2024-04-16 11:31:08</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:07:17</oboInOwl:date>
         <rdfs:comment xml:lang="en">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.</rdfs:comment>
         <rdfs:comment xml:lang="en">The BSD license on the BFO project site refers to code used to build BFO.</rdfs:comment>
         <rdfs:comment xml:lang="en">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.</rdfs:comment>

external-dev/ncit-slim.owl

@@ -21,7 +21,7 @@
         <terms:title>NCI Thesaurus OBO Edition</terms:title>
         <pav:importedFrom>http://purl.obolibrary.org/obo/ncit.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:30:19</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:06:28</oboInOwl:date>
         <rdfs:comment>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.</rdfs:comment>
         <owl:versionInfo>23.09d</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>

external-dev/npo-slim.owl

@@ -17,7 +17,7 @@
         <dc:identifier>http://purl.bioontology.org/ontology/npo</dc:identifier>
         <pav:importedFrom>https://raw.githubusercontent.com/enanomapper/npo/master/npo-inferred.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:30:22</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:06:31</oboInOwl:date>
         <rdfs:comment>Inferred version created with Pellet reasoner in Protege editor (v. 4.1)</rdfs:comment>
         <rdfs:comment>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.</rdfs:comment>
         <owl:versionInfo>2013-05-31 (yyyy-mm-dd)</owl:versionInfo>

external-dev/oae-slim.owl

@@ -58,7 +58,7 @@
         <dc:title xml:lang="en">OAE: Ontology of Adverse Events</dc:title>
         <pav:importedFrom>http://purl.obolibrary.org/obo/oae.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:30:28</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:06:37</oboInOwl:date>
         <owl:versionInfo xml:lang="en">1.2.47</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>

external-dev/obcs-slim.owl

@@ -37,7 +37,7 @@
         <terms:license rdf:resource="http://creativecommons.org/licenses/by/4.0/"/>
         <pav:importedFrom>http://purl.obolibrary.org/obo/obcs.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:30:32</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:06:41</oboInOwl:date>
         <owl:versionInfo>2023-12-08</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>

external-dev/obi-slim.owl

@@ -82,7 +82,7 @@
         <terms:title>Ontology for Biomedical Investigations</terms:title>
         <pav:importedFrom>http://purl.obolibrary.org/obo/obi.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:30:37</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:06:46</oboInOwl:date>
         <rdfs:comment>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.</rdfs:comment>
         <owl:versionInfo>2024-01-09</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>

external-dev/pato-slim.owl

@@ -39,7 +39,7 @@
         <terms:license rdf:resource="https://creativecommons.org/licenses/by/3.0/"/>
         <pav:importedFrom>http://purl.obolibrary.org/obo/pato.owl</pav:importedFrom>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2024-04-16 11:30:44</oboInOwl:date>
+        <oboInOwl:date>2024-04-16 14:06:53</oboInOwl:date>
         <oboInOwl:default-namespace>quality</oboInOwl:default-namespace>
         <oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>
         <owl:versionInfo>2024-03-28</owl:versionInfo>