Release 9.0

enanomapper · Jan 4, 2023 · 080eb85 · 080eb85
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diff --git a/CITATION.cff b/CITATION.cff
@@ -2,7 +2,7 @@
 # Visit https://bit.ly/cffinit to generate yours today!
 
 cff-version: 1.2.0
-title: eNanoMapper 8.0
+title: eNanoMapper 9.0
 message: >-
   If you use this ontology, please cite the specific
   version and the article.
@@ -38,5 +38,5 @@ keywords:
   - nanomaterials
   - ontologies
 license: CC-BY-3.0
-version: '8.0'
-date-released: '2022-08-11'
+version: '9.0'
+date-released: '2023-01-04'
diff --git a/README.md b/README.md
@@ -118,14 +118,18 @@ Making Releases
 
 
 1. Test if the `enanomapper.owl` can be loaded without errors in Protégé
-   * And run the Makefile with ```make check``` in the ```internal/``` folder
 2. check if the metadata in the enanomapper.owl is up to data (e.g. names of people who submitted PRs)
 3. Copy the internal ontologies in `ontologies/internal-dev/` to `ontologies/internal` and  `ontologies/external-dev/` to `ontologies/external`
-4. Update the owl.versionInfo of `enanomapper.owl`
-5. Update the owl.versionInfo of `enanomapper-dev.owl`
-6. Write markdown for the release with the changes since the previous release
-7. Update the CITATION.cff
-8. Tag the git commit matching the release
+4. Update for `enanomapper.owl` and `enanomapper-dev.owl`:
+   * `owl:versionInfo`
+   * `owl:versionIRI` (only `enanomapper.owl`)
+5. Create a folder `releases/{version}` and store there a copy of the latest `enanomapper.owl` file
+6. Update the CITATION.cff
+   * `title`
+   * `version`
+   * `date-released`
+7. Make a git commit with the changes and tag that commit matching the release
+8. Write markdown for the release with the changes since the previous release
 9. Release the whole repository in GitHub https://github.com/enanomapper/ontologies/releases 
 10. Update the DOI number for new release: https://zenodo.org/record/260098
 

diff --git a/enanomapper-dev.owl b/enanomapper-dev.owl
@@ -53,7 +53,7 @@
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal-dev/pato-ext.owl"/>
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal-dev/wikidata.owl"/>
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies//enanomapper-auto-dev.owl"/>
-        <owl:versionInfo>9.0-SNAPSHOT</owl:versionInfo>
+        <owl:versionInfo>10.0-SNAPSHOT</owl:versionInfo>
         <dc:contributor>The eNanoMapper Consortium</dc:contributor>
         <dc:contributor>The NanoCommons Consortium</dc:contributor>
         <dc:contributor>The RiskGONE Consortium</dc:contributor>

diff --git a/enanomapper.owl b/enanomapper.owl
@@ -42,7 +42,7 @@
      xmlns:dc="http://purl.org/dc/elements/1.1/"
      xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#">
     <owl:Ontology rdf:about="http://enanomapper.github.io/ontologies/enanomapper.owl">
-        <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal/bao-ext.owl"/>
+    <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal/bao-ext.owl"/>
 	<owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal/bfo-ext.owl"/>
 	<owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal/chebi-ext.owl"/>
 	<owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal/chmo-ext.owl"/>
@@ -53,7 +53,8 @@
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal/pato-ext.owl"/>
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies/internal/wikidata.owl"/>
         <owl:imports rdf:resource="http://enanomapper.github.io/ontologies//enanomapper-auto.owl"/>
-        <owl:versionInfo>8.0</owl:versionInfo>
+        <owl:versionInfo>9.0</owl:versionInfo>
+        <owl:versionIRI rdf:resource="http://enanomapper.github.io/ontologies/releases/9.0/enanomapper.owl"/>
         <dc:contributor>The eNanoMapper Consortium</dc:contributor>
         <dc:contributor>The NanoCommons Consortium</dc:contributor>
         <dc:contributor>The RiskGONE Consortium</dc:contributor>

diff --git a/external/bao-slim.owl b/external/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>2022-08-11 21:04:10</oboInOwl:date>
+        <oboInOwl:date>2023-01-04 12:24:20</oboInOwl:date>
         <rdfs:comment>Contact:
 Stephan Schurer
 stephan dot schurer at gmail dot com</rdfs:comment>

diff --git a/external/bfo-slim.owl b/external/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>2022-08-11 21:08:15</oboInOwl:date>
+        <oboInOwl:date>2023-01-04 12:50:01</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. 
@@ -468,36 +468,6 @@ See the BFO 2 release notes for further information about BFO 2. Please note tha
 
 
 
-    <!-- http://purl.obolibrary.org/obo/BFO_0000031 -->
-
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031">
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
-        <obo:BFO_0000179>gdc</obo:BFO_0000179>
-        <obo:BFO_0000180>GenericallyDependentContinuant</obo:BFO_0000180>
-        <obo:IAO_0000112 xml:lang="en">The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">the pdf file on your laptop, the pdf file that is a copy thereof on my laptop</obo:IAO_0000112>
-        <obo:IAO_0000112 xml:lang="en">the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.</obo:IAO_0000112>
-        <obo:IAO_0000115 xml:lang="en">b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])</obo:IAO_0000115>
-        <obo:IAO_0000602>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </obo:IAO_0000602>
-        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
-        <rdfs:label xml:lang="en">generically dependent continuant</rdfs:label>
-    </owl:Class>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
-        <owl:annotatedTarget xml:lang="en">b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])</owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/074-001"/>
-    </owl:Axiom>
-    <owl:Axiom>
-        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
-        <owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
-        <owl:annotatedTarget>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </owl:annotatedTarget>
-        <obo:IAO_0010000 rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/074-001"/>
-    </owl:Axiom>
-
-
-
     <!-- http://purl.obolibrary.org/obo/BFO_0000034 -->
 
 
@@ -599,13 +569,6 @@ See the BFO 2 release notes for further information about BFO 2. Please note tha
 
 
 
-    <!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
-
-
-    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030"/>
-
-
-
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //

diff --git a/external/bto-slim.owl b/external/bto-slim.owl
@@ -18,7 +18,7 @@
         <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>2022-08-11 21:03:54</oboInOwl:date>
+        <oboInOwl:date>2023-01-04 12:24:30</oboInOwl:date>
         <oboInOwl:date>23:10:2021 16:56</oboInOwl:date>
         <oboInOwl:default-namespace>BrendaTissueOBO</oboInOwl:default-namespace>
         <oboInOwl:hasOBOFormatVersion>1.2</oboInOwl:hasOBOFormatVersion>

diff --git a/external/ccont-slim.owl b/external/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, matthias.ganzinger@med.uni-heidelberg.de</efo:creator>
         <oboInOwl:auto-generated-by>Slimmer</oboInOwl:auto-generated-by>
-        <oboInOwl:date>2022-08-11 21:04:15</oboInOwl:date>
+        <oboInOwl:date>2023-01-04 12:24:32</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>