Merge pull request #671 from enanomapper/endpoints_assays_sbd4nano

Batch adding assays and endpoints needed for the Causal links network (SbD4Nano) merge to avoid linking too many issues
enanomapper · Apr 4, 2024 · b991f38 · b991f38
2 parents 8c94a04 + 354a010
commit b991f38
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diff --git a/config/cheminf.iris b/config/cheminf.iris
@@ -1,4 +1,4 @@
-+(http://purl.obolibrary.org/obo/BFO_0000019):http://semanticscience.org/resource/CHEMINF_000247 surface area
++(http://www.bioassayontology.org/bao#BAO_0002128):http://semanticscience.org/resource/CHEMINF_000247 surface area as a physical property endpoint
 +D(http://purl.obolibrary.org/obo/BFO_0000019):http://semanticscience.org/resource/CHEMINF_000101 chemical substance quality
 +D(http://purl.obolibrary.org/obo/BFO_0000019):http://semanticscience.org/resource/CHEMINF_000031 molecular entity quality
 +D(http://purl.obolibrary.org/obo/IAO_0000030):http://semanticscience.org/resource/CHEMINF_000014 chemical entity information format description

diff --git a/internal-dev/bao-ext.owl b/internal-dev/bao-ext.owl
@@ -154,6 +154,121 @@
         <rdfs:label xml:lang="en">Impedance-based cell assay</rdfs:label>
     </owl:Class>
 
+    <!-- http://purl.enanomapper.net/onto/ENM_5562662 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_5562662">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHMO_0000087"/>
+	<rdfs:label xml:lang="en">Rhodamine fluorescence microscopy assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.org/onto/ENM_0000037"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_3221617 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_3221617">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001501"/>
+	<rdfs:label xml:lang="en">H2DCFDA fluorescence assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.org/onto/ENM_0000037"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_5562662 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_5562662">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHMO_0000087"/>
+	<rdfs:label xml:lang="en">Rhodamine 123 fluorescence microscopy assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.net/onto/ENM_0295914"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_3323766 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_3323766">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000916"/>
+	<rdfs:label xml:lang="en">DHE flow cytometry assay</rdfs:label>
+	<rdfs:label xml:lang="en">Dihydroethidium flow cytometry assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.net/onto/ENM_0295914"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_9802609 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_9802609">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000916"/>
+	<rdfs:label xml:lang="en">DHR123 flow cytometry assay</rdfs:label>
+	<rdfs:label xml:lang="en">Dihydrorhodamine 123 flow cytometry assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.net/onto/ENM_0295914"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_3323768 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_3323768">
+	<rdfs:subClassOf rdf:resource="http://www.bioassayontology.org/bao#BAO_0002168"/>
+	<rdfs:label xml:lang="en">Cellular glutathione quantification assay</rdfs:label>
+	<rdfs:label xml:lang="en">Cellular GSH quantification assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.net/onto/ENM_7011632"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_5666044 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_5666044">
+	<rdfs:subClassOf rdf:resource="http://purl.enanomapper.net/onto/ENM_3323768"/>
+	<rdfs:label xml:lang="en">Monochlorobimane cellular GSH quantification assay</rdfs:label>
+	<rdfs:label xml:lang="en">MCB cellular GSH quantification assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.net/onto/ENM_7011632"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+
+    <!-- http://purl.enanomapper.net/onto/ENM_0801504 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_0801504">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000916"/>
+	<rdfs:label xml:lang="en">TMRM flow cytometry assay</rdfs:label>
+	<rdfs:label xml:lang="en">Tetramethylrhodamine methyl ester flow cytometry assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.net/onto/ENM_0295914"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_4869361 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_4869361">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000916"/>
+	<rdfs:label xml:lang="en">DCF flow cytometry assay</rdfs:label>
+	<rdfs:label xml:lang="en">Dichlorodihydrofluorescein flow cytometry assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.org/onto/ENM_0000037"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
 </rdf:RDF>
 
 <!-- Generated by the OWL API (version 4.2.8.20170104-2310) https://github.com/owlcs/owlapi -->

diff --git a/internal-dev/cheminf-ext.owl b/internal-dev/cheminf-ext.owl
@@ -106,6 +106,14 @@
         <rdfs:label xml:lang="en">Oxygen vacancies</rdfs:label>
     </owl:Class>
 
+
+    <!-- http://purl.enanomapper.net/onto/ENM_5933788 -->
+
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_5933788">
+        <rdfs:subClassOf rdf:resource="http://semanticscience.org/resource/CHEMINF_000247"/>
+        <rdfs:label xml:lang="en">BET surface area endpoint</rdfs:label>
+    </owl:Class>
+
 </rdf:RDF>
 
 

diff --git a/internal-dev/chmo-ext.owl b/internal-dev/chmo-ext.owl
@@ -8,9 +8,9 @@
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:obo="http://purl.obolibrary.org/obo/"
      xmlns:dc="http://purl.org/dc/elements/1.1/">
-
     <owl:Ontology rdf:about="http://enanomapper.github.io/ontologies/internal/chmo-ext.owl">
         <dc:contributor>Laurent Winckers</dc:contributor>
+	<dc:contributor>Javier Millan Acosta</dc:contributor>
 	<dc:license>CC-BY 4.0 https://creativecommons.org/licenses/by/4.0/</dc:license>
 	<rdfs:comment>This ontology contains proposed extensions to the Chemical Methods Ontology, which in due course will be submitted to the CHMO. </rdfs:comment>
     </owl:Ontology>
@@ -39,7 +39,5 @@
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHMO_0001075"/>
         <rdfs:label xml:lang="en">CHN analysis</rdfs:label>
     </owl:Class>
-
-
 
 </rdf:RDF>
diff --git a/internal-dev/endpoints.owl b/internal-dev/endpoints.owl
@@ -446,7 +446,13 @@
         <rdfs:label xml:lang="en">Oxidative stress</rdfs:label>
     </owl:Class>
 
+    <!-- http://purl.enanomapper.net/onto/ENM_7011632 -->
 
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_7011632">
+        <rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_0000037"/>
+        <rdfs:label xml:lang="en">Cellular glutathione content</rdfs:label>
+        <rdfs:label xml:lang="en">Cellular GSH content</rdfs:label>
+    </owl:Class>
 
     <!-- http://purl.enanomapper.org/onto/ENM_0000038 -->
 
@@ -686,7 +692,11 @@
         <rdfs:label xml:lang="en">cytotoxicity endpoint</rdfs:label>
     </owl:Class>
 
-
+    <!-- http://purl.enanomapper.net/onto/ENM_0295914 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_0295914">
+	<rdfs:subClassOf rdf:resource="http://purl.enanomapper.org/onto/ENM_0000063"/>
+	<rdfs:label xml:lang="en">Mitochondrial membrane potential endpoint</rdfs:label>
+    </owl:Class>
 
     <!-- http://purl.enanomapper.org/onto/ENM_0000066 -->
 

diff --git a/internal-dev/npo-ext.owl b/internal-dev/npo-ext.owl
@@ -3235,4 +3235,28 @@
         <rdfs:label xml:lang="en">TiO2@SiO2 nanocomposite</rdfs:label>
     </owl:Class>
 
+    <!-- http://purl.enanomapper.net/onto/ENM_3323767 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_3323767">
+	<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000070"/>
+	<rdfs:label xml:lang="en">Surface area assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://semanticscience.org/resource/CHEMINF_000247"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
+    <!-- http://purl.enanomapper.net/onto/ENM_2012430 -->
+    <owl:Class rdf:about="http://purl.enanomapper.net/onto/ENM_2012430">
+	<rdfs:subClassOf rdf:resource="http://purl.enanomapper.net/onto/ENM_3323767"/>
+	<rdfs:label xml:lang="en">BET surface area assay</rdfs:label>
+	<rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.bioassayontology.org/bao#BAO_0000208"/>
+                <owl:someValuesFrom rdf:resource="http://purl.enanomapper.net/onto/ENM_5933788"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+
 </rdf:RDF>