Merge branch 'master' into cd8_receptor_353

obi-ontology · Nov 30, 2023 · d15ded3 · d15ded3
2 parents 524212a + 471ed83
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diff --git a/src/ontology/modules/data-transformations.owl b/src/ontology/modules/data-transformations.owl
@@ -22,6 +22,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
@@ -40,6 +46,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
+
+    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/IAO_0000233 -->
 
     <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000233"/>
@@ -69,6 +81,12 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0000312 -->
+
+    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312"/>
+
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -80,6 +98,24 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/CHMO_0000701 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/CHMO_0000701"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/IAO_0000027 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/OBI_0003097 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003097"/>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0003327 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003327"/>
@@ -109,12 +145,12 @@
             </owl:Restriction>
         </rdfs:subClassOf>
         <obo:IAO_0000115>The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item.</obo:IAO_0000115>
-        <obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899 "William D. Duncan"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith"</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899 &quot;William D. Duncan&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0001-9676-7377 &quot;Alexander D. Bartnik&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0001-9990-8331 &quot;Alexander D. Diehl&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0002-2104-0568 &quot;Lucas M. Serra&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0002-7245-3450 &quot;Lauren M. Wishnie&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0002-9821-4132 &quot;Mackenzie T. Smith&quot;</obo:IAO_0000117>
         <obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1481</obo:IAO_0000233>
         <rdfs:label>image data set analysis</rdfs:label>
     </owl:Class>
@@ -139,23 +175,134 @@
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <obo:IAO_0000112>A Fourier transform of raw "k-space" data produced into an image data set that represents the anatomical structure of the tissue examined.</obo:IAO_0000112>
+        <obo:IAO_0000112>A Fourier transform of raw &quot;k-space&quot; data produced into an image data set that represents the anatomical structure of the tissue examined.</obo:IAO_0000112>
         <obo:IAO_0000115>A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set.</obo:IAO_0000115>
-        <obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899 "William D. Duncan"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0001-9676-7377 "Alexander D. Bartnik"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0001-9990-8331 "Alexander D. Diehl"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0002-2104-0568 "Lucas M. Serra"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0002-7245-3450 "Lauren M. Wishnie"</obo:IAO_0000117>
-        <obo:IAO_0000117>https://orcid.org/0000-0002-9821-4132 "Mackenzie T. Smith"</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899 &quot;William D. Duncan&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0001-9676-7377 &quot;Alexander D. Bartnik&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0001-9990-8331 &quot;Alexander D. Diehl&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0002-2104-0568 &quot;Lucas M. Serra&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0002-7245-3450 &quot;Lauren M. Wishnie&quot;</obo:IAO_0000117>
+        <obo:IAO_0000117>https://orcid.org/0000-0002-9821-4132 &quot;Mackenzie T. Smith&quot;</obo:IAO_0000117>
         <obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1481</obo:IAO_0000233>
         <rdfs:label>raw magnetic resonance image data set reconstruction</rdfs:label>
     </owl:Class>
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0003540 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003540"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/OBI_0003647 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003647">
+        <owl:equivalentClass>
+            <owl:Class>
+                <owl:intersectionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200085"/>
+                    <owl:Restriction>
+                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
+                        <owl:someValuesFrom>
+                            <owl:Class>
+                                <owl:intersectionOf rdf:parseType="Collection">
+                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
+                                    <owl:Restriction>
+                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0003540"/>
+                                    </owl:Restriction>
+                                </owl:intersectionOf>
+                            </owl:Class>
+                        </owl:someValuesFrom>
+                    </owl:Restriction>
+                </owl:intersectionOf>
+            </owl:Class>
+        </owl:equivalentClass>
+        <obo:IAO_0000111>tandem mass spectrometry analysis</obo:IAO_0000111>
+        <obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
+        <obo:IAO_0000119>A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay.</obo:IAO_0000119>
+        <obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1684</obo:IAO_0000233>
+        <rdfs:label>tandem mass spectrometry analysis</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/OBI_0003648 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003648">
+        <owl:equivalentClass>
+            <owl:Class>
+                <owl:intersectionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200085"/>
+                    <owl:Restriction>
+                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
+                        <owl:someValuesFrom>
+                            <owl:Class>
+                                <owl:intersectionOf rdf:parseType="Collection">
+                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
+                                    <owl:Restriction>
+                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0003097"/>
+                                    </owl:Restriction>
+                                </owl:intersectionOf>
+                            </owl:Class>
+                        </owl:someValuesFrom>
+                    </owl:Restriction>
+                </owl:intersectionOf>
+            </owl:Class>
+        </owl:equivalentClass>
+        <obo:IAO_0000111>liquid chromatography mass spectrometry analysis</obo:IAO_0000111>
+        <obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
+        <obo:IAO_0000119>A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography mass spectrometry assay.</obo:IAO_0000119>
+        <obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1684</obo:IAO_0000233>
+        <rdfs:label>liquid chromatrography mass spectrometry analysis</rdfs:label>
+    </owl:Class>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/OBI_0003649 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003649">
+        <owl:equivalentClass>
+            <owl:Class>
+                <owl:intersectionOf rdf:parseType="Collection">
+                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0200085"/>
+                    <owl:Restriction>
+                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
+                        <owl:someValuesFrom>
+                            <owl:Class>
+                                <owl:intersectionOf rdf:parseType="Collection">
+                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000027"/>
+                                    <owl:Restriction>
+                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
+                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHMO_0000701"/>
+                                    </owl:Restriction>
+                                </owl:intersectionOf>
+                            </owl:Class>
+                        </owl:someValuesFrom>
+                    </owl:Restriction>
+                </owl:intersectionOf>
+            </owl:Class>
+        </owl:equivalentClass>
+        <obo:IAO_0000111>liquid chromatography tandem mass spectrometry analysis</obo:IAO_0000111>
+        <obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
+        <obo:IAO_0000119>A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography tandem mass spectrometry assay.</obo:IAO_0000119>
+        <obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1684</obo:IAO_0000233>
+        <rdfs:label>liquid chromatography-tandem mass spectrometry analysis</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0200000 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200000"/>
+
+
+
+    <!-- http://purl.obolibrary.org/obo/OBI_0200085 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0200085"/>
 </rdf:RDF>
 
 

diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl
@@ -1043,7 +1043,6 @@
         <obo:IAO_0000117>PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119>GROUP:&lt;http://msi-ontology.sourceforge.net&gt;</obo:IAO_0000119>
         <obo:IAO_0000119>http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072</obo:IAO_0000119>
-        <obo:IAO_0000232>check on definition !</obo:IAO_0000232>
         <rdfs:label>solvent mixer</rdfs:label>
     </owl:Class>
 
@@ -1964,7 +1963,6 @@
         <obo:IAO_0000117>PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119>GROUP:&lt;http://msi-ontology.sourceforge.net&gt;</obo:IAO_0000119>
         <obo:IAO_0000119>http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055</obo:IAO_0000119>
-        <obo:IAO_0000232>chromatography device, check on definition !</obo:IAO_0000232>
         <rdfs:label>column cartridge</rdfs:label>
     </owl:Class>
 
@@ -2192,7 +2190,6 @@
         <obo:IAO_0000117>PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119>GROUP:&lt;http://msi-ontology.sourceforge.net&gt;</obo:IAO_0000119>
         <obo:IAO_0000119>http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054</obo:IAO_0000119>
-        <obo:IAO_0000232>check on definition !</obo:IAO_0000232>
         <rdfs:label>column cartridger</rdfs:label>
     </owl:Class>
 
@@ -2223,7 +2220,6 @@
         <obo:IAO_0000117>PERSON:Daniel Schober</obo:IAO_0000117>
         <obo:IAO_0000119>GROUP:&lt;http://msi-ontology.sourceforge.net&gt;</obo:IAO_0000119>
         <obo:IAO_0000119>http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065</obo:IAO_0000119>
-        <obo:IAO_0000232>chromatography device, check on definition !</obo:IAO_0000232>
         <rdfs:label>needle assembly</rdfs:label>
     </owl:Class>
 
@@ -6949,12 +6945,12 @@
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002131">
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001870"/>
-        <obo:IAO_0000111>Illumina Infinium MethylationEPIC BeadChip</obo:IAO_0000111>
+        <obo:IAO_0000111>Illumina Infinium MethylationEPIC v1.0 BeadChip</obo:IAO_0000111>
         <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
         <obo:IAO_0000115>An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution.</obo:IAO_0000115>
         <obo:IAO_0000117>Person: Chris Stoeckert, Jason Hilton</obo:IAO_0000117>
         <obo:IAO_0000119>http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/humanmethylationepic-data-sheet-1070-2015-008.pdf</obo:IAO_0000119>
-        <rdfs:label>Illumina Infinium MethylationEPIC BeadChip</rdfs:label>
+        <rdfs:label>Illumina Infinium MethylationEPIC v1.0 BeadChip</rdfs:label>
     </owl:Class>
 
 
@@ -9136,6 +9132,20 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0003650 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003650">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001870"/>
+        <obo:IAO_0000111>Illumina Infinium MethylationEPIC v2.0 BeadChip</obo:IAO_0000111>
+        <obo:IAO_0000115>An Illumina methylation BeadChip that targets  935,000 methylation sites per sample at single-nucleotide resolution.</obo:IAO_0000115>
+        <obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
+        <obo:IAO_0000119>https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html</obo:IAO_0000119>
+        <obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1665</obo:IAO_0000233>
+        <rdfs:label>Illumina Infinium MethylationEPIC v2.0 BeadChip</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0302886 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0302886"/>

diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl
@@ -22422,6 +22422,18 @@ b) that the amount of analyte/measurand detected is over some predetermined thre
 
 
 
+    <!-- http://purl.obolibrary.org/obo/OBI_0003651 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003651">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OGMS_0000123"/>
+        <obo:IAO_0000115>A clinical data item that quantifies the severity of a person&apos;s fatigue as measured by a 20-item self-report instrument.</obo:IAO_0000115>
+        <obo:IAO_0000117>Sebastian Duesing</obo:IAO_0000117>
+        <obo:IAO_0000119>https://pubmed.ncbi.nlm.nih.gov/7636775/ DOI: 10.1016/0022-3999(94)00125-o</obo:IAO_0000119>
+        <rdfs:label xml:lang="en">multidimensional fatigue inventory score</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/OBI_0005246 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0005246">

diff --git a/src/ontology/templates/data-transformations.tsv b/src/ontology/templates/data-transformations.tsv
@@ -2,3 +2,6 @@ ontology ID	label	editor preferred term	has curation status	alternative term	def
 ID	A rdfs:label	A editor preferred term	AI has curation status	A alternative term SPLIT=|	A definition SPLIT=|	A definition source SPLIT=|	A example of usage SPLIT=|	A term editor SPLIT=|	A editor note SPLIT=|	A curator note SPLIT=|	A term tracker item	CLASS_TYPE	C %	C has_specified_input some %	C has_specified_output some %	C achieves_planned_objective some %	C %
 OBI:0003355	image data set analysis				The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item.			https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith""			https://github.com/obi-ontology/obi/issues/1481	subclass	data transformation	image data set			
 OBI:0003356	raw magnetic resonance image data set reconstruction				A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set.		A Fourier transform of raw ""k-space"" data produced into an image data set that represents the anatomical structure of the tissue examined.	https://orcid.org/0000-0001-9676-7377 ""Alexander D. Bartnik""|https://orcid.org/0000-0001-9990-8331 ""Alexander D. Diehl""|https://orcid.org/0000-0001-9625-1899 ""William D. Duncan""|https://orcid.org/0000-0002-2104-0568 ""Lucas M. Serra""|https://orcid.org/0000-0002-7245-3450 ""Lauren M. Wishnie""|https://orcid.org/0000-0002-9821-4132 ""Mackenzie T. Smith""			https://github.com/obi-ontology/obi/issues/1481	equivalent	image data set analysis	raw magnetic resonance image data set	reconstructed magnetic resonance image data set		
+OBI:0003647	tandem mass spectrometry analysis	tandem mass spectrometry analysis				A mass spectrometry analysis in which the data being analyzed is the result of a tandem mass spectrometry assay.		Sebastian Duesing			https://github.com/obi-ontology/obi/issues/1684	equivalent	mass spectrometry analysis	('data item' and is_specified_output_of some 'tandem mass spectrometry assay')			
+OBI:0003648	liquid chromatrography mass spectrometry analysis	liquid chromatography mass spectrometry analysis				A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography mass spectrometry assay.		Sebastian Duesing			https://github.com/obi-ontology/obi/issues/1684	equivalent	mass spectrometry analysis	('data item' and is_specified_output_of some 'liquid chromatography mass spectrometry assay')			
+OBI:0003649	liquid chromatography-tandem mass spectrometry analysis	liquid chromatography tandem mass spectrometry analysis				A mass spectrometry analysis in which the data being analyzed is the result of a liquid chromatography tandem mass spectrometry assay.		Sebastian Duesing			https://github.com/obi-ontology/obi/issues/1684	equivalent	mass spectrometry analysis	('data item' and is_specified_output_of some 'liquid chromatography-tandem mass spectrometry')