Skip to content

Commit

Permalink
Merge branch 'master' into administration_1703
Browse files Browse the repository at this point in the history
  • Loading branch information
@jamesaoverton
jamesaoverton authored Nov 30, 2023
2 parents e809a75 + 6a4587e commit 21039d0
Show file tree
Hide file tree
Showing 7 changed files with 218 additions and 39 deletions.
173 changes: 160 additions & 13 deletions src/ontology/modules/data-transformations.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -69,6 +81,12 @@



<!-- http://purl.obolibrary.org/obo/OBI_0000312 -->

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000312"/>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
Expand All @@ -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"/>
Expand Down Expand Up @@ -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>
Expand All @@ -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>


Expand Down
22 changes: 16 additions & 6 deletions src/ontology/modules/devices.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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>

Expand Down Expand Up @@ -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>

Expand Down Expand Up @@ -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>

Expand Down Expand Up @@ -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>

Expand Down Expand Up @@ -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>


Expand Down Expand Up @@ -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"/>
Expand Down
20 changes: 20 additions & 0 deletions src/ontology/modules/obsolete.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,12 @@



<!-- http://purl.obolibrary.org/obo/IAO_0000234 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000234"/>



<!-- http://purl.obolibrary.org/obo/IAO_0100001 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0100001"/>
Expand Down Expand Up @@ -1140,6 +1146,20 @@



<!-- http://purl.obolibrary.org/obo/OBI_1110132 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_1110132">
<rdfs:subClassOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
<obo:IAO_0000115>A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor.</obo:IAO_0000115>
<obo:IAO_0000118>CD8</obo:IAO_0000118>
<obo:IAO_0000234>https://github.com/obi-ontology/obi/issues/353</obo:IAO_0000234>
<obo:IAO_0100001 rdf:resource="http://purl.obolibrary.org/obo/PR_000025402"/>
<rdfs:label>obsolete CD8 receptor</rdfs:label>
<owl:deprecated rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/REO_0000171 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/REO_0000171">
Expand Down
Loading

0 comments on commit 21039d0

Please sign in to comment.