Merge pull request #1818 from obi-ontology/fix_reasoned_hierarchy

Fix classes that reasoned into places too high in the hierarchy
obi-ontology · Aug 30, 2024 · 47a538e · 47a538e
2 parents c1348e4 + f0463fe
commit 47a538e
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diff --git a/src/ontology/modules/devices.owl b/src/ontology/modules/devices.owl
@@ -6212,57 +6212,53 @@
  <!-- http://purl.obolibrary.org/obo/OBI_0001870 -->
 
  <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0001870">
- <owl:equivalentClass>
- <owl:Class>
- <owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0001869"/>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
- <owl:someValuesFrom>
- <owl:Class>
- <owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000034"/>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
- <owl:allValuesFrom>
- <owl:Class>
- <owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
- <owl:someValuesFrom>
- <owl:Class>
- <owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
- <owl:someValuesFrom>
- <owl:Class>
- <owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_4431"/>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
- <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_32875"/>
- </owl:Restriction>
- </owl:intersectionOf>
- </owl:Class>
- </owl:someValuesFrom>
- </owl:Restriction>
- </owl:intersectionOf>
- </owl:Class>
- </owl:someValuesFrom>
- </owl:Restriction>
- </owl:intersectionOf>
- </owl:Class>
- </owl:allValuesFrom>
- </owl:Restriction>
- </owl:intersectionOf>
- </owl:Class>
- </owl:someValuesFrom>
- </owl:Restriction>
- </owl:intersectionOf>
- </owl:Class>
- </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001869"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
+ <owl:someValuesFrom>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000034"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
+ <owl:allValuesFrom>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
+ <owl:someValuesFrom>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ <owl:someValuesFrom>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description rdf:about="http://purl.obolibrary.org/obo/CHEBI_4431"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+ <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/CHEBI_32875"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
  <obo:IAO_0000115 xml:lang="en">A BeadChip made for an analyte assay that generates information about DNA methylation.</obo:IAO_0000115>
  <obo:IAO_0000117>PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg</obo:IAO_0000117>

diff --git a/src/ontology/obi-edit.owl b/src/ontology/obi-edit.owl
@@ -6511,6 +6511,7 @@ Proposal is to obsolete.</obo:IAO_0000116>
  </owl:intersectionOf>
  </owl:Class>
  </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000427"/>
  <obo:IAO_0000111 xml:lang="en">reverse transcriptase</obo:IAO_0000111>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
  <obo:IAO_0000115 xml:lang="en">enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase
@@ -6643,6 +6644,7 @@ activity)</obo:IAO_0000115>
  </owl:intersectionOf>
  </owl:Class>
  </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000040"/>
  <obo:IAO_0000111 xml:lang="en">enzyme</obo:IAO_0000111>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
  <obo:IAO_0000115 xml:lang="en">(protein or rna) or has_part (protein or rna) and
@@ -6679,6 +6681,7 @@ that has_part some material entity is a material entity. If we add as equivalent
  </owl:intersectionOf>
  </owl:Class>
  </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHEBI_4705"/>
  <obo:IAO_0000111 xml:lang="en">plasmid</obo:IAO_0000111>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
  <obo:IAO_0000115 xml:lang="en">plasmid = DNA and has_quality circular and has_function
@@ -9168,6 +9171,7 @@ http://en.wikipedia.org/wiki/Survival_rate</obo:IAO_0000119>
  </owl:intersectionOf>
  </owl:Class>
  </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000826"/>
  <obo:IAO_0000111>double blind study execution</obo:IAO_0000111>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
  <obo:IAO_0000115 xml:lang="en">A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated</obo:IAO_0000115>
@@ -9641,6 +9645,7 @@ http://en.wikipedia.org/wiki/Survival_rate</obo:IAO_0000119>
  </owl:intersectionOf>
  </owl:Class>
  </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000826"/>
  <obo:IAO_0000111>single blind study execution</obo:IAO_0000111>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
  <obo:IAO_0000115 xml:lang="en">A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated</obo:IAO_0000115>
@@ -18117,6 +18122,7 @@ PMID: 23587118.
  </owl:intersectionOf>
  </owl:Class>
  </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000300"/>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
  <obo:IAO_0000115 xml:lang="en">A textual entity that is used to denote a sequence assembly.</obo:IAO_0000115>
  <obo:IAO_0000117>PERSON: Jie Zheng, Chris Stoeckert</obo:IAO_0000117>
@@ -26544,6 +26550,7 @@ determinations of compounds.</obo:IAO_0000115>
  </owl:intersectionOf>
  </owl:Class>
  </owl:equivalentClass>
+ <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0100051"/>
  <obo:IAO_0000111 xml:lang="en">pool of specimens</obo:IAO_0000111>
  <obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
  <obo:IAO_0000115 xml:lang="en">A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.</obo:IAO_0000115>

diff --git a/src/ontology/templates/devices.tsv b/src/ontology/templates/devices.tsv
@@ -309,7 +309,7 @@ OBI:0001204 SNP microarray SNP microarray metadata complete A DNA microarray us
 OBI:0001307 tiling microarray tiling microarray metadata complete genome tiling array A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions. EFO_0002704: tiling array Person: Helen Parkinson DNA microarray 
 OBI:0001865 assay array metadata complete A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg device solid support function 
 OBI:0001869 Illumina BeadChip metadata complete An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides. http://www.illumina.com/technology/beadarray_technology.ilmn PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg, Venkat Malladi assay array Illumina 
-OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg equivalent Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group')))))))))
+OBI:0001870 Illumina methylation BeadChip metadata complete A BeadChip made for an analyte assay that generates information about DNA methylation. Penn Group PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg Illumina BeadChip ('bearer of' some (function and ('realized in' only (assay and (has_specified_output some ('measurement datum' and ('is about' some (deoxyribonucleotide and ('has part' some 'methyl group')))))))))
 OBI:0001871 LSRFortessa X-20 metadata complete A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously. http://www.bdbiosciences.com/instruments/lsrx20/index.jsp?WT.srch=1&gclid=CJjJ8JTR5LoCFXBo7AodZycAbg Anna Maria Masci flow cytometer analyzer Becton Dickinson (BD Biosciences) 
 OBI:0001971 Ion 316 Chip v2 Ion 316 Chip v2 Ion PGM 316 Chip|Ion 316 Chip|Ion PGM 316 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #774 https://sourceforge.net/p/obi/obi-terms/774/ ion semiconductor chip 
 OBI:0001972 Ion 318 Chip v2 Ion 318 Chip v2 Ion 318 Chip|Ion PGM 318 Chip|Ion PGM 318 Chip v2 An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb. http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-pgm-ion-proton-system-chips.html PERSON: Sagar Jain Issue Tracker #775 https://sourceforge.net/p/obi/obi-terms/775/ ion semiconductor chip