Merge pull request #1830 from obi-ontology/specimen_hierarchy_cleanup…

…_1821 Proposed cleanup of specimen hierarchy
obi-ontology · Nov 6, 2024 · b180777 · b180777
2 parents 76ace83 + d26a303
commit b180777
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Showing 10 changed files with 3,009 additions and 3,236 deletions.
diff --git a/Makefile b/Makefile
@@ -105,7 +105,7 @@ MODULE_NAMES := administration\
  antibody-purification\
  assays\
  biopsy\
- biobank-specimens\
+ specimens\
  organizations\
  data-sets\
  data-transformations\

diff --git a/README.md b/README.md
@@ -20,7 +20,7 @@ Our ontology terms come in three groups. Depending on what type of term you want
     - [`assays.tsv`](src/ontology/templates/assays.tsv) for general assays
     - [`epitope-assays.tsv`](src/ontology/templates/epitope-assays.tsv) specifically for immune epitope assays
     - [`value-specifications.tsv`](src/ontology/templates/value-specifications.tsv)
-    - [`biobank-specimens.tsv`](src/ontology/templates/biobank-specimens.tsv)
+    - [`specimens.tsv`](src/ontology/templates/specimens.tsv) for specimens
     - [`medical-history.tsv`](src/ontology/templates/medical-history.tsv) for medical history classifications and related selection criteria
     - [`study-designs.tsv`](src/ontology/templates/study-designs.tsv) for study designs
     - [`data-sets.tsv`](src/ontology/templates/data-sets.tsv) for data sets

diff --git a/src/ontology/OntoFox_inputs/Uberon_input.txt b/src/ontology/OntoFox_inputs/Uberon_input.txt
@@ -14,6 +14,7 @@ http://purl.obolibrary.org/obo/UBERON_0000010 # peripheral nervous system
 http://purl.obolibrary.org/obo/UBERON_0000029
 http://purl.obolibrary.org/obo/UBERON_0000057 # urethra
 http://purl.obolibrary.org/obo/UBERON_0000105
+http://purl.obolibrary.org/obo/UBERON_0000162 # cloaca
 http://purl.obolibrary.org/obo/UBERON_0000165
 http://purl.obolibrary.org/obo/UBERON_0000165 # mouth
 http://purl.obolibrary.org/obo/UBERON_0000173

diff --git a/src/ontology/OntoFox_outputs/Uberon_imports.owl b/src/ontology/OntoFox_outputs/Uberon_imports.owl
@@ -149,6 +149,18 @@
 
 
 
+    <!-- http://purl.obolibrary.org/obo/UBERON_0000162 -->
+
+    <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000162">
+        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/UBERON_0000465"/>
+        <obo:IAO_0000111>cloaca</obo:IAO_0000111>
+        <obo:IAO_0000115>Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures.</obo:IAO_0000115>
+        <obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/uberon.owl"/>
+        <rdfs:label>cloaca</rdfs:label>
+    </owl:Class>
+
+
+
     <!-- http://purl.obolibrary.org/obo/UBERON_0000165 -->
 
     <owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000165">

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -30,7 +30,6 @@
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/antibody-purification.owl" uri="modules/antibody-purification.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/assays.owl" uri="modules/assays.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/biopsy.owl" uri="modules/biopsy.owl"/>
-    <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-specimens.owl" uri="modules/biobank-specimens.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/biobank-tissue-specimen.owl" uri="modules/biobank-tissue-specimen.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/data-sets.owl" uri="modules/data-sets.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/data-transformations.owl" uri="modules/data-transformations.owl"/>
@@ -43,6 +42,7 @@
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/sample-collection.owl" uri="modules/sample-collection.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/sequence-analysis.owl" uri="modules/sequence-analysis.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/specimen-assay-data.owl" uri="modules/specimen-assay-data.owl"/>
+    <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/specimens.owl" uri="modules/specimens.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/study-designs.owl" uri="modules/study-designs.owl"/>
     <uri name="http://purl.obolibrary.org/obo/obi/dev/modules/value-specifications.owl" uri="modules/value-specifications.owl"/>
 </catalog>