Merge pull request #613 from monarch-initiative/issue-577cellcountupd…

…ates

replaced MAXO_0001006 hematopoietic cell count with MAXO_0001509 blood cell count. close #577

src/ontology/components/maxo-deprecated.owl

@@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/maxo/components/maxo-deprecated.owl>
-<http://purl.obolibrary.org/obo/maxo/releases/2023-10-03/components/maxo-deprecated.owl>
-Annotation(owl:versionInfo "2023-10-03")
+<http://purl.obolibrary.org/obo/maxo/releases/2023-11-02/components/maxo-deprecated.owl>
+Annotation(owl:versionInfo "2023-11-02")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000008>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000032>))
@@ -59,6 +59,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000807>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000862>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000896>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0000916>))
+Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0001006>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0001023>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0001112>))
 Declaration(Class(<http://purl.obolibrary.org/obo/MAXO_0001132>))
@@ -363,6 +364,12 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0000916> "obsolete airway endoscopy")
 AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/MAXO_0000916> "true"^^xsd:boolean)
 
+# Class: <http://purl.obolibrary.org/obo/MAXO_0001006> (obsolete hematopoeitic cell count)
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/MAXO_0001006> <http://purl.obolibrary.org/obo/MAXO_0001509>)
+AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0001006> "obsolete hematopoeitic cell count")
+AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/MAXO_0001006> "true"^^xsd:boolean)
+
 # Class: <http://purl.obolibrary.org/obo/MAXO_0001023> (obsolete tranquilizing agent therapy)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0100001> <http://purl.obolibrary.org/obo/MAXO_0001023> <http://purl.obolibrary.org/obo/MAXO_0000023>)

src/ontology/maxo-edit.owl

@@ -10023,13 +10023,6 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynony
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0001005> "opioid antagonist agent therapy"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/MAXO_0001005> <http://purl.obolibrary.org/obo/MAXO_0000219>)
 
-# Class: <http://purl.obolibrary.org/obo/MAXO_0001006> (hematopoietic cell count)
-
-AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasSynonymType> <http://purl.obolibrary.org/obo/maxo#ABBREVIATION>) <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MAXO_0001006> "CBC")
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MAXO_0001006> "complete blood count")
-AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/MAXO_0001006> "full blood count")
-SubClassOf(<http://purl.obolibrary.org/obo/MAXO_0001006> <http://purl.obolibrary.org/obo/MAXO_0000829>)
-
 # Class: <http://purl.obolibrary.org/obo/MAXO_0001007> (erythrocyte count)
 
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/MAXO_0001007> "NCIT:C51946")
@@ -10485,6 +10478,10 @@ AnnotationAssertion(dcterms:creator <http://purl.obolibrary.org/obo/MAXO_0001502
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/MAXO_0001502> "tyrosine metabolism inhibitor")
 SubClassOf(<http://purl.obolibrary.org/obo/MAXO_0001502> <http://purl.obolibrary.org/obo/MAXO_0000058>)
 
+# Class: <http://purl.obolibrary.org/obo/MAXO_0001509> (blood cell count)
+
+SubClassOf(<http://purl.obolibrary.org/obo/MAXO_0001509> <http://purl.obolibrary.org/obo/MAXO_0000829>)
+
 # Class: <http://purl.obolibrary.org/obo/MAXO_0009003> (preimplantation genetic testing)
 
 AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "NCBIBook:NBK5191") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/MAXO_0009003> "Genetic testing of one or more cells removed from early embryos conceived by in vitro fertilization and transferring to the mother's uterus only those embryos determined not to have the pathogenic variant(s)/chromosome anomaly(ies) of concern.")

src/ontology/reports/equivalent-classes-violation.csv

@@ -0,0 +1,2 @@
+baseClass,baseLabel,equivalentClass,equivalentLabel
+http://purl.obolibrary.org/obo/MAXO_0000829,blood cell measurement,http://purl.obolibrary.org/obo/MAXO_0001509,blood cell count

src/patterns/data/manual/cellcount.tsv

@@ -17,4 +17,4 @@ MAXO:0001372	burr cell count	CL:0002155	echynocyte	http://orcid.org/0000-0001-79
 MAXO:0001373		CL:0000786	plasma cell	http://orcid.org/0000-0001-7941-2961	2023-03-03T20:39:14Z				
 MAXO:0001374		CL:0000451	dendritic cell	http://orcid.org/0000-0001-7941-2961	2023-03-03T20:39:14Z				
 MAXO:0001375		CL:0000815	regulatory T cell	http://orcid.org/0000-0001-7941-2961	2023-03-03T20:39:14Z				T reg cell count
-MAXO:0001509		CL:0000081	blood cell	http://orcid.org/0000-0001-7941-2961	2023-11-01T20:39:14Z				
+MAXO:0001509		CL:0000081	blood cell	http://orcid.org/0000-0001-7941-2961	2023-11-01T20:39:14Z				CBC|complete blood cell count|complete blood count|full blood count