diff --git a/src/ontology/components/maxo-deprecated.owl b/src/ontology/components/maxo-deprecated.owl index a0277e2d..100fedd0 100644 --- a/src/ontology/components/maxo-deprecated.owl +++ b/src/ontology/components/maxo-deprecated.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2023-10-03") + +Annotation(owl:versionInfo "2023-11-02") Declaration(Class()) Declaration(Class()) @@ -59,6 +59,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -363,6 +364,12 @@ AnnotationAssertion( "obsolete airway endoscopy") AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) +# Class: (obsolete hematopoeitic cell count) + +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "obsolete hematopoeitic cell count") +AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) + # Class: (obsolete tranquilizing agent therapy) AnnotationAssertion( ) diff --git a/src/ontology/maxo-edit.owl b/src/ontology/maxo-edit.owl index c283bf84..9b882149 100644 --- a/src/ontology/maxo-edit.owl +++ b/src/ontology/maxo-edit.owl @@ -10023,13 +10023,6 @@ AnnotationAssertion( "opioid antagonist agent therapy"@en) SubClassOf( ) -# Class: (hematopoietic cell count) - -AnnotationAssertion(Annotation( ) "CBC") -AnnotationAssertion( "complete blood count") -AnnotationAssertion( "full blood count") -SubClassOf( ) - # Class: (erythrocyte count) AnnotationAssertion( "NCIT:C51946") @@ -10485,6 +10478,10 @@ AnnotationAssertion(dcterms:creator "tyrosine metabolism inhibitor") SubClassOf( ) +# Class: (blood cell count) + +SubClassOf( ) + # Class: (preimplantation genetic testing) AnnotationAssertion(Annotation( "NCBIBook:NBK5191") "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.") diff --git a/src/ontology/reports/equivalent-classes-violation.csv b/src/ontology/reports/equivalent-classes-violation.csv new file mode 100644 index 00000000..61edf63b --- /dev/null +++ b/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 diff --git a/src/patterns/data/manual/cellcount.tsv b/src/patterns/data/manual/cellcount.tsv index 624ec604..20a99815 100644 --- a/src/patterns/data/manual/cellcount.tsv +++ b/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 \ No newline at end of file +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 \ No newline at end of file diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 1563c654..f34faa02 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -271,6 +271,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -681,7 +682,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -1126,6 +1126,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -3279,8 +3280,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of eosinophil in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "eosinophil cell count") -AnnotationAssertion( "eosinophil cell count measurement") AnnotationAssertion( "eosinophil count test") AnnotationAssertion(rdfs:label "eosinophil count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3290,8 +3289,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of granulocyte in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "granulocyte cell count") -AnnotationAssertion( "granulocyte cell count measurement") AnnotationAssertion( "granulocyte count test") AnnotationAssertion(rdfs:label "granulocyte count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3301,8 +3298,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of basophil in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "basophil cell count") -AnnotationAssertion( "basophil cell count measurement") AnnotationAssertion( "basophil count test") AnnotationAssertion(rdfs:label "basophil count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3312,8 +3307,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of lymphocyte in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "lymphocyte cell count") -AnnotationAssertion( "lymphocyte cell count measurement") AnnotationAssertion( "lymphocyte count test") AnnotationAssertion(rdfs:label "lymphocyte count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3645,8 +3638,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of reticulocyte in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "reticulocyte cell count") -AnnotationAssertion( "reticulocyte cell count measurement") AnnotationAssertion( "reticulocyte count test") AnnotationAssertion(rdfs:label "reticulocyte count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3775,24 +3766,11 @@ AnnotationAssertion( "surgical procedure on nervous system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) -# Class: (hematopoietic cell count) - -AnnotationAssertion( "A determination of the number of hematopoietic cell in a blood sample.") -AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") -AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "hematopoietic cell cell count") -AnnotationAssertion( "hematopoietic cell cell count measurement") -AnnotationAssertion( "hematopoietic cell count test") -AnnotationAssertion(rdfs:label "hematopoietic cell count") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) - # Class: (erythrocyte count) AnnotationAssertion( "A determination of the number of erythrocyte in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "erythrocyte cell count") -AnnotationAssertion( "erythrocyte cell count measurement") AnnotationAssertion( "erythrocyte count test") AnnotationAssertion(rdfs:label "erythrocyte count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3802,8 +3780,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of platelet in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "platelet cell count") -AnnotationAssertion( "platelet cell count measurement") AnnotationAssertion( "platelet count test") AnnotationAssertion(rdfs:label "platelet count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3813,8 +3789,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of neutrophil in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "neutrophil cell count") -AnnotationAssertion( "neutrophil cell count measurement") AnnotationAssertion( "neutrophil count test") AnnotationAssertion(rdfs:label "neutrophil count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -3824,8 +3798,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of leukocyte in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2019-05-16T18:20:55Z") -AnnotationAssertion( "leukocyte cell count") -AnnotationAssertion( "leukocyte cell count measurement") AnnotationAssertion( "leukocyte count test") AnnotationAssertion(rdfs:label "leukocyte count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7090,8 +7062,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of sperm in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "sperm cell count") -AnnotationAssertion( "sperm cell count measurement") AnnotationAssertion( "sperm count test") AnnotationAssertion(rdfs:label "sperm count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7101,8 +7071,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of helper T cell in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "helper T cell cell count") -AnnotationAssertion( "helper T cell cell count measurement") AnnotationAssertion( "helper T cell count test") AnnotationAssertion(rdfs:label "helper T cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7112,8 +7080,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of T cell in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "T cell cell count") -AnnotationAssertion( "T cell cell count measurement") AnnotationAssertion( "T cell count test") AnnotationAssertion(rdfs:label "T cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7123,8 +7089,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of B cell in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "B cell cell count") -AnnotationAssertion( "B cell cell count measurement") AnnotationAssertion( "B cell count test") AnnotationAssertion(rdfs:label "B cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7134,8 +7098,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of natural killer cell in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "natural killer cell cell count") -AnnotationAssertion( "natural killer cell cell count measurement") AnnotationAssertion( "natural killer cell count test") AnnotationAssertion(rdfs:label "natural killer cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7145,8 +7107,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of echinocyte in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "echinocyte cell count") -AnnotationAssertion( "echinocyte cell count measurement") AnnotationAssertion( "echinocyte count test") AnnotationAssertion(rdfs:label "burr cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7156,8 +7116,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of plasma cell in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "plasma cell cell count") -AnnotationAssertion( "plasma cell cell count measurement") AnnotationAssertion( "plasma cell count test") AnnotationAssertion(rdfs:label "plasma cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7167,8 +7125,6 @@ EquivalentClasses( ObjectIntersecti AnnotationAssertion( "A determination of the number of dendritic cell in a blood sample.") AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") -AnnotationAssertion( "dendritic cell cell count") -AnnotationAssertion( "dendritic cell cell count measurement") AnnotationAssertion( "dendritic cell count test") AnnotationAssertion(rdfs:label "dendritic cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -7179,8 +7135,6 @@ AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") AnnotationAssertion( "2023-03-03T20:39:14Z") AnnotationAssertion( "T reg cell count") -AnnotationAssertion( "regulatory T cell cell count") -AnnotationAssertion( "regulatory T cell cell count measurement") AnnotationAssertion( "regulatory T cell count test") AnnotationAssertion(rdfs:label "regulatory T cell count") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) @@ -8110,6 +8064,19 @@ AnnotationAssertion( "surgical procedure on musculoskeletal system") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) +# Class: (blood cell count) + +AnnotationAssertion( "A determination of the number of blood cell in a blood sample.") +AnnotationAssertion( "http://orcid.org/0000-0001-7941-2961") +AnnotationAssertion( "2023-11-01T20:39:14Z") +AnnotationAssertion( "CBC") +AnnotationAssertion( "blood cell count test") +AnnotationAssertion( "complete blood cell count") +AnnotationAssertion( "complete blood count") +AnnotationAssertion( "full blood count") +AnnotationAssertion(rdfs:label "blood cell count") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) + # Class: (surgical procedure on pancreatic system) AnnotationAssertion( "Any surgical procedure conducted on the pancreatic system.") diff --git a/src/templates/replaced.tsv b/src/templates/replaced.tsv index 39bab2ec..bc35059e 100644 --- a/src/templates/replaced.tsv +++ b/src/templates/replaced.tsv @@ -51,3 +51,4 @@ http://purl.obolibrary.org/obo/MAXO_0010358 obsolete angiography procedure true http://purl.obolibrary.org/obo/MAXO_0010359 obsolete pulmonary angiography procedure true http://purl.obolibrary.org/obo/MAXO_0001313 http://purl.obolibrary.org/obo/MAXO_0001023 obsolete tranquilizing agent therapy true http://purl.obolibrary.org/obo/MAXO_0000023 http://purl.obolibrary.org/obo/MAXO_0000386 obsolete biopsy of muscle true http://purl.obolibrary.org/obo/MAXO_0000387 +http://purl.obolibrary.org/obo/MAXO_0001006 obsolete hematopoeitic cell count true http://purl.obolibrary.org/obo/MAXO_0001509