diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md index 9025ccc..d774b6d 100644 --- a/docs/odk-workflows/RepoManagement.md +++ b/docs/odk-workflows/RepoManagement.md @@ -45,9 +45,9 @@ Note: our ODK file should only have one `import_group` which can contain multipl 1. Add an import statement to your `src/ontology/gcbo-edit.owl` file. We suggest to do this using a text editor, by simply copying an existing import declaration and renaming it to the new ontology import, for example as follows: ``` ... - Ontology( - Import() - Import() + Ontology( + Import() + Import() ... ``` 2. Add your imports redirect to your catalog file `src/ontology/catalog-v001.xml`, for example: @@ -68,7 +68,7 @@ Import() in your editors file (the ontology) and ``` - + ``` in your catalog, tools like `robot` or Protégé will recognize the statement diff --git a/docs/odk-workflows/components.md b/docs/odk-workflows/components.md index 0072fbe..d00abc5 100644 --- a/docs/odk-workflows/components.md +++ b/docs/odk-workflows/components.md @@ -17,20 +17,20 @@ components: 3) Add the component to your catalog file (src/ontology/catalog-v001.xml) ``` - + ``` 4) Add the component to the edit file (src/ontology/gcbo-edit.obo) for .obo formats: ``` -import: https://github.com/bmir-radx/gbco/gcbo/components/your-component-name.owl +import: https://github.com/bmir-radx/gcbo/components/your-component-name.owl ``` for .owl formats: ``` -Import() +Import() ``` 5) Refresh your repo by running `sh run.sh make update_repo` - this should create a new file in src/ontology/components. diff --git a/gcbo-base.json b/gcbo-base.json index ecfc5e2..0ad73fb 100644 --- a/gcbo-base.json +++ b/gcbo-base.json @@ -1,6 +1,6 @@ { "graphs" : [ { - "id" : "https://github.com/bmir-radx/gbco/gcbo/gcbo-base.json", + "id" : "https://github.com/bmir-radx/gcbo/gcbo-base.json", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/type", @@ -16,9 +16,9 @@ "val" : "Global Code Book Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-30" + "val" : "2024-05-01" } ], - "version" : "https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo-base.json" + "version" : "https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo-base.json" } } ] } \ No newline at end of file diff --git a/gcbo-base.obo b/gcbo-base.obo index fd3a4e7..9c2fbd7 100644 --- a/gcbo-base.obo +++ b/gcbo-base.obo @@ -1,9 +1,9 @@ format-version: 1.2 -data-version: https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo-base.owl -ontology: https://github.com/bmir-radx/gbco/gcbo/gcbo-base.owl +data-version: https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo-base.owl +ontology: https://github.com/bmir-radx/gcbo/gcbo-base.owl property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 property_value: http://purl.org/dc/terms/description "None" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified property_value: http://purl.org/dc/terms/title "Global Code Book Ontology" xsd:string -property_value: owl:versionInfo "2024-04-30" xsd:string +property_value: owl:versionInfo "2024-05-01" xsd:string diff --git a/gcbo-base.owl b/gcbo-base.owl index 892862a..2f6f81b 100644 --- a/gcbo-base.owl +++ b/gcbo-base.owl @@ -1,6 +1,6 @@ - - - + + None Global Code Book Ontology - 2024-04-30 + 2024-05-01 diff --git a/gcbo-full.json b/gcbo-full.json index b5867c2..d5b4f91 100644 --- a/gcbo-full.json +++ b/gcbo-full.json @@ -1,6 +1,6 @@ { "graphs" : [ { - "id" : "https://github.com/bmir-radx/gbco/gcbo/gcbo-full.json", + "id" : "https://github.com/bmir-radx/gcbo/gcbo-full.json", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", @@ -13,9 +13,9 @@ "val" : "Global Code Book Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-30" + "val" : "2024-05-01" } ], - "version" : "https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo-full.json" + "version" : "https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo-full.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", diff --git a/gcbo-full.obo b/gcbo-full.obo index 673ab1b..1473e0a 100644 --- a/gcbo-full.obo +++ b/gcbo-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo-full.owl +data-version: https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo-full.owl subsetdef: attribute_slim "" subsetdef: clingen "" subsetdef: disease_grouping "" @@ -200,11 +200,11 @@ synonymtypedef: CLINGEN_LABEL "" synonymtypedef: DEPRECATED "" synonymtypedef: DUBIOUS "" synonymtypedef: OMO:0003005 "" -ontology: https://github.com/bmir-radx/gbco/gcbo/gcbo-full.owl +ontology: https://github.com/bmir-radx/gcbo/gcbo-full.owl property_value: http://purl.org/dc/terms/description "None" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified property_value: http://purl.org/dc/terms/title "Global Code Book Ontology" xsd:string -property_value: owl:versionInfo "2024-04-30" xsd:string +property_value: owl:versionInfo "2024-05-01" xsd:string [Term] id: BFO:0000001 @@ -33450,8 +33450,8 @@ subset: NCIT:C157711 subset: NCIT:C177537 synonym: "Smoking" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Smoking" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} -synonym: "Smoking" EXACT [] {NCIT:P384="CTRP", NCIT:P383="DN"} synonym: "Smoking" EXACT [] {NCIT:P383="PT", NCIT:P384="CPTAC"} +synonym: "Smoking" EXACT [] {NCIT:P384="CTRP", NCIT:P383="DN"} synonym: "Smoking" EXACT [] {NCIT:P383="PT", NCIT:P384="GDC"} is_a: NCIT:C19683 ! Personal Behavior property_value: NCIT:A32 NCIT:C16457 @@ -34063,8 +34063,8 @@ synonym: "Education" EXACT [] {NCIT:P384="SeroNet", NCIT:P383="PT"} synonym: "Education" EXACT [] {NCIT:P386="PCC", NCIT:P383="PT", NCIT:P384="ACC/AHA"} synonym: "Education Level" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Education Level" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} -synonym: "Education Level" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} synonym: "Education Level" EXACT [] {NCIT:P383="PT", NCIT:P384="OORO", NCIT:P386="PC"} +synonym: "Education Level" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} synonym: "education level" EXACT [] {NCIT:P383="SY", NCIT:P385="VAR", NCIT:P384="GDC"} synonym: "Education Level Completed" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} synonym: "education_level" EXACT [] {NCIT:P383="PT", NCIT:P385="VAR", NCIT:P384="GDC"} @@ -38839,8 +38839,8 @@ id: NCIT:C20189 name: Property or Attribute def: "A distinguishing quality or prominent aspect of a person, object, action, process, or substance." [] {NCIT:P378="NCI"} subset: NCIT:C90259 -synonym: "Property or Attribute" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Property or Attribute" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} +synonym: "Property or Attribute" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} disjoint_from: NCIT:C43431 ! Activity disjoint_from: NCIT:C7057 ! Disease, Disorder or Finding disjoint_from: NCIT:C97325 ! Manufactured Object @@ -38907,11 +38907,11 @@ subset: NCIT:C97181 subset: NCIT:C97185 synonym: "CODE" EXACT [] {NCIT:P385="CDISC-OBSCLS", NCIT:P383="PT", NCIT:P384="CDISC"} synonym: "Code" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} -synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="CDISC", NCIT:P385="DDF-DDF Entities"} synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} +synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="CDISC", NCIT:P385="DDF-DDF Entities"} synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="CDISC", NCIT:P385="DDF-Attr Response Code"} -synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 3.0.3"} +synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="PCDC"} synonym: "Code Name" EXACT [] {NCIT:P386="eCTD", NCIT:P383="PT", NCIT:P384="FDA"} synonym: "Coding System" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} @@ -38957,8 +38957,8 @@ subset: NCIT:C89506 subset: NCIT:C90259 synonym: "Individual" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} -synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 3.0.3"} +synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} synonym: "Person" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} is_a: NCIT:C20181 ! Conceptual Entity @@ -39003,8 +39003,8 @@ synonym: "Intervention or Procedure" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Intervention Strategies" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} synonym: "Interventional" EXACT [] {NCIT:P383="AD", NCIT:P384="NCI"} synonym: "Interventional Procedure Type" EXACT [] {NCIT:P383="PT", NCIT:P384="OORO", NCIT:P386="PC"} -synonym: "interventionDescription" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "interventionDescription" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 3.0.3"} +synonym: "interventionDescription" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "Procedure" EXACT [] {NCIT:P383="SY", NCIT:P384="NICHD"} synonym: "Procedure" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} synonym: "procedure" EXACT [] {NCIT:P383="PT", NCIT:P386="ICDC", NCIT:P384="ICDC"} @@ -39592,8 +39592,8 @@ synonym: "Immune disorder, NOS" EXACT [] {NCIT:P383="PT", NCIT:P384="CTEP", NCIT synonym: "Immune Disorders" EXACT [] {NCIT:P383="SY", NCIT:P384="CPTAC"} synonym: "Immune Dysfunction" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} -synonym: "Immune System Disorder" EXACT [] {NCIT:P384="CTRP", NCIT:P383="DN"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="CPTAC"} +synonym: "Immune System Disorder" EXACT [] {NCIT:P384="CTRP", NCIT:P383="DN"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="Cellosaurus"} synonym: "Immunologic Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="PCDC", NCIT:P386="HL"} @@ -39959,8 +39959,8 @@ subset: NCIT:C159501 subset: NCIT:C159503 synonym: "Activity" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} synonym: "Activity" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} -synonym: "Activity" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "Activity" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 3.0.3"} +synonym: "Activity" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "General activity" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} disjoint_from: NCIT:C7057 ! Disease, Disorder or Finding disjoint_from: NCIT:C97325 ! Manufactured Object @@ -40138,8 +40138,8 @@ subset: NCIT:C124325 subset: NCIT:C61410 subset: NCIT:C69186 subset: NCIT:C77526 -synonym: "Pregnancy Status" EXACT [] {NCIT:P383="SY", NCIT:P384="CDISC"} synonym: "Pregnancy Status" EXACT [] {NCIT:P385="SEND-PYTEST", NCIT:P383="PT", NCIT:P384="CDISC"} +synonym: "Pregnancy Status" EXACT [] {NCIT:P383="SY", NCIT:P384="CDISC"} synonym: "Pregnancy Status" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Pregnancy Status" EXACT [] {NCIT:P383="PT", NCIT:P384="DICOM"} synonym: "PREGSTAT" EXACT [] {NCIT:P383="PT", NCIT:P384="CDISC", NCIT:P385="SEND-PYTESTCD"} @@ -40336,8 +40336,8 @@ id: NCIT:C92720 name: Pregnancy Finding def: "Symptoms, signs, diagnostic examinations or a test results in a pregnant mother." [] {NCIT:P378="NCI"} subset: NCIT:C90259 -synonym: "Pregnancy Finding" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} synonym: "Pregnancy Finding" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} +synonym: "Pregnancy Finding" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} is_a: NCIT:C117720 ! Female Reproductive System Finding property_value: NCIT:NHC0 "C92720" xsd:string property_value: NCIT:P106 "Finding" xsd:string @@ -40384,8 +40384,8 @@ synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} synonym: "Cancer" EXACT [] {NCIT:P384="SeroNet", NCIT:P383="PT"} synonym: "Cancer" EXACT [] {NCIT:P383="PT", NCIT:P385="3262", NCIT:P386="CDRH", NCIT:P384="FDA"} synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="CDISC"} -synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="GDC"} synonym: "Cancer" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} +synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="GDC"} synonym: "cancer" EXACT [] {NCIT:P383="PT", NCIT:P385="CDR0000045333", NCIT:P384="NCI-GLOSS"} synonym: "Malignancy" EXACT [] {NCIT:P383="SY", NCIT:P384="CDISC"} synonym: "Malignancy" EXACT [] {NCIT:P383="SY", NCIT:P384="GDC"} @@ -51112,7 +51112,7 @@ def: "A relation that holds between the disease and a process where the physical comment: Editor note: TODO property chain: disease_has_location <- dhbido o occurs_in xref: RO:0004021 range: BFO:0000015 ! process -is_a: disease_disrupts ! disease disrupts +is_a: disease_disrupts ! disease causes disruption of is_a: RO:0004019 ! disease has basis in transitive_over: part_of ! part_of diff --git a/gcbo-full.owl b/gcbo-full.owl index a56b2f1..8828d46 100644 --- a/gcbo-full.owl +++ b/gcbo-full.owl @@ -1,6 +1,6 @@ - - - + + None Global Code Book Ontology - 2024-04-30 + 2024-05-01 diff --git a/gcbo-simple.json b/gcbo-simple.json index 0fd4e42..d9122ef 100644 --- a/gcbo-simple.json +++ b/gcbo-simple.json @@ -1,6 +1,6 @@ { "graphs" : [ { - "id" : "https://github.com/bmir-radx/gbco/gcbo/gcbo-simple.json", + "id" : "https://github.com/bmir-radx/gcbo/gcbo-simple.json", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", @@ -13,9 +13,9 @@ "val" : "Global Code Book Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-30" + "val" : "2024-05-01" } ], - "version" : "https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo-simple.json" + "version" : "https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo-simple.json" }, "nodes" : [ { "id" : "http://purl.org/dc/terms/description", diff --git a/gcbo-simple.obo b/gcbo-simple.obo index 7a92b8b..cc42b22 100644 --- a/gcbo-simple.obo +++ b/gcbo-simple.obo @@ -1,8 +1,8 @@ format-version: 1.2 -data-version: https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo-simple.owl -ontology: https://github.com/bmir-radx/gbco/gcbo/gcbo-simple.owl +data-version: https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo-simple.owl +ontology: https://github.com/bmir-radx/gcbo/gcbo-simple.owl property_value: http://purl.org/dc/terms/description "None" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified property_value: http://purl.org/dc/terms/title "Global Code Book Ontology" xsd:string -property_value: owl:versionInfo "2024-04-30" xsd:string +property_value: owl:versionInfo "2024-05-01" xsd:string diff --git a/gcbo-simple.owl b/gcbo-simple.owl index 39af30a..2014996 100644 --- a/gcbo-simple.owl +++ b/gcbo-simple.owl @@ -1,6 +1,6 @@ - - - + + None Global Code Book Ontology - 2024-04-30 + 2024-05-01 diff --git a/gcbo.json b/gcbo.json index 12517a3..cad9b7a 100644 --- a/gcbo.json +++ b/gcbo.json @@ -1,6 +1,6 @@ { "graphs" : [ { - "id" : "https://github.com/bmir-radx/gbco/gcbo.json", + "id" : "https://github.com/bmir-radx/gcbo.json", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/terms/description", @@ -13,9 +13,9 @@ "val" : "Global Code Book Ontology" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-04-30" + "val" : "2024-05-01" } ], - "version" : "https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo.json" + "version" : "https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", diff --git a/gcbo.obo b/gcbo.obo index 4460dca..139659a 100644 --- a/gcbo.obo +++ b/gcbo.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: https://github.com/bmir-radx/gbco/gcbo/releases/2024-04-30/gcbo.owl +data-version: https://github.com/bmir-radx/gcbo/releases/2024-05-01/gcbo.owl subsetdef: attribute_slim "" subsetdef: clingen "" subsetdef: disease_grouping "" @@ -200,11 +200,11 @@ synonymtypedef: CLINGEN_LABEL "" synonymtypedef: DEPRECATED "" synonymtypedef: DUBIOUS "" synonymtypedef: OMO:0003005 "" -ontology: https://github.com/bmir-radx/gbco/gcbo.owl +ontology: https://github.com/bmir-radx/gcbo.owl property_value: http://purl.org/dc/terms/description "None" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/unspecified property_value: http://purl.org/dc/terms/title "Global Code Book Ontology" xsd:string -property_value: owl:versionInfo "2024-04-30" xsd:string +property_value: owl:versionInfo "2024-05-01" xsd:string [Term] id: BFO:0000001 @@ -33450,8 +33450,8 @@ subset: NCIT:C157711 subset: NCIT:C177537 synonym: "Smoking" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Smoking" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} -synonym: "Smoking" EXACT [] {NCIT:P383="PT", NCIT:P384="CPTAC"} synonym: "Smoking" EXACT [] {NCIT:P384="CTRP", NCIT:P383="DN"} +synonym: "Smoking" EXACT [] {NCIT:P383="PT", NCIT:P384="CPTAC"} synonym: "Smoking" EXACT [] {NCIT:P383="PT", NCIT:P384="GDC"} is_a: NCIT:C19683 ! Personal Behavior property_value: NCIT:A32 NCIT:C16457 @@ -38907,11 +38907,11 @@ subset: NCIT:C97181 subset: NCIT:C97185 synonym: "CODE" EXACT [] {NCIT:P385="CDISC-OBSCLS", NCIT:P383="PT", NCIT:P384="CDISC"} synonym: "Code" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} -synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="CDISC", NCIT:P385="DDF-DDF Entities"} synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} +synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="CDISC", NCIT:P385="DDF-DDF Entities"} synonym: "Code" EXACT [] {NCIT:P383="PT", NCIT:P384="CDISC", NCIT:P385="DDF-Attr Response Code"} -synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 3.0.3"} +synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "code" EXACT [] {NCIT:P383="PT", NCIT:P384="PCDC"} synonym: "Code Name" EXACT [] {NCIT:P386="eCTD", NCIT:P383="PT", NCIT:P384="FDA"} synonym: "Coding System" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} @@ -38957,8 +38957,8 @@ subset: NCIT:C89506 subset: NCIT:C90259 synonym: "Individual" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} -synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 3.0.3"} +synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="BRIDG 5.3"} synonym: "Person" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} synonym: "Person" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} is_a: NCIT:C20181 ! Conceptual Entity @@ -39592,8 +39592,8 @@ synonym: "Immune disorder, NOS" EXACT [] {NCIT:P383="PT", NCIT:P384="CTEP", NCIT synonym: "Immune Disorders" EXACT [] {NCIT:P383="SY", NCIT:P384="CPTAC"} synonym: "Immune Dysfunction" EXACT [] {NCIT:P383="SY", NCIT:P384="caDSR"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} -synonym: "Immune System Disorder" EXACT [] {NCIT:P384="CTRP", NCIT:P383="DN"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="CPTAC"} +synonym: "Immune System Disorder" EXACT [] {NCIT:P384="CTRP", NCIT:P383="DN"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Immune System Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="Cellosaurus"} synonym: "Immunologic Disorder" EXACT [] {NCIT:P383="PT", NCIT:P384="PCDC", NCIT:P386="HL"} @@ -40336,8 +40336,8 @@ id: NCIT:C92720 name: Pregnancy Finding def: "Symptoms, signs, diagnostic examinations or a test results in a pregnant mother." [] {NCIT:P378="NCI"} subset: NCIT:C90259 -synonym: "Pregnancy Finding" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} synonym: "Pregnancy Finding" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} +synonym: "Pregnancy Finding" EXACT [] {NCIT:P383="PT", NCIT:P384="NCI"} is_a: NCIT:C117720 ! Female Reproductive System Finding property_value: NCIT:NHC0 "C92720" xsd:string property_value: NCIT:P106 "Finding" xsd:string @@ -40384,8 +40384,8 @@ synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="NCI"} synonym: "Cancer" EXACT [] {NCIT:P384="SeroNet", NCIT:P383="PT"} synonym: "Cancer" EXACT [] {NCIT:P383="PT", NCIT:P385="3262", NCIT:P386="CDRH", NCIT:P384="FDA"} synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="CDISC"} -synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="GDC"} synonym: "Cancer" EXACT [] {NCIT:P383="PT", NCIT:P384="NICHD"} +synonym: "Cancer" EXACT [] {NCIT:P383="SY", NCIT:P384="GDC"} synonym: "cancer" EXACT [] {NCIT:P383="PT", NCIT:P385="CDR0000045333", NCIT:P384="NCI-GLOSS"} synonym: "Malignancy" EXACT [] {NCIT:P383="SY", NCIT:P384="CDISC"} synonym: "Malignancy" EXACT [] {NCIT:P383="SY", NCIT:P384="GDC"} @@ -51112,7 +51112,7 @@ def: "A relation that holds between the disease and a process where the physical comment: Editor note: TODO property chain: disease_has_location <- dhbido o occurs_in xref: RO:0004021 range: BFO:0000015 ! process -is_a: disease_disrupts ! disease causes disruption of +is_a: disease_disrupts ! disease disrupts is_a: RO:0004019 ! disease has basis in transitive_over: part_of ! part_of diff --git a/gcbo.owl b/gcbo.owl index c1f411b..d6f26ba 100644 --- a/gcbo.owl +++ b/gcbo.owl @@ -1,6 +1,6 @@ - - - + + None Global Code Book Ontology - 2024-04-30 + 2024-05-01 diff --git a/patterns/definitions.owl b/patterns/definitions.owl index 5262871..221bf65 100644 --- a/patterns/definitions.owl +++ b/patterns/definitions.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,9 +6,9 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - -Annotation(owl:versionInfo "2024-04-30") +Ontology( + +Annotation(owl:versionInfo "2024-05-01") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 43d584a..43ea056 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 6104b1946933ac730934d10fb19766a81202c01448823d72879e6a6610533441 +CONFIG_HASH= fd4792a5b818d4783baec205d067e9cc25f438ab4ff94e3526180e316dbf5f78 # ---------------------------------------- @@ -19,9 +19,9 @@ CONFIG_HASH= 6104b1946933ac730934d10fb19766a81202c01448823d72879e # these can be overwritten on the command line OBOBASE= http://purl.obolibrary.org/obo -URIBASE= https://github.com/bmir-radx/gbco +URIBASE= https://github.com/bmir-radx ONT= gcbo -ONTBASE= https://github.com/bmir-radx/gbco/gcbo +ONTBASE= https://github.com/bmir-radx/gcbo EDIT_FORMAT= owl SRC = $(ONT)-edit.$(EDIT_FORMAT) MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false diff --git a/src/ontology/gcbo-odk.yaml b/src/ontology/gcbo-odk.yaml index 6886c7e..5b33f18 100644 --- a/src/ontology/gcbo-odk.yaml +++ b/src/ontology/gcbo-odk.yaml @@ -6,7 +6,7 @@ use_dosdps: true dosdp_tools_options: "--obo-prefixes=true --prefixes=config/prefixes.yaml" git_main_branch: main use_context: true -uribase: "https://github.com/bmir-radx/gbco" +uribase: "https://github.com/bmir-radx" release_artefacts: - base - full diff --git a/src/ontology/imports/mondo_import.owl b/src/ontology/imports/mondo_import.owl index 4f8337b..09791e1 100644 --- a/src/ontology/imports/mondo_import.owl +++ b/src/ontology/imports/mondo_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2024-04-30") +Annotation(owl:versionInfo "2024-05-01") Declaration(Class()) Declaration(Class()) @@ -4920,7 +4920,7 @@ SubObjectPropertyOf( ) ObjectPropertyDomain( ) -# Object Property: (disease causes disruption of) +# Object Property: (disease disrupts) AnnotationAssertion( "A relationship between a disease and a process where the disease process disrupts the execution of the process.") AnnotationAssertion( "RO:0004024") diff --git a/src/ontology/imports/nbo_import.owl b/src/ontology/imports/nbo_import.owl index d1d03ff..4875940 100644 --- a/src/ontology/imports/nbo_import.owl +++ b/src/ontology/imports/nbo_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2024-04-30") +Annotation(owl:versionInfo "2024-05-01") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/ncit_import.owl b/src/ontology/imports/ncit_import.owl index 019c1ee..d00a5c4 100644 --- a/src/ontology/imports/ncit_import.owl +++ b/src/ontology/imports/ncit_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2024-04-30") +Annotation(owl:versionInfo "2024-05-01") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl index 26f20de..313007c 100644 --- a/src/ontology/imports/pato_import.owl +++ b/src/ontology/imports/pato_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2024-04-30") +Annotation(owl:versionInfo "2024-05-01") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/imports/symp_import.owl b/src/ontology/imports/symp_import.owl index c12300b..4f7811c 100644 --- a/src/ontology/imports/symp_import.owl +++ b/src/ontology/imports/symp_import.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,10 +6,10 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - +Ontology( + Annotation( ) -Annotation(owl:versionInfo "2024-04-30") +Annotation(owl:versionInfo "2024-05-01") Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv index 4601161..42d346f 100644 --- a/src/ontology/reports/basic-report.tsv +++ b/src/ontology/reports/basic-report.tsv @@ -137,7 +137,7 @@ "An inflammatory process affecting a joint. Causes include infection, autoimmune processes, degenerative processes, and trauma. Signs and symptoms may include swelling around the affected joint and pain." "DOID:848 EFO:0005856 MESH:D001168 SCTID:3723001 Wikipedia:Arthritis UMLS:C0003864 NCIT:C2883" "A carcinoma arising in the oral cavity. Most oral cavity carcinomas are squamous cell carcinomas of the tongue, buccal mucosa, or gums. Less frequent morphologic variants include mucoepidermoid carcinoma and adenocarcinoma." "NCIT:C8990 UMLS:C0151546" "Disorders that are causes by overuse of tendons." "SCTID:68172002 EFO:1001434 MESH:D052256" - "Failure of the heart to pump a sufficient amount of blood to meet the needs of the body tissues, resulting in tissue congestion and edema. Signs and symptoms include shortness of breath, pitting edema, enlarged tender liver, engorged neck veins, and pulmonary rales." "ICD9:428.9 ICD9:404.13 ICD9:404.01 NCIT:C3080 ICD9:428 SCTID:42343007 EFO:0000373 DOID:6000 ICD9:428.0 ICD9:404.11 UMLS:C0018802" + "Failure of the heart to pump a sufficient amount of blood to meet the needs of the body tissues, resulting in tissue congestion and edema. Signs and symptoms include shortness of breath, pitting edema, enlarged tender liver, engorged neck veins, and pulmonary rales." "ICD9:428.9 ICD9:404.13 ICD9:404.01 SCTID:42343007 NCIT:C3080 ICD9:428 EFO:0000373 DOID:6000 ICD9:428.0 ICD9:404.11 UMLS:C0018802" "An immune response that occurs following re-exposure to an innocuous antigen, and that requires the presence of existing antibodies against that antigen. This response involves the binding of IgE to mast cells, and may worsen with repeated exposures." "DOID:1205 UMLS:C0020517 SCTID:609328004 ICD9:V15.09 EFO:0003785 NCIT:C114476 MESH:D006967 ICD9:995.3" "Acute inflammation of the conjunctiva." "ICD9:372.03 UMLS:C0155141 DOID:11184 ICD9:372.00 SCTID:53726008 NCIT:C35195" @@ -338,8 +338,8 @@ - "A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table." "An inflammatory disease involving a pathogenic inflammatory response in the muscle tissue." "SCTID:128496001 EFO:0000783 MESH:D009220 DOID:633 ICD9:728.9 NCIT:C27578" + "A molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table." "A carcinoma that arises from the head and neck region. Representative examples include oral cavity squamous cell carcinoma, laryngeal squamous cell carcinoma, and salivary gland carcinoma." "NCIT:C35850 UMLS:C3887461 DOID:1542" @@ -357,8 +357,8 @@ "The inhalation and exhalation of tobacco smoke." - "A sensation perception that is characterized by an unpleasant sensation that usually indicates the body is threatened or damaged. The sensation may be sharp or dull, short-lived or chronic, intermittent or continual, confined to one area or spread over the entire body." + @@ -373,9 +373,9 @@ "A heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms." + "An abnormal chest sound that is characterized by breathing with difficulty usually with a whistling sound." "UMLS_ICD9CM_2005_AUI:A0133941 UMLS_CUI:C0043144 ICD9CM_2005:786.07" "A primary or metastatic malignant neoplasm affecting the head and neck. Representative examples include oral cavity squamous cell carcinoma, laryngeal squamous cell carcinoma, and salivary gland carcinoma." "UMLS:C0278996 DOID:11934 EFO:0006859 NCIT:C4013" - "An abnormal chest sound that is characterized by breathing with difficulty usually with a whistling sound." "UMLS_ICD9CM_2005_AUI:A0133941 UMLS_CUI:C0043144 ICD9CM_2005:786.07" "Acute or chronic inflammation of the fallopian tube. It is most often caused by Neisseria gonorrhoeae and Chlamydia trachomatis infections. The infections usually originate in the vagina and ascend to the fallopian tube. Symptoms include abdominal, pelvic, and lower back pain, pain during ovulation and sexual intercourse, fever, nausea, and vomiting. Complications include infertility and ectopic pregnancy." "NCIT:C26880 DOID:5733 MESH:D012488 SCTID:88157006 UMLS:C0036130" "Any variation from the normal rate or rhythm (which may include the origin of the impulse and/or its subsequent propagation) in the heart." "NCIT:C2881 SCTID:698247007 EFO:0004269 ICD9:427.9" @@ -468,8 +468,8 @@ "A size quality inhering in an bearer by virtue of the bearer's extension in one dimension." "A benign or malignant neoplasm that affects the colon or rectum. Representative examples of benign neoplasms include lipoma and leiomyoma. Representative examples of malignant neoplasms include carcinoma, lymphoma, and sarcoma. Colorectal adenomas always exhibit epithelial dysplasia and are considered premalignant neoplasms." "NCIT:C2956 EFO:0004142 MESH:D015179" - "Any organic molecular entity that is acidic and contains carbon in covalent linkage." "A respiratory system and chest symptom that is characterized by an explosive expulsion of air from the lungs acting as a protective mechanism to clear the air passages or as a symptom of pulmonary disturbance." "UMLS_ICD9CM_2005_AUI:A0043303 UMLS_CUI:C0010200 ICD9CM_2005:786.2" + "Any organic molecular entity that is acidic and contains carbon in covalent linkage." "A neoplasm (disease) that involves the brain." "NCIT:C2907" @@ -488,8 +488,8 @@ "A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions." "ICD10CM:G40 DOID:1826 ICD10WHO:G40 ICD9:345.9 SCTID:84757009 ICD9:345.90 MESH:D004827 NCIT:C3020 ICD9:345.80 ICD9:345 NIFSTD:birnlex_12718 ICD9:345.8 EFO:0000474 ICD9:345.91" "A cyclic compound having as ring members atoms of at least two different elements." - "A substance used locally on humans and other animals to destroy harmful microorganisms or to inhibit their activity (cf. disinfectants, which destroy microorganisms found on non-living objects, and antibiotics, which can be transported through the lymphatic system to destroy bacteria within the body)." + "A substance used locally on humans and other animals to destroy harmful microorganisms or to inhibit their activity (cf. disinfectants, which destroy microorganisms found on non-living objects, and antibiotics, which can be transported through the lymphatic system to destroy bacteria within the body)." "Neoplasms of the hematopoietic system, including hematopoietic cell neoplasms (e.g. leukemias, lymphomas) and non-hematopoietic cell neoplasms that can affect the hematopoietic system (e.g. lymph node and splenic sarcomas). --2003" "SCTID:129154003 NCIT:C35813 DOID:2531 UMLS:C1512393 MESH:D019337" @@ -499,8 +499,8 @@ "A well differentiated, low or intermediate grade tumor with neuroendocrine differentiation that arises from the small intestine." "EFO:1001928 UMLS:C3272528 NCIT:C96061" - "Heavy nuclear particle: proton or neutron." + "Heavy nuclear particle: proton or neutron." "A non-neoplastic or neoplastic disorder that affects the pancreas. Representative examples of non-neoplastic disorders include pancreatitis and pancreatic insufficiency. Representative examples of neoplastic disorders include cystadenomas, carcinomas, lymphomas, and neuroendocrine neoplasms." "MESH:D010182 NCIT:C26842 ICD9:577.9 SCTID:3855007 DOID:26 ICD9:577.8" @@ -527,8 +527,8 @@ "An instance of muscle tissue disorder that is caused by an inherited genomic modification in an individual." "A chronic inflammatory process causing damage and fibrosis of the pancreatic parenchyma. Signs and symptoms include abdominal pain, malabsorption and diabetes mellitus." "SCTID:235494005 NCIT:C84637 EFO:0000342 ICD9:577.1 UMLS:C0149521 MESH:D050500" - "Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli." "A non-neoplastic or neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and cholecystitis. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, and cholangiocarcinoma." "UMLS:C0267792 NCIT:C3959 DOID:3118" + "Any process that modulates the frequency, rate or extent of consumption behavior, the specific actions or reactions of an organism in response to external or internal stimuli." "A malignant glioma that involves the brain." "SCTID:254937005 EFO:0005543 DOID:0060108 UMLS:C0349661" "Infections of the INTESTINES with PARASITES, commonly involving PARASITIC WORMS. Infections with roundworms (NEMATODE INFECTIONS) and tapeworms (CESTODE INFECTIONS) are also known as HELMINTHIASIS." "MESH:D007411 UMLS:C0021832" @@ -689,8 +689,8 @@ - "A skin and integumentary tissue symptom that is characterized by the excretion of moisture in visible quantities through the opening of the sweat glands." + "Vasculitis represents a clinically heterogenous group of diseases of multifactorial etiology characterized by inflammation of either large-sized vessels (large-vessel vasculitis, e.g. Giant-cell arteritis and Takayasu arteritis), medium-sized vessels (medium-vessel vasculitis e.g. polyarteritis nodosa and Kawasaki disease), or small-sized vessels (small-vessel vasculitis, e.g. granulomatosis with polyangiitis, microscopic polyangiitis, immunoglobulin A vasculitis, and cutaneous leukocytoclastic angiitis). Vasculitis occurs at any age, may be acute or chronic, and manifests with general symptoms such as fever, weight loss and fatigue, as well as more specific clinical signs depending on the type of vessels and organs affected. The degree of severity is variable, ranging from life or sight threatening disease (e.g. Behcet disease) to relatively minor skin disease." "MESH:D014657 SCTID:31996006 EFO:0006803 MedDRA:10036023 GARD:18844 UMLS:C0042384 Orphanet:52759 Wikipedia:Vasculitis DOID:865 MedDRA:10047115 NCIT:C26912 Orphanet:280369" @@ -708,8 +708,8 @@ "A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life." - "An agonist that selectively binds to and activates a protein kinase receptor." + "An agonist that selectively binds to and activates a protein kinase receptor." @@ -729,8 +729,8 @@ - "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en "An autoimmune form of uveitis (disease)." "DOID:0040088" + "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en @@ -904,7 +904,7 @@ "An adenocarcinoma that arises from the ovary. It is the most common type of ovarian carcinoma. It includes the serous adenocarcinoma, mucinous adenocarcinoma, clear cell adenocarcinoma, and endometrioid adenocarcinoma." "EFO:0006460 Orphanet:213504 DOID:3713 MedDRA:10051938 GARD:20466 NCIT:C7700" - "A carcinoma that arises from epithelial cells of the fallopian tube." "NCIT:C3867 EFO:1000251 DOID:1963 UMLS:C0238122 SCTID:276870001" + "A carcinoma that arises from epithelial cells of the fallopian tube." "EFO:1000251 DOID:1963 UMLS:C0238122 SCTID:276870001 NCIT:C3867" "Infections with nematodes of the order rhabditida." "UMLS:C0162631 EFO:0007468 MESH:D017196" @@ -953,9 +953,9 @@ "A respiratory system disease with a basis in a pathological type I hypersensitivity reaction." "DOID:0060496" + "An iron group element atom that has atomic number 26." - "A malignant germ cell tumor that involves the uterine cervix." "GARD:20501 ICD10CM:C53.0 UMLS:C4750752 Orphanet:213837" @@ -987,8 +987,8 @@ - "A poison that interferes with the functions of the nervous system." + "A poison that interferes with the functions of the nervous system." "A primary or metastatic malignant neoplasm involving the cardiovascular system." "NCIT:C114940 DOID:176 UMLS:C3898472" @@ -1038,7 +1038,7 @@ "A malignant neoplasm involving the myocardium." "UMLS:C0346611 DOID:9299 NCIT:C4569" - "A carcinoma involving a uterus." "EFO:0002919 UMLS:C2960452 SCTID:446022000" + "A carcinoma involving a uterus." "SCTID:446022000 EFO:0002919 UMLS:C2960452" "A benign or malignant neoplasm affecting the kidney. Representative examples of benign renal neoplasms include fibroma, lipoma, oncocytoma, and juxtaglomerular cell tumor. Representative examples of malignant renal neoplasms include renal cell carcinoma, renal pelvis carcinoma, Wilms tumor, rhabdoid tumor, sarcoma, and lymphoma." "SCTID:126880001 ICD9:239.5 NCIT:C3150 ONCOTREE:KIDNEY" @@ -1137,8 +1137,8 @@ "Any alkali metal salt having sodium(1+) as the cation." "A hypersensitivity reaction type II disease that involves the alimentary part of gastrointestinal system." "DOID:0060031" - "Arrhythmia is a cardiovascular system symptom consisting of an alteration in rhythm of the heartbeat either in time or force." + "A rare adenocarcinoma that arises from the uterine ligament." "NCIT:C40135 DOID:3700 UMLS:C1519866" "An impairment of the structure or function of the blood vessels which carry blood away from the heart." "SCTID:359557001 ICD9:447.8 NCIT:C35317 DOID:0050828 UMLS:C0852949 ICD9:447.9" @@ -1148,8 +1148,8 @@ "Gastritis resulting from bacteria." "DOID:4033 SCTID:723096000 NCIT:C27340 UMLS:C0948039" "A bone disease that results in formation or resorption abnormalities located in bone." "DOID:0080005" - "A main group molecular entity that contains one or more atoms of a p-block element." "A disease involving the spinal cord." "UMLS:C0037928 ICD9:336.9 DOID:319 ICD9:336.8 NCIT:C97110 SCTID:48522003 MESH:D013118" + "A main group molecular entity that contains one or more atoms of a p-block element." @@ -1166,9 +1166,9 @@ + "A pain that is characterized by a pain in the head." "UMLS_CUI:C0018681 ICD9CM_2005:784.0 UMLS_ICD9CM_2005_AUI:A0065994" - "A pain that is characterized by a pain in the head." "UMLS_CUI:C0018681 ICD9CM_2005:784.0 UMLS_ICD9CM_2005_AUI:A0065994" @@ -1265,8 +1265,8 @@ "The act of bringing an object or substance into the body by swallowing, surrounding or absorbing it [NBO:SMAC]" "A neoplasm with neuroendocrine differentiation that arises from the gallbladder. It includes well differentiated neuroendocrine tumors (low and intermediate grade) and poorly differentiated neuroendocrine carcinomas (high grade)." "UMLS:C3273115 NCIT:C96917" "A hypersensitivity reaction type II disease that involves the exocrine system." "DOID:0060029" - "Inflammation of the stomach that is chronic in nature." "ICD9:535.4 NCIT:C26929 HP:0005231 ICD9:535.41 ICD9:535.40 UMLS:C0085695 SCTID:8493009 EFO:0000337" + "Inflammation of the stomach that is chronic in nature." "ICD9:535.4 NCIT:C26929 HP:0005231 ICD9:535.41 ICD9:535.40 UMLS:C0085695 SCTID:8493009 EFO:0000337" "A hematologic disorder which does not display the morphologic and/or clinical characteristics of an overt malignancy. Representative examples include atypical lymphoproliferative disorders and myelodysplastic syndromes." "NCIT:C27274 UMLS:C1335471" @@ -1382,8 +1382,8 @@ "Compounds based on a biladiene skeleton." - + "Inflammation of the small intestine." "SCTID:64613007 NCIT:C26765 UMLS:C0014335 MESH:D004751" @@ -1404,9 +1404,9 @@ "Any fungal metabolite produced during a metabolic reaction in Baker's yeast (Saccharomyces cerevisiae)." + "Orphanet:309001 UMLS:CN227180 GARD:21313" - @@ -1537,8 +1537,8 @@ "A chronic and progressive lung disorder characterized by the loss of elasticity of the bronchial tree and the air sacs, destruction of the air sacs wall, thickening of the bronchial wall, and mucous accumulation in the bronchial tree. The pathologic changes result in the disruption of the air flow in the bronchial airways. Signs and symptoms include shortness of breath, wheezing, productive cough, and chest tightness. The two main types of chronic obstructive pulmonary disease are chronic obstructive bronchitis and emphysema." "ICD9:496 NCIT:C3199 MESH:D029424 ICD9:490-496.99 OMIM:606963 EFO:0000341 DOID:3083 SCTID:13645005" - "An agonist that selectively binds to and activates a protein kinase C receptor" + "An agonist that selectively binds to and activates a protein kinase C receptor" "A malignant neoplasm involving the heart" "ICD9:164.1 DOID:117 NCIT:C3548 MESH:D006338" @@ -1558,8 +1558,8 @@ "Conditions in which the primary symptom is headache and the headache cannot be attributed to any known causes." "HP:0012459 MESH:D051270 Orphanet:276429 ICD9:339.81 GARD:10796 SCTID:122711000119109" "Squamous cell carcinoma of the gallbladder and extrahepatic biliary tract is a rare hepatic and biliary tract tumor, arising either in the gallbladder itself or in the epithelium lining the extrahepatic biliary tree, the cystic duct and peribiliary glands. It is characterized by a substantial keratinization with abundant keratohyalin pearls and central deposition of dense keratin material within infiltrative nests and locally aggressive nature. In the early stages of the disease symptoms are vague and nonspecific (abdominal pain, jaundice and vomiting). In the advanced stages it may present with a bulky tumor and symptoms of adjacent organ involvement." "UMLS:C4707898 SCTID:766978002 GARD:21792 Orphanet:424996" - "Any habitual use of the tobacco plant leaf and its products." "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." + "Any habitual use of the tobacco plant leaf and its products." "An autosomal dominant heart condition that causes disruptions in the heart's normal rhythm. This condition is characterized by uncoordinated electrical activity in the heart's upper chambers (the atria), which causes the heartbeat to become fast and irregular." "OMIMPS:608583 Orphanet:334 GARD:9740 SCTID:715395008 DOID:0050650 UMLS:C3468561" "A battery-powered electronic device designed to atomize a nicotine-containing liquid solution for inhalation in a manner that simulates smoking a tobacco cigarette." @@ -1596,7 +1596,7 @@ "A malignant neoplasm involving the thyroid gland" "DOID:1781 ICD9:193 UMLS:C0007115 SCTID:363478007 NCIT:C7510" - "Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area, as in coronary thrombosis." "UMLS:C0027051 HP:0001658 DOID:5844 SCTID:22298006 EFO:0000612 NCIT:C27996 ICD10CM:I21 MESH:D009203" + "Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area, as in coronary thrombosis." "UMLS:C0027051 HP:0001658 DOID:5844 SCTID:22298006 EFO:0000612 ICD10CM:I21 NCIT:C27996 MESH:D009203" "An acute infectious process that affects the brain tissue. It is usually caused by viruses and less often by bacteria, parasites, and fungi." "ICD9:323.4 MESH:D000069544 SCTID:312215006 ICD9:049.8 NCIT:C79550" @@ -1661,8 +1661,8 @@ "An indication of a person's current tobacco and nicotine consumption as well as some indication of smoking history." "A well differentiated, low grade neuroendocrine tumor (carcinoid tumor) that arises from the small intestine. The mitotic count is less than 2 per 10 HPF and/or the Ki67 index is equal to or less than 2 percent." "UMLS:C0349536 SCTID:276818002 DOID:0050925 NCIT:C4638" - "Behavior related to the intake of substances." "Natural pigments containing a fundamental skeleton of four pyrrole nuclei united through the alpha-positions by four methine groups to form a macrocyclic structure." + "Behavior related to the intake of substances." @@ -1718,7 +1718,7 @@ "Any process that modulates the frequency, rate or extent of consumption of food or liquid" - "A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis)." "MESH:D001327 NCIT:C2889 UMLS:C0004364 OMIM:109100 ICD9:279.49 EFO:0005140 ICD9:279.4 DOID:417 ICD9:720 OBI:1110054 SCTID:85828009" + "A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis)." "MESH:D001327 NCIT:C2889 UMLS:C0004364 OMIM:109100 EFO:0005140 ICD9:279.49 ICD9:279.4 DOID:417 ICD9:720 OBI:1110054 SCTID:85828009" @@ -1870,8 +1870,8 @@ "A feeding behavior associated with the intake or the frequency of intake or preference or manner of intake of food." "A slow growing neuroendocrine tumor, composed of uniform, round, or polygonal cells having monotonous, centrally located nuclei and small nucleoli, infrequent mitoses, and no necrosis. The tumor may show a variety of patterns, such as solid, trabecular, and acinar. Electron microscopy shows small secretory granules. Immunohistochemical studies reveal NSE, as well as chromogranin immunoreactivity. Malignant histology (cellular pleomorphism, hyperchromatic nuclei, prominent nucleoli, necrosis, and mitoses) can occasionally be seen. Such cases may have an aggressive clinical course. Gastrointestinal tract and lung are common sites of involvement." "ICD9:209.60 NCIT:C2915 HP:0100570 MESH:D002276 EFO:0004243 SCTID:443492008 ICDO:8240/3 ICDO:8241/3" "An inherited metabolic disease that is has its basis in the disruption of glucose transport." "GARD:18957 UMLS:CN227593 Orphanet:79178" - "A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties." "A cell that is capable of detection of a stimulus involved in sensory perception." + "A biological role which describes how a drug interacts within a biological system and how the interactions affect its medicinal properties." "An inherited disorder characterized by structural alterations of a globin chain within the hemoglobin molecule." "MESH:D006453 ICD10CM:D58.1 MedDRA:10060892 Orphanet:68364 ICD9:282.7 GARD:18883 ICD10CM:D58.0 NCIT:C3092 DOID:2860 SCTID:427306008" "A carcinoma arising from the squamous cells of the epidermis. Skin squamous cell carcinoma is most commonly found on sun-exposed areas. The majority of the tumors are well-differentiated." "EFO:1001927 ONCOTREE:CSCC DOID:3151 UMLS:C0553723 SCTID:254651007 NCIT:C4819" "A melancholy feeling of sadness and despair." "UMLS:C0011581 DOID:1596 ICD9:311 NCIT:C2982 SCTID:35489007 MESH:D003866 MFOMD:0000013 ICD10CM:F32" @@ -1880,8 +1880,8 @@ "A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition." "UMLS:C0039082 DOID:225 NCIT:C28193 OGMS:0000086 MESH:D013577" "An immune system disease that has basis in dysregulation of the hypersensitivity reaction, an inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system." "DOID:0060056 SCTID:473010000 EFO:1002003 NCIT:C3114" - "UMLS_ICD9CM_2005_AUI:A0284173 UMLS_CUI:C0476247 ICD9CM_2005:784" + "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." "Inflammation of the iris and anterior chamber of the eye." "UMLS:C0042165 NCIT:C35109 HP:0012122 CSP:1114-9593 MESH:D014606 MedDRA:10002709 DOID:1407 Orphanet:280886 SCTID:410692006 GARD:10941 EFO:1000811" @@ -1924,9 +1924,9 @@ "Autoimmune oophoritis is a rare cause of primary ovarian insufficiency (POI). It happens when the body's immune system mistakenly attacks the ovaries causing inflammation, atrophy and fibrosis. These changes stop the ovaries from working normally. The main symptoms of autoimmune oophorotis are irregular or absent menstrual period (amenorrhea) and symptoms related to ovarian cysts such as abdominal cramping, bloating, nausea and vomiting. Autoimmune oophoritis may occur as part of autoimmune polyglandular syndrome type I and type II but has also been associated with lupus, pernicious anemia, myasthenia gravis and other autoimmune conditions. The underlying cause of autoimmune oophoritis is unknown. Diagnosis involves a special blood test which looks for anti-steroid or anti-ovarian antibodies, a pelvic ultrasound to look for enlarged cystic ovaries and tests to rule out other possible causes of POI. Management of autoimmune oophoritis involves emotional support, possible estrogen replacement therapy and management of other autoimmune conditions." "MESH:C538274 UMLS:C0878654" - "An organic compound having at least one hydroxy group attached to a carbon atom." + "An organic compound having at least one hydroxy group attached to a carbon atom." "A unique group of rare tumors of the central nervous system that affect mainly children and adolescents. Their morphologic and biologic profile corresponds to that of homologous germ cell tumors that arise in the gonads and in other extragonadal sites. Representative examples include: germinoma, embryonal carcinoma, yolk sac tumor, choriocarcinoma, and teratoma." "UMLS:C1332880 NCIT:C5461 DOID:4439" "A malignant mesenchymal neoplasm arising from adipocytes." "ICD9:171.9 DOID:3939 SCTID:254828009 NCIT:C4501" "A disorder directly resulting from the presence and activity of a microbial, viral, or parasitic agent in humans. It can be transmitted by direct or indirect contact." "ICD9:136.9 ICD10CM:A00-B99 DOID:0050117 ICD9:079.0 MESH:D003141 NCIT:C26726 EFO:0005741 SCTID:40733004 ICD9:136.8 IDO:0000436" @@ -1937,8 +1937,8 @@ "A disease involving the ocular adnexa." "SCTID:118941004 UMLS:C1290855 ICD10WHO:H00-H06 DOID:0050815 Orphanet:519266" - "The inflammation of one or more joints caused by a bacterial infection within the joint space. Symptoms include pain, stiffness, and decreased range of motion in the affected joint." "EFO:1001351 ICD9:711.94 MESH:D001170 ICD9:711.97 ICD9:711.96 ICD9:711.0 ICD9:711.91 ICD9:711.90 SCTID:48245008 NCIT:C26700 NCIT:C26699 ICD9:711.9 ICD9:711.93 DOID:813 ICD9:711.40 ICD9:711.95 ICD9:711.92" "An alteration of appetite that is characterized by a loss of desire to eat, i.e. no desire to eat." + "The inflammation of one or more joints caused by a bacterial infection within the joint space. Symptoms include pain, stiffness, and decreased range of motion in the affected joint." "EFO:1001351 ICD9:711.94 MESH:D001170 ICD9:711.97 ICD9:711.96 ICD9:711.0 ICD9:711.91 ICD9:711.90 SCTID:48245008 NCIT:C26700 NCIT:C26699 ICD9:711.9 ICD9:711.93 DOID:813 ICD9:711.40 ICD9:711.95 ICD9:711.92" "A congenital disorder (due to inherited enzyme abnormality) or acquired (due to failure of a metabolically important organ) disorder resulting from an abnormal metabolic process." "SCTID:75934005 DOID:0014667 MESH:D008659 UMLS:C0025517 ICD10WHO:E70-E90 NCIT:C3235 ICD9:277.9 EFO:0000589 ICD10CM:E70-E88 ICD9:277.8" @@ -1951,9 +1951,9 @@ "Orphanet:280914 SCTID:231947004 GARD:21098 UMLS:C0339315" - "A quality which inheres in a continuant." "snap:Quality" "A pathological process with signs indicating it may become cancerous. Representative examples include leukoplakia, dysplastic nevus, actinic keratosis, xeroderma pigmentosum, and intraepithelial neoplasia." "MESH:D011230 NCIT:C3341" + "A quality which inheres in a continuant." "snap:Quality" @@ -2095,8 +2095,8 @@ "A grouping of occupations and fields of study." "A question about whether an individual has or had trouble using stairs." - + "A germ cell tumor that arises within the myocardium or cardiac chambers. The reported cases have been teratomas and yolk sac tumors." "NCIT:C147005" "Paraneoplastic syndrome that involves the renal system." @@ -2184,9 +2184,9 @@ "A benign or malignant neoplasm affecting the fallopian tube. Representative examples of benign neoplasms include papilloma, adenofibroma, and leiomyoma. Representative examples of malignant neoplasms include carcinoma, carcinosarcoma, and adenosarcoma." "MESH:D005185 NCIT:C3032 UMLS:C0015558 ICD9:239.5 SCTID:126916003" - "Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances." "Myocarditis is a condition that is characterized by inflammation of the heart muscle (myocardium). Some affected people have no noticeable symptoms of the condition. When present, signs and symptoms may include chest pain, abnormal heartbeat, shortness of breath, fatigue, signs of infection (i.e. fever, headache, sore throat, diarrhea), and leg swelling. Myocarditis can be caused by a variety of factors including infections (viral, bacterial, parasitic, and fungal), allergic reactions to certain medications, and exposure to certain chemicals. It can also be associated with other inflammatory conditions such as lupus, Wegener's granulomatosis, giant cell arteritis and Takayasu's arteritis. Most cases occur sporadically in people with no family history of the condition. Treatment aims to address the underlying cause of the condition. Medications and rarely, a heart transplant may be needed if the heart muscle becomes weak." "MESH:D009205 SCTID:50920009 ICD10CM:I40 NORD:1882 UMLS:C0027059 ICD9:429.0 NCIT:C34831 DOID:820" + "Substance that attaches to and blocks cell receptors that normally bind naturally occurring substances." "An inherited metabolic disease that is has its basis in the disruption of carbohydrate metabolic process." "GARD:18946 EFO:1000061 MESH:D002239 ICD9:271.8 NCIT:C97089 Orphanet:79161 DOID:2978 MedDRA:10061023" @@ -2332,8 +2332,8 @@ "A benign or malignant, primary or metastatic neoplasm involving the lungs. Representative examples of benign neoplasms include adenoma, papilloma, chondroma, and endobronchial lipoma. Representative examples of malignant neoplasms include carcinoma, carcinoid tumor, sarcoma, and lymphoma." "NCIT:C3200 ONCOTREE:LUNG MESH:D008175" - "A molecular entity consisting of two or more chemical elements." "A natural pigment containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next." + "A molecular entity consisting of two or more chemical elements." "Any carboxylic acid containing two carboxy groups." @@ -2382,9 +2382,9 @@ "Any of the activities associated with tobacco smoking." + "A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease." - "A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease." "An amino acid zwitterion obtained by transfer of a proton from the carboxy to the amino group of any alpha-amino acid; major species at pH 7.3." @@ -2409,8 +2409,8 @@ "An element whose atom has an incomplete d sub-shell, or which can give rise to cations with an incomplete d sub-shell." "A benign, intermediate, or malignant neoplasm arising from vascular tissue including arteries, veins, venous sinuses, lymphatic vessels, arterioles and capillaries. It may occur in essentially any body location and is characterized by the presence of vascular channel formation and endothelial cells." "NCIT:C7388" - + "A morphologic qualifier indicating that a cancerous lesion is undifferentiated." "NCIT:C28082" @@ -2430,8 +2430,8 @@ - "A substance used in the prophylaxis or therapy of infectious diseases." + "A substance used in the prophylaxis or therapy of infectious diseases." "Nausea is a digestive system symptom characterized by an uneasy or unsettled feeling in the stomach together with an urge to vomit." "UMLS_ICD9CM_2005_AUI:A0750850 UMLS_CUI:C0375548 ICD9CM_2005:787.02" @@ -2570,8 +2570,8 @@ - + "A carcinoma arising from the renal parenchyma. There is a strong correlation between cigarette smoking and the development of renal cell carcinoma. The clinical presentation includes : hematuria, flank pain and a palpable lumbar mass. A high percentage of renal cell carcinomas are diagnosed when an ultrasound is performed for other purposes. Radical nephrectomy is the standard intervention procedure. Renal cell carcinoma is generally considered to be resistant to radiation treatment and chemotherapy." "ICDO:8312/3 ICDO:8311/1 EFO:0005708 NCIT:C9385" "A non-infectious or infectious inflammatory process affecting the vagina." "DOID:2170 ICD9:616.10 HP:0030683 ICD9:616.1 NCIT:C26911 SCTID:30800001 MESH:D014627 UMLS:C0042267 EFO:0005757" "Hydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-))." @@ -2615,8 +2615,8 @@ "An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects." "A Disease due to or propagated by sexual contact." "ICD9:099.9 MESH:D012749 SCTID:8098009 ICD10CM:A50-A64 ICD9:099.8 NCIT:C3365 UMLS:C0036916" "The effect of insurance coverage on medical care and practices." - "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." "Reactome:R-HSA-8868783 EC:2.-.-.- Reactome:R-HSA-5668414 Reactome:R-HSA-1483186 Reactome:R-HSA-1483089" + "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." "Reactome:R-HSA-8868783 EC:2.-.-.- Reactome:R-HSA-5668414 Reactome:R-HSA-1483186 Reactome:R-HSA-1483089" "Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization." "ICD9:275.49 DOID:10575 ICD9:275.4 MESH:D002128 EFO:0005769 SCTID:71638002 ICD9:275.40 UMLS:C0006705" @@ -2705,16 +2705,16 @@ "NCIT:C171201 SCTID:46536000 DOID:10972 UMLS:C0036133 ICD9:614.2" - "Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea." + "Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea." "A neurodegenerative disease that involves the optic choroid." "ICD9:363.4 SCTID:406446000 ICD9:363.40 MESH:C535358 DOID:980" - + @@ -2723,8 +2723,8 @@ "A disease that involves the rectum." "MESH:D012002 ICD9:569.49 DOID:1285 SCTID:5964004 UMLS:C0034882" - "A nucleus or any of its constituents in any of their energy states." + "A nucleus or any of its constituents in any of their energy states." "Overactivity of the thyroid gland resulting in overproduction of thyroid hormone and increased metabolic rate. Causes include diffuse hyperplasia of the thyroid gland (Graves' disease), single nodule in the thyroid gland, and thyroiditis. The symptoms are related to the increased metabolic rate and include weight loss, fatigue, heat intolerance, excessive sweating, diarrhea, tachycardia, insomnia, muscle weakness, and tremor." "MESH:D006980 NCIT:C3123 ICD9:242.90 DOID:7998 EFO:0009189 SCTID:34486009" @@ -2756,8 +2756,8 @@ - "A neurological and physiological symptom that is characterized by a diminished or reduced ability to remember things such as dates and names, and increased forgetfulness." + "Inflammation of the tracheobronchial tree." "NCIT:C122784 UMLS:C0040586 SCTID:13617004" "The inflammation of one or more joints caused by any infectious pathogen within the joint space. Symptoms include pain, stiffness, and decreased range of motion in the affected joint." "NCIT:C26700" @@ -2808,8 +2808,8 @@ "A rare squamous cell carcinoma that arises from the mucosal lining of the trachea. It usually grows as an intraluminal mass and later invades extraluminal structures. The majority of patients present with hemoptysis, coughing, dyspnea, or stridor." "SCTID:254620000 DOID:12003 NCIT:C4448 UMLS:C0345946 EFO:1000600" "Abnormal appearance of material expectorated (coughed up) from the respiratory system and that is composed of mucus but may contain other substances such as pus, blood, microorganisms, and fibrin." - "Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds." + "Any eukaryotic metabolite produced during a metabolic reaction in fungi, the kingdom that includes microorganisms such as the yeasts and moulds." "An inflammatory process affecting the skin, caused by bacteria, viruses, parasites, or fungi. Examples of bacterial infection include carbuncles, furuncles, impetigo, erysipelas, and abscesses. Examples of viral infection include shingles, warts, molluscum contagiosum, and pityriasis rosea. Examples of parasitic infection include scabies and lice. Examples of fungal infection include athlete's foot, yeast infection, and ringworm." "NCIT:C35025 SCTID:19824006 UMLS:C0037278" "Gastritis resulting from herpes virus." "UMLS:C1333996 DOID:6102 NCIT:C27341" @@ -2854,8 +2854,8 @@ - "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en + "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en "An attribute of a disease." "NCIT:C41009" @@ -3128,8 +3128,8 @@ - "An adenocarcinoma arising from the pancreas. It is characterized by the presence of relatively uniform malignant cells which form acinar patterns. It usually occurs during adulthood. Signs and symptoms include abdominal pain, weight loss, nausea, and diarrhea. It may metastasize to regional lymph nodes and the liver. A minority of patients develop lipase hypersecretion syndrome. This syndrome may be seen in patients with liver metastases and it is characterized by excessive secretion of lipase in the serum, polyarthralgia, and subcutaneous fat necrosis." "NCIT:C7977 GARD:21777 Orphanet:424046 UMLS:C0279661 DOID:5742 ONCOTREE:PAAC EFO:1000439" "A skin and integumentary tissue symptom that is characterized by a bluish or purplish discoloration (as of skin) due to deficient oxygenation of the blood." "UMLS_ICD9CM_2005_AUI:A0044296 UMLS_CUI:C0010520 ICD9CM_2005:782.5" + "An adenocarcinoma arising from the pancreas. It is characterized by the presence of relatively uniform malignant cells which form acinar patterns. It usually occurs during adulthood. Signs and symptoms include abdominal pain, weight loss, nausea, and diarrhea. It may metastasize to regional lymph nodes and the liver. A minority of patients develop lipase hypersecretion syndrome. This syndrome may be seen in patients with liver metastases and it is characterized by excessive secretion of lipase in the serum, polyarthralgia, and subcutaneous fat necrosis." "NCIT:C7977 GARD:21777 Orphanet:424046 UMLS:C0279661 DOID:5742 ONCOTREE:PAAC EFO:1000439" "A neoplasm (disease) that involves the nervous system." "NCIT:C3268" "A primary or metastatic malignant neoplasm that affects the uterine ligament." "DOID:5727 UMLS:C0864950 NCIT:C126498" @@ -3148,10 +3148,10 @@ - "Sore eyes is a eye symptom characterized by an inflammation of the thin covering of the eyeball and the inner eyelid brought about by a viral infection which may be highly contagious." - "Any polyatomic entity that is an electrically neutral entity consisting of more than one atom." + + "Any polyatomic entity that is an electrically neutral entity consisting of more than one atom." "Cholangitis that is both sudden in onset and of a relatively short duration." "NCIT:C35334 UMLS:C0267917 SCTID:6215006 DOID:14271" "An inherited metabolic disorder caused by an enzyme deficiency, resulting in an inability to oxidize fatty acids for energy production." "GARD:21314 ICD9:272.8 DOID:3146 MedDRA:10061227 NCIT:C97092 ICD9:272.9 SCTID:267431006 UMLS:C0154251 Orphanet:309005" @@ -3181,8 +3181,8 @@ "A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." - "An entity that has temporal parts and that happens, unfolds or develops through time."@en + "An entity that has temporal parts and that happens, unfolds or develops through time."@en "Chronic form of salpingo-oophoritis." "SCTID:198142001 DOID:12265 UMLS:C0156328 ICD9:614.1" @@ -3203,7 +3203,7 @@ - "A disease affects cognitive processes." "SCTID:443265004 NCIT:C92196 MESH:D019965 DOID:1561 EFO:1001457 ICD9:294.9 DOID:0080832" + "A disease affects cognitive processes." "SCTID:443265004 NCIT:C92196 DOID:1561 EFO:1001457 MESH:D019965 ICD9:294.9 DOID:0080832" @@ -3220,7 +3220,7 @@ "Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds." "GARD:21554 Orphanet:363582" - "An acute or chronic inflammatory process affecting the biliary tract." "UMLS:C0008311 ICD9:576.1 NCIT:C26718 MESH:D002761 ICD10CM:K83.0 DOID:9446 SCTID:82403002" + "An acute or chronic inflammatory process affecting the biliary tract." "UMLS:C0008311 ICD9:576.1 NCIT:C26718 ICD10CM:K83.0 MESH:D002761 DOID:9446 SCTID:82403002" @@ -3320,11 +3320,11 @@ - "A liquid that can dissolve other substances (solutes) without any change in their chemical composition." "A malignant neoplasm involving the musculoskeletal system" "DOID:0060100" + "A liquid that can dissolve other substances (solutes) without any change in their chemical composition." + "A respiratory system and chest symptom that is characterized by a sound of breathing that is not similar to that of the sound of moving air and may include: rhonchi (a low-pitched breath sound), crackles (a high-pitched breath sound), wheezing (a high-pitched whistling sound caused by narrowing of the bronchial tubes), and stridor (a harsh, vibratory sound caused by narrowing of the upper airway)." "UMLS_ICD9CM_2005_AUI:A0284219 UMLS_CUI:C0159056 ICD9CM_2005:786.7" - "A respiratory system and chest symptom that is characterized by a sound of breathing that is not similar to that of the sound of moving air and may include: rhonchi (a low-pitched breath sound), crackles (a high-pitched breath sound), wheezing (a high-pitched whistling sound caused by narrowing of the bronchial tubes), and stridor (a harsh, vibratory sound caused by narrowing of the upper airway)." "UMLS_ICD9CM_2005_AUI:A0284219 UMLS_CUI:C0159056 ICD9CM_2005:786.7" "An autoinflammatory condition following an infection with Group A Beta Hemolytic Streptococcus (GABHS), in which the heart is attacked by antibodies formed in reaction to a recent GABHS infection. Chief anatomic changes of the valve include leaflet thickening, commissural fusion, and shortening and thickening of the tendinous cords, all of which can result in valvular dysfunction." 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_:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + + - + @@ -4547,12 +4473,13 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + + @@ -4563,6 +4490,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -4574,8 +4502,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -4586,6 +4514,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -4608,10 +4537,11 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + - + @@ -4634,8 +4564,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -4739,6 +4669,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -4749,15 +4680,18 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + + + @@ -4771,6 +4705,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -4798,16 +4733,16 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + - + @@ -4838,8 +4773,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -4944,6 +4879,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5014,6 +4950,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 +_:B7b1a61e8X2D2500X2D47a8X2Da03dX2Dae82be793e50genid20177 @@ -5030,10 +4967,10 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5057,8 +4994,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5100,6 +5037,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5119,6 +5057,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5132,8 +5071,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5188,6 +5127,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5197,6 +5137,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5212,12 +5153,14 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + + + @@ -5253,6 +5196,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5261,22 +5205,24 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + + + - + @@ -5289,8 +5235,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5311,8 +5257,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5351,9 +5297,10 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + - + @@ -5364,8 +5311,10 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + + @@ -5377,6 +5326,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5398,8 +5348,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5417,6 +5367,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5429,6 +5380,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5454,8 +5406,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5472,6 +5424,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5486,6 +5439,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5502,15 +5456,15 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - - + + @@ -5596,8 +5550,10 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + + @@ -5617,11 +5573,11 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - - + + @@ -5656,14 +5612,15 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + + @@ -5703,6 +5660,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 +_:B7b1a61e8X2D2500X2D47a8X2Da03dX2Dae82be793e50genid20181 @@ -5724,8 +5682,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -5761,18 +5719,19 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + - + - + @@ -5813,9 +5772,10 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + + - @@ -5824,6 +5784,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5842,6 +5803,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5859,6 +5821,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -5892,11 +5855,12 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - - + + + @@ -5904,13 +5868,14 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + + @@ -5954,11 +5919,11 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + - @@ -5999,6 +5964,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -6029,8 +5995,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -6051,6 +6017,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + @@ -6058,6 +6025,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + + @@ -6189,8 +6158,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 - + @@ -6243,12 +6212,13 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 + - + @@ -6263,7 +6233,6 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20173 -_:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 @@ -6272,8 +6241,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + @@ -6293,6 +6262,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6306,9 +6276,11 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + + @@ -6353,10 +6325,12 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + + @@ -6386,9 +6360,9 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + @@ -6396,6 +6370,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6416,16 +6391,17 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + - + @@ -6477,6 +6453,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6539,6 +6516,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6547,8 +6525,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + @@ -6569,8 +6547,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + @@ -6650,6 +6628,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6684,12 +6663,14 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + + + @@ -6716,6 +6697,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6738,8 +6720,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + @@ -6756,15 +6738,15 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + - + @@ -6844,6 +6826,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6853,22 +6836,22 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + - + - + @@ -6879,9 +6862,9 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + - @@ -6931,6 +6914,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -6961,15 +6945,15 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + - - + @@ -6992,9 +6976,10 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 - + + @@ -7006,10 +6991,11 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + - + @@ -7063,6 +7049,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -7096,6 +7083,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -7103,10 +7091,11 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 +_:B7b1a61e8X2D2500X2D47a8X2Da03dX2Dae82be793e50genid20173 - + @@ -7130,6 +7119,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 + @@ -7154,7 +7144,6 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20325 -_:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 @@ -7181,8 +7170,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 - + @@ -7200,6 +7189,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + @@ -7238,6 +7228,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + @@ -7277,6 +7268,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + @@ -7321,13 +7313,14 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + - + - + @@ -7335,6 +7328,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + @@ -7359,6 +7353,7 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + @@ -7458,6 +7453,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + + @@ -7481,10 +7478,12 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + + @@ -7498,67 +7497,68 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -7602,11 +7602,11 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 + - @@ -7665,8 +7665,8 @@ _:B3b620877X2D91f3X2D44c2X2Da81eX2D2894b7511b68genid20181 - + diff --git a/src/ontology/reports/gcbo-edit.owl-obo-report.tsv b/src/ontology/reports/gcbo-edit.owl-obo-report.tsv index 729186c..196280a 100644 --- a/src/ontology/reports/gcbo-edit.owl-obo-report.tsv +++ b/src/ontology/reports/gcbo-edit.owl-obo-report.tsv @@ -1 +1,152 @@ Level Rule Name Subject Property Value +ERROR duplicate_label Chronic obstructive pulmonary disease data element rdfs:label Chronic obstructive pulmonary disease data element +ERROR duplicate_label Chronic obstructive pulmonary disease data element rdfs:label Chronic obstructive pulmonary disease data element +ERROR duplicate_label Chronic lung disease data element rdfs:label Chronic lung disease data element +ERROR duplicate_label Chronic lung disease data element rdfs:label Chronic lung disease data element +WARN missing_definition Age Section IAO:0000115 +WARN missing_definition Disability Status Section IAO:0000115 +WARN missing_definition Domicile Section IAO:0000115 +WARN missing_definition Education Level Section IAO:0000115 +WARN missing_definition Education Years Section IAO:0000115 +WARN missing_definition Employment Section IAO:0000115 +WARN missing_definition Ethnicity Section IAO:0000115 +WARN missing_definition Health Status Section IAO:0000115 +WARN missing_definition Identity Section IAO:0000115 +WARN missing_definition Insurance Status Section IAO:0000115 +WARN missing_definition Medical History Section IAO:0000115 +WARN missing_definition Race Section IAO:0000115 +WARN missing_definition Sex Section IAO:0000115 +WARN missing_definition Symptoms Section IAO:0000115 +WARN missing_definition Abdom pain data element IAO:0000115 +WARN missing_definition Atrial fibrillation data element IAO:0000115 +WARN missing_definition Age data element IAO:0000115 +WARN missing_definition Alcohol substance abuse data element IAO:0000115 +WARN missing_definition Alcohol frequency data element IAO:0000115 +WARN missing_definition Alcohol use data element IAO:0000115 +WARN missing_definition Alcohol past year data element IAO:0000115 +WARN missing_definition Alzheimers data element IAO:0000115 +WARN missing_definition Anemia data element IAO:0000115 +WARN missing_definition Anxiety data element IAO:0000115 +WARN missing_definition Appetite data element IAO:0000115 +WARN missing_definition Arrhythmia data element IAO:0000115 +WARN missing_definition Arthritis data element IAO:0000115 +WARN missing_definition Asthma data element IAO:0000115 +WARN missing_definition Autoimmune disease data element IAO:0000115 +WARN missing_definition Balance data element IAO:0000115 +WARN missing_definition Blind data element IAO:0000115 +WARN missing_definition Blue lips data element IAO:0000115 +WARN missing_definition Cancer data element IAO:0000115 +WARN missing_definition Active cancer treatment data element IAO:0000115 +WARN missing_definition Cancer diagnosis past year data element IAO:0000115 +WARN missing_definition Cardiovascular disease data element IAO:0000115 +WARN missing_definition Cystic fibrosis data element IAO:0000115 +WARN missing_definition Chronic heart disease data element IAO:0000115 +WARN missing_definition Congestive heart failure data element IAO:0000115 +WARN missing_definition Cholesterol data element IAO:0000115 +WARN missing_definition Chronic kidney disease data element IAO:0000115 +WARN missing_definition Chronic kidney disease treatment data element IAO:0000115 +WARN missing_definition Chronic lung disease data element IAO:0000115 +WARN missing_definition Chronic lung disease data element IAO:0000115 +WARN missing_definition Chronic pain data element IAO:0000115 +WARN missing_definition Cigarettes smoke frequency data element IAO:0000115 +WARN missing_definition Chronic lung disease bronchopulmonary dysplasia data element IAO:0000115 +WARN missing_definition Confusion data element IAO:0000115 +WARN missing_definition Conjunctivitis data element IAO:0000115 +WARN missing_definition Chronic obstructive pulmonary disease data element IAO:0000115 +WARN missing_definition Chronic obstructive pulmonary disease data element IAO:0000115 +WARN missing_definition Coronary artery disease data element IAO:0000115 +WARN missing_definition Coronary artery disease angina data element IAO:0000115 +WARN missing_definition Cough data element IAO:0000115 +WARN missing_definition Deaf data element IAO:0000115 +WARN missing_definition Depression data element IAO:0000115 +WARN missing_definition Diabetes data element IAO:0000115 +WARN missing_definition Difficulty breathing data element IAO:0000115 +WARN missing_definition Disability data element IAO:0000115 +WARN missing_definition Dress/Bathe data element IAO:0000115 +WARN missing_definition Education data element IAO:0000115 +WARN missing_definition Education years data element IAO:0000115 +WARN missing_definition Employment data element IAO:0000115 +WARN missing_definition Errand data element IAO:0000115 +WARN missing_definition Ethnicity data element IAO:0000115 +WARN missing_definition Fatigue data element IAO:0000115 +WARN missing_definition Fever chills data element IAO:0000115 +WARN missing_definition Fibromyalgia data element IAO:0000115 +WARN missing_definition Gastroesophageal reflux disease data element IAO:0000115 +WARN missing_definition Gestational diabetes data element IAO:0000115 +WARN missing_definition Headache data element IAO:0000115 +WARN missing_definition Health status data element IAO:0000115 +WARN missing_definition Heart attack data element IAO:0000115 +WARN missing_definition Heart condition data element IAO:0000115 +WARN missing_definition Height data element IAO:0000115 +WARN missing_definition Height category data element IAO:0000115 +WARN missing_definition High temperature data element IAO:0000115 +WARN missing_definition Smoking history data element IAO:0000115 +WARN missing_definition HIV data element IAO:0000115 +WARN missing_definition Hypertension data element IAO:0000115 +WARN missing_definition Inflammatory bowel disease data element IAO:0000115 +WARN missing_definition Irritable bowel syndrome data element IAO:0000115 +WARN missing_definition Immuno compromised solid organ data element IAO:0000115 +WARN missing_definition Immunocompromised data element IAO:0000115 +WARN missing_definition Immunodeficiency data element IAO:0000115 +WARN missing_definition Immunosuppressive condition data element IAO:0000115 +WARN missing_definition Insomnia data element IAO:0000115 +WARN missing_definition Insurance data element IAO:0000115 +WARN missing_definition Intravenous drug use data element IAO:0000115 +WARN missing_definition Lifetime alcohol use data element IAO:0000115 +WARN missing_definition Liver disease data element IAO:0000115 +WARN missing_definition Lupus data element IAO:0000115 +WARN missing_definition Memory data element IAO:0000115 +WARN missing_definition Mental health disorder data element IAO:0000115 +WARN missing_definition Migraines data element IAO:0000115 +WARN missing_definition Multiple sclerosis data element IAO:0000115 +WARN missing_definition Muscle ache data element IAO:0000115 +WARN missing_definition Nausea/vomiting/diarrhea data element IAO:0000115 +WARN missing_definition Shaking data element IAO:0000115 +WARN missing_definition Neurodegenerative disease data element IAO:0000115 +WARN missing_definition Neurological condition data element IAO:0000115 +WARN missing_definition Nicotine data element IAO:0000115 +WARN missing_definition No chronic condition data element IAO:0000115 +WARN missing_definition No symptoms data element IAO:0000115 +WARN missing_definition Numb extremities data element IAO:0000115 +WARN missing_definition Obesity data element IAO:0000115 +WARN missing_definition Loss of taste or smell data element IAO:0000115 +WARN missing_definition Osteoporosis data element IAO:0000115 +WARN missing_definition Other chronic condition data element IAO:0000115 +WARN missing_definition Other symptoms data element IAO:0000115 +WARN missing_definition Other mental health disorder data element IAO:0000115 +WARN missing_definition Polycystic ovary syndrome data element IAO:0000115 +WARN missing_definition Pregnancy data element IAO:0000115 +WARN missing_definition Premature birth data element IAO:0000115 +WARN missing_definition Osoriasis data element IAO:0000115 +WARN missing_definition Rheumatoid arthritis data element IAO:0000115 +WARN missing_definition Race data element IAO:0000115 +WARN missing_definition Rash/toes data element IAO:0000115 +WARN missing_definition Record ID data element IAO:0000115 +WARN missing_definition Red eyes data element IAO:0000115 +WARN missing_definition Renal disease data element IAO:0000115 +WARN missing_definition Restless leg data element IAO:0000115 +WARN missing_definition Seasonal allergies data element IAO:0000115 +WARN missing_definition Seizures data element IAO:0000115 +WARN missing_definition Serious mental illness data element IAO:0000115 +WARN missing_definition Sex data element IAO:0000115 +WARN missing_definition Sickle cell disease data element IAO:0000115 +WARN missing_definition Skin rash data element IAO:0000115 +WARN missing_definition Sleep apnea data element IAO:0000115 +WARN missing_definition Slurred speech data element IAO:0000115 +WARN missing_definition Smoking data element IAO:0000115 +WARN missing_definition Stroke data element IAO:0000115 +WARN missing_definition Substance use data element IAO:0000115 +WARN missing_definition Sweating data element IAO:0000115 +WARN missing_definition Type 1 diabetes data element IAO:0000115 +WARN missing_definition Type 2 diabetes data element IAO:0000115 +WARN missing_definition Thalassemia data element IAO:0000115 +WARN missing_definition Throat/congestion/nose data element IAO:0000115 +WARN missing_definition Thyroid data element IAO:0000115 +WARN missing_definition Tobacco use data element IAO:0000115 +WARN missing_definition Vape frequency data element IAO:0000115 +WARN missing_definition Vaping data element IAO:0000115 +WARN missing_definition Walk/Climb data element IAO:0000115 +WARN missing_definition Weight data element IAO:0000115 +WARN missing_definition Weight category data element IAO:0000115 +WARN missing_definition Wheezing data element IAO:0000115 +WARN missing_definition ZIP code data element IAO:0000115 diff --git a/src/ontology/reports/synonyms.tsv b/src/ontology/reports/synonyms.tsv index 41dd86e..b193277 100644 --- a/src/ontology/reports/synonyms.tsv +++ b/src/ontology/reports/synonyms.tsv @@ -1,157 +1,65 @@ ?cls ?pred ?val ?synType - "molecular entity"@en - "ethanol" - "mouse metabolite" - "catalytic activity" - "anion" - "chemical entity" - "central nervous system depressant" - "protein-containing macromolecular complex" - "protein-containing complex" - "tobacco smoking behavior"@en - "specifically dependent continuant"@en - "quality of a liquid" - "neurotoxin" - "s-block molecular entity" - "antagonist" - "food" - "multicellular organismal process" - "physical quality" - "food consumption" - "lepton" - "process"@en - "animal metabolite" - "teratogenic agent" - "quality"@en - "carbon group element atom" - "behavior" - "s-block element atom" - "independent continuant"@en - "biological_process" - "biological process"@en - "mass"@en - "mass" - "drug" - "material entity"@en - "fundamental particle" - "metabolite" - "inorganic group" - "nucleon" - "complex of molecular entities" - "quality of a substance" - "hydroxy group" - "prokaryotic metabolite" - "agonist" - "feeding behavior" - "protein kinase C agonist" - "ethanols" - "regulation of drinking behavior" - "function"@en - "antiinfective agent" - "composite particle" - "realizable"@en - "realizable entity"@en - "physiological role" - "antiseptic drug" - "gene product" - "mammalian metabolite" - "continuant"@en - "quality" - "characteristic"@en - "smoking behavior"@en - "biochemical role" - "poison" - "consumption behavior"@en - "macronutrient" - "central nervous system drug" - "regulation of behavior"@en - "primary alcohol" - "atom"@en - "chalcogen" - "behavior process" - "aetiopathogenetic role" - "pharmacological role" - "organic molecule" - "ethoxide" - "tobacco consumption"@en - "fermion" - "antimicrobial agent" - "occurrent"@en - "pharmaceutical" - "heteroatomic molecular entity" - "polar solvent" - "p-block element atom" - "organic hydroxy compound" - "alkyl alcohol" - "ion" - "application" - "atomic nucleus"@en - "atomic nucleus" - "polyatomic entity" - "oxygen atom" - "cellular_component" - "nuclear particle" - "organic ion" - "group" - "protein kinase agonist" - "Saccharomyces cerevisiae metabolite" - "regulation of eating behavior" - "chalcogen molecular entity" - "hydroxides" - "NMDA receptor antagonist" - "molecule" - "transferase activity, transferring phosphorus-containing groups" - "carbon group molecular entity" - "electron" - "electron"@en - "nucleic acid polymer" - "liquid consumption" - "entity"@en - "p-block molecular entity" - "main group element atom" - "nutrient" - "nonmetal atom" - "Escherichia coli metabolite" - "regulation of alcohol consumption"@en - "role" - "inorganic molecular entity" - "uncharged atom" - "atom" - "regulation of consumption behavior"@en - "oxygen molecular entity" - "aliphatic alcohol" - "transferase activity" - "eukaryotic metabolite" - "main group molecular entity" - "baryon" - "chemical role" - "physical object quality" - "role"@en - "molecular_function" - "gene product or complex activity"@en - "excitatory amino acid antagonist" - "molecular entity" - "hydrogen molecular entity" - "biological role" - "food component" - "alcohol consumption" - "hadron" - "organic anion" - "disinfectant" - "alcohol" - "kinase activity" - "organic molecular entity" - "solvent" - "hydrogen atom" - "fungal metabolite" - "disposition"@en - "bacterial metabolite" - "volatile organic compound" - "regulation of feeding behavior"@en - "subatomic particle"@en - "subatomic particle" - "carbon atom" - "human metabolite" + "general symptom" + "congestion" + "sore eyes" + "memory loss" + "hypoesthesia" + "feces and droppings symptom" + "bloodshot eye" + "alteration of consciousness" + "disturbances of sensation of smell and taste" + "wheezing" + "arrhythmia" + "extreme fatigue" + "fever" + "cyanosis" + "obsolete myalgia"@en + "ear symptom" + "head and neck symptom" + "diaphoresis" + "rash" + "mouth symptom" + "neurological and physiological symptom" + "shakes" + "fatigue" + "nausea" + "ageusia" + "loss of balance" + "nutrition, metabolism, and development symptom" + "cough" + "symptom" + "abdominal pain" + "sweaty" + "seizure" + "diarrhea" + "throat pain" + "slurred speech" + "cardiovascular system symptom" + "balance symptom"@en + "nervous system symptom" + "sensation perception" + "inability to think clearly" + "concentration difficulty" + "decreased appetite" + "eye symptom" + "loss of appetite" + "nose symptom" + "confusion" + "abnormal chest sound" + "alteration of appetite" + "pain" + "inability to concentrate" + "vomiting" + "respiratory abnormality" + "respiratory system and chest symptom" + "dyspnea" + "head symptom" + "skin and integumentary tissue symptom" + "headache" + "memory impairment" + "rhinorrhea" + "digestive system symptom" + "deafness" "esophageal neuroendocrine tumor" "lobule" "Saurischia" @@ -183,6 +91,7 @@ "heart primordium" "spinal nerve" "duodenal neuroendocrine tumor, well differentiated, low or intermediate grade" + "physiological role" "bronchial endocrine tumor" "excretory duct" "larval stage" @@ -201,9 +110,9 @@ "mental disorder" "contractility" "chronic conjunctivitis" + "crista terminalis" "polychromatophilic cytoplasm" "stroke disorder" - "crista terminalis" "paraxial mesoderm" "sclera" "proerythroblast" @@ -216,6 +125,7 @@ "urethra cancer" "inflammatory response" "synapse" + "disposition"@en "presumptive pronephric mesoderm" "developmental anomaly of metabolic origin" "duration" @@ -223,16 +133,17 @@ "somatodendritic compartment" "future mouth" "size" - "autoimmune oophoritis" "colon adenocarcinoma" "Obesity" "tracheobronchitis" "chronic bronchitis" + "autoimmune oophoritis" "steroid metabolic process" "small intestine neuroendocrine neoplasm" "Abnormal myocardium morphology" "secretion" "elastic fiber" + "oxygen atom" "olfactory apparatus chamber" "intraciliary transport particle" "Neognathae" @@ -253,20 +164,23 @@ "Dipnomorpha" "hepatoblast"@en "hemolytic anemia" + "catalytic activity" "renal pelvis adenocarcinoma" "presumptive gut" "onium cation" "carcinoma of esophagus" - "epithelial tube" "mesenchyme from somatopleure" - "macromolecule metabolic process" + "epithelial tube" "developing mesenchymal condensation" - "parneoplastic endocrine syndrome" "material anatomical entity" + "parneoplastic endocrine syndrome" + "macromolecule metabolic process" + "composite particle" "common bile duct neoplasm" "nitrogen compound metabolic process" - "peptide zwitterion" "islet of Langerhans" + "peptide zwitterion" + "polyatomic entity" "psoriatic arthritis" "Abnormal respiratory system physiology" "cellular modified amino acid metabolic process" @@ -278,6 +192,7 @@ "allergic asthma" "Abnormality of bone mineral density" "collagenopathy" + "entity"@en "brainstem neoplasm" "hepatobiliary system" "Sarcopterygii" @@ -304,6 +219,8 @@ "intracellular vesicle" "central nervous system" "upper urinary tract" + "mass" + "mass"@en "upper respiratory tract" "Autoimmunity" "conjunctival cancer" @@ -320,25 +237,31 @@ "hepatocellular carcinoma" "skin of head" "viral myocarditis" + "realizable entity"@en + "realizable"@en "abdominal segment of trunk" + "quality" + "characteristic"@en "right hepatic duct" "tracheobronchial epithelium" "erythrocyte" - "pancreatic neuroendocrine tumor" "Sleep-related breathing disorders" "neuroendocrine tumor of rectum, well differentiated, low or intermediate grade" + "pancreatic neuroendocrine tumor" "developing neuroepithelium" + "animal metabolite" "nutritional disorder" "calcium metabolic disease" "euploid" + "chemical entity" "muscle cancer" - "organic acid" "tumor grade 1, general grading system" + "organic acid" "bodily gas" "liver bud" "intestine" - "biomacromolecule" "renal pelvis neoplasm" + "biomacromolecule" "intracranial hypertension" "enzyme inhibitor" "Endopterygota" @@ -355,6 +278,7 @@ "epithelial cell" "iris disorder" "blood vessel endothelium" + "bacterial metabolite" "myomatous neoplasm" "mesenchyme condensation cell" "optic neural crest" @@ -374,8 +298,8 @@ "chordamesoderm" "neurula stage" "stomach glandular region" - "cellular response to peptide hormone stimulus" "immature eye" + "cellular response to peptide hormone stimulus" "lipid" "squamous cell carcinoma of rectum" "bowel dysfunction" @@ -402,14 +326,20 @@ "neurectoderm" "Protostomia" "vasculature of central nervous system plus retina" + "function"@en "secretion of exocrine gland" + "biological_process" + "biological process"@en "multi-unit eye" "vagina" + "electron" + "electron"@en + "nucleic acid polymer" "tissue development" "idiopathic" + "myocardial disorder" "secretion by tissue" "cellular response to peptide" - "myocardial disorder" "colon neuroendocrine tumor G1" "dermatocranium" "tauopathy" @@ -450,11 +380,11 @@ "small molecule biosynthetic process" "information content entity"@en "demyelinating disease" - "pelvic girdle skeleton" "simple eye" - "coronary vessel" + "pelvic girdle skeleton" "tendinitis" "adaptive immune response" + "coronary vessel" "muscle contraction" "conducting tissue of heart" "internal genitalia" @@ -503,10 +433,13 @@ "salpingitis" "ocular adnexa" "protein secreting cell" + "baryon" + "subatomic particle" + "subatomic particle"@en "reproductive system" "subdivision of tube" - "optic choroid disorder" "Vomiting" + "optic choroid disorder" "developing anatomical structure" "early embryonic cell (metazoa)" "biological sex" @@ -520,11 +453,12 @@ "mesodermal cell" "natural product fundamental parent" "inherited hemoglobinopathy" - "tube development" "Phenotypic abnormality" + "tube development" "midbrain" "chromatin" "retinal disorder" + "p-block element atom" "dermatomyositis" "systemic arterial system" "chronic endophthalmitis" @@ -539,15 +473,16 @@ "polysaccharide biosynthetic process" "exocrine system" "endoderm formation" + "behavior" "right cardiac chamber" + "skeletal muscle organ, vertebrate" "cytoplasm" "mesenchyme" "skeletal joint" "organic substance catabolic process" "glandular epithelium" - "skeletal muscle organ, vertebrate" - "pancreatic neuroendocrine tumor G1" "cleaving embryo" + "pancreatic neuroendocrine tumor G1" "paraneoplastic neurologic syndrome" "anatomical structure development" "epilepsy, idiopathic generalized" @@ -568,6 +503,7 @@ "skeletal muscle cancer" "organic acid biosynthetic process" "pyloric sphincter" + "quality of a liquid" "glycogen catabolic process" "neoplasm of esophagus" "anus disorder" @@ -589,9 +525,9 @@ "uveitis" "arteriole" "biological_region" + "anatomical histological quality" "multi fate stem cell" "azane" - "anatomical histological quality" "pancreas" "trunk" "univalent carboacyl group" @@ -621,16 +557,17 @@ "1st arch mandibular component" "refrigerant" "pyelitis" + "specifically dependent continuant"@en "entire pharyngeal arch endoderm" "cell-cell junction" "dermomyotome" "renal duct" - "disease characteristic" "vasculature of eye" + "disease characteristic" "hemolymphoid system" "thoracic cancer" - "anterior neural tube" "choroidal sclerosis" + "anterior neural tube" "visceral muscle cell"@en "autoimmune primary ovarian failure" "Rhabditomorpha" @@ -643,6 +580,7 @@ "epithelium of biliary system" "intraembryonic coelom" "detection of external stimulus" + "main group element atom" "nucleate cell" "pair of lungs" "transporter activity" @@ -684,11 +622,13 @@ "muscle organ" "electrically signaling cell" "anatomical structure quality" + "physical quality" "hereditary fallopian tube carcinoma" "chromosome" "smooth muscle myoblast" "liver neuroendocrine carcinoma" "nerve" + "chalcogen" "cervical cancer" "ciliated columnar epithelium" "rhombencephalon neural crest" @@ -701,6 +641,7 @@ "Peploviricota" "inflammatory disease" "regulation of biological quality" + "lepton" "post-viral disorder" "hypertensive disorder" "pancreatic acinar cell carcinoma" @@ -715,6 +656,8 @@ "alkali metal atom" "dorsal pancreatic bud" "megakaryocyte differentiation" + "atomic nucleus" + "atomic nucleus"@en "progenitor cell of endocrine pancreas" "organ part" "germ line cell" @@ -731,6 +674,7 @@ "neural tube ventricular layer" "virus associated tumor" "lung neoplasm" + "transferase activity, transferring phosphorus-containing groups" "organism subdivision" "Drosophilini" "bile" @@ -753,6 +697,7 @@ "colorectal adenocarcinoma" "transitional anatomical structure" "skin carcinoma" + "eukaryotic metabolite" "system" "proctitis" "upper respiratory tract epithelium" @@ -773,6 +718,7 @@ "encephalomyelitis" "myocyte of sinoatrial node" "Arthropoda" + "oxygen molecular entity" "tube formation" "unipotent" "melanogaster subgroup" @@ -793,6 +739,8 @@ "extracellular vesicle biogenesis" "skull disorder" "tracheobronchial tree" + "protein-containing complex" + "protein-containing macromolecular complex" "immune response" "mucopolysaccharide" "Xenopus " @@ -806,11 +754,13 @@ "skin neoplasm" "macromolecule localization" "sensory system cancer" + "group" "constipation disorder" "anatomical surface region" "Pancrustacea" "carboxylic acid metabolic process" "mesothelium" + "hydroxy group" "oral cavity" "tumor grading characteristic" "Sleep apnea" @@ -824,15 +774,16 @@ "eye blink reflex" "pharynx cancer" "pancreatic adenocarcinoma" - "blepharoconjunctivitis" "caudal part of nephrogenic cord" + "blepharoconjunctivitis" "pyelocystitis" "dicarboxylic acid dianion" "acute myocarditis" "primary subdivision of skull" "dermal skeleton" - "epithelial tube morphogenesis" "capillary disorder" + "epithelial tube morphogenesis" + "hadron" "immaterial anatomical entity" "disorder of organic acid metabolism" "gastric acid secretion" @@ -849,6 +800,7 @@ "blepharitis" "skin disorder" "orthochromatic erythroblast" + "continuant"@en "appendage girdle complex" "cellular organisms" "rheumatic myocarditis" @@ -862,10 +814,12 @@ "chronic obstructive pulmonary disease" "elliptic" "neuromuscular disease" + "Escherichia coli metabolite" "bile acid and bile salt transport" "heart" "ovarian adenocarcinoma" "Mode of inheritance" + "mammalian metabolite" "serous sac" "Stroke" "ovarian disorder" @@ -878,15 +832,15 @@ "capsule" "mesonephric tubule" "skeletal system development" + "gastric carcinoma" "endothelial cell" "branching morphogenesis of an epithelial tube" - "gastric carcinoma" "acute" "tumor grade 2, general grading system" "cystitis" - "embryonic cloacal fold" "heart failure" "bronchus" + "embryonic cloacal fold" "malignant germ cell tumor of cervix uteri" "ciliopathy" "gallbladder" @@ -894,10 +848,10 @@ "Seizure" "lung" "Chondrichthyes" - "retinal vasculitis" "cyclic polypyrrole" - "ciliated epithelial cell" + "retinal vasculitis" "cardiopharyngeal field" + "ciliated epithelial cell" "organic substance transport" "future central nervous system" "left hepatic duct" @@ -944,11 +898,12 @@ "hyperplasia" "plasma membrane organization" "IgG4-related ophthalmic disorder" - "colorectum" - "neural crest-derived structure" "paraneoplastic hematological syndrome" - "pharyngeal arch 3" + "neural crest-derived structure" + "colorectum" + "aetiopathogenetic role" "structural epilepsy" + "pharyngeal arch 3" "polysaccharide derivative" "head or neck skin" "hereditary chronic pancreatitis" @@ -973,9 +928,11 @@ "brain ischemia" "non-neural ectoderm" "pancreas disorder" + "organic molecule" "colon neuroendocrine neoplasm" "morphogenesis of a branching structure" "Retroviridae" + "organic ion" "zygote"@en "Eutheria" "female organism" @@ -1011,6 +968,7 @@ "lung carcinoma" "embryonic morphogenesis" "convex 3-D shape" + "biological role" "nasal cavity mucosa" "Columbiformes" "neural rod" @@ -1019,6 +977,7 @@ "extrahepatic part of hepatic duct" "nuclear lumen" "cornea squamous cell carcinoma" + "inorganic molecular entity" "thoracic cavity element" "osteochondrodysplasia" "inflammation of heart layer" @@ -1107,6 +1066,7 @@ "arterial system" "tracheal cancer" "encephalitis" + "food component" "nervous system disorder" "subdivision of skeletal system" "motor neuron" @@ -1118,6 +1078,7 @@ "mesoderm formation" "neural fold" "ureteritis" + "fungal metabolite" "organic substance biosynthetic process" "abdomen element" "blood vessel" @@ -1129,8 +1090,8 @@ "Cyclorrhapha" "tunica fibrosa of eyeball" "epithelial cell of tracheobronchial tree" - "arterial blood vessel" "epicranial aponeurosis" + "arterial blood vessel" "lipid transport" "neurological pain disorder" "tumor grade 3 or 4, general grading system" @@ -1166,8 +1127,8 @@ "opacity" "Neopterygii" "mucus" - "neural crest cell" "biconcave" + "neural crest cell" "colon" "progenitor cell" "anatomical wall" @@ -1197,6 +1158,7 @@ "axial skeleton plus cranial skeleton" "cognitive disorder" "transition element coordination entity" + "hydroxides" "precursor cell" "familial colorectal cancer" "Drosophilidae" @@ -1204,9 +1166,9 @@ "smooth muscle of eye" "bone disorder" "reproductive system cancer" + "heart rudiment" "inorganic ion homeostasis" "plasma membrane region" - "heart rudiment" "Blindness" "syndromic or isolated" "musculoskeletal system" @@ -1220,18 +1182,20 @@ "anus adenocarcinoma" "striated visceral muscle cell"@en "hereditary renal cell carcinoma" + "chemical role" "pancreatitis" "lung germ cell tumor" "acquired skeletal muscle disease" + "macronutrient" "organic hydroxy compound transport" - "Weight loss" "Amphibia" + "Weight loss" "neoplasm of thorax" - "midbrain basal plate" "linear tetrapyrrole anion" "cell differentiation" - "acellular membrane" + "midbrain basal plate" "ventral pancreatic duct" + "acellular membrane" "extracellular matrix secreting cell" "squamous cell carcinoma of pancreas" "camera-type eye photoreceptor cell" @@ -1244,13 +1208,14 @@ "blood vasculature" "endo-epithelial cell" "Eczematoid dermatitis" - "presomitic mesoderm" "epiblast (generic)" - "anatomical cluster" + "presomitic mesoderm" "bile duct disorder" + "anatomical cluster" "Craniata " "skeletal muscle myoblast" "Constitutional symptom"@en + "chalcogen molecular entity" "somatostatin secretion" "preplacodal ectoderm" "liver lobule" @@ -1269,6 +1234,7 @@ "primitive streak" "ovarian dysfunction" "localization" + "s-block molecular entity" "primary ovarian failure" "hepatic acinus" "smooth muscle tumor" @@ -1298,13 +1264,14 @@ "Teleostei" "neuroendocrine carcinoma" "CNS demyelinating autoimmune disease" + "developing mesenchymal structure" "protein-DNA complex" "rectum neuroendocrine neoplasm" "Actinopterygii" "bile salt" - "developing mesenchymal structure" "sphincter muscle" "detection of visible light" + "mouse metabolite" "parasitic eye infection" "nasal disorder" "germinal epithelium of ovary" @@ -1326,8 +1293,9 @@ "bile duct adenocarcinoma" "metanephric ureteric bud" "fibrinogen complex" - "Duplodnaviria" "inborn errors of metabolism" + "Duplodnaviria" + "nucleon" "thoracic cavity" "optical quality" "cellular response to hexose stimulus" @@ -1349,6 +1317,7 @@ "biliary tract neoplasm" "organic hydride" "cancer or benign tumor" + "inorganic group" "venule" "neoplastic disease or syndrome" "organic divalent group" @@ -1390,9 +1359,9 @@ "striated muscle cell" "dermis disorder" "low grade glioma" - "rostral part of nephrogenic cord" "gastrointestinal system epithelium" "Bronsted acid" + "rostral part of nephrogenic cord" "epithelial cell of stomach" "amide transport" "spinal cord neural crest" @@ -1416,13 +1385,14 @@ "squamous cell neoplasm" "bile duct cancer" "Abnormality of the respiratory system" + "occurrent"@en "metanephric mesenchyme" "post-juvenile adult stage" "transient arthritis" "micronutrient" "Mandibulata" - "vision disorder" "dorsum" + "vision disorder" "posterior uveitis" "digestive tract epithelium" "acute cholangitis" @@ -1446,18 +1416,20 @@ "response to abiotic stimulus" "coordination entity" "erythroblast" - "lens placode" "Abnormal inflammatory response" "hereditary disorder of connective tissue" + "lens placode" "organic polycyclic compound" "monosaccharide transmembrane transport" "oxoacid metabolic process" "cylindrical" "Archosauria" "Rhabditidae" + "quality"@en "biliary tract disorder" "postcranial axial skeletal system" "chronic pancreatitis" + "heteroatomic molecular entity" "ectodermal placode" "Xenopus laevis" "autoimmune disorder of exocrine system" @@ -1494,9 +1466,10 @@ "action potential" "dorsal region element" "intracellular non-membrane-bounded organelle" + "application" "monoatomic monocation" - "oligopotent" "renal cell carcinoma" + "oligopotent" "duct epithelial cell" "bacterial gastritis" "ciliary body" @@ -1522,6 +1495,7 @@ "diarrheal disease" "height" "response to hexose" + "molecular entity" "exocrine pancreatic carcinoma" "autosomal recessive disease" "respiratory system mucosa" @@ -1535,6 +1509,7 @@ "Abnormal cardiovascular system physiology" "gastritis" "inborn carbohydrate metabolic disorder" + "molecule" "substance-related disorder" "epithelium of gonad" "myelitis" @@ -1574,8 +1549,8 @@ "overnutrition" "hereditary gastric cancer" "esophageal cancer" - "Sabellida" "small intestine adenocarcinoma" + "Sabellida" "nodal myocyte" "hypertensive encephalopathy" "photoreceptor array" @@ -1623,6 +1598,7 @@ "alpha-amino-acid anion" "bone tissue" "hereditary otorhinolaryngologic disease" + "carbon atom" "ocular surface region" "gastric gland" "Caenorhabditis" @@ -1660,10 +1636,11 @@ "cornea cancer" "hepatobiliary neoplasm" "rectal carcinoma" + "prokaryotic metabolite" "Struthio" "presumptive neural retina" - "external encapsulating structure" "autoimmune disease" + "external encapsulating structure" "alkali metal cation" "acinar" "hematologic disorder" @@ -1675,12 +1652,13 @@ "developmental defect during embryogenesis" "transmembrane transport" "duodenal adenocarcinoma" - "zygote stage" "intrahepatic bile duct" + "zygote stage" "type B pancreatic cell" "axon ensheathment" "phlebitis" "ammonia" + "role"@en "intrahepatic bile duct epithelium" "eye carcinoma" "Abnormal brain morphology" @@ -1703,12 +1681,12 @@ "sense organ" "saccular" "Palaeognathae" - "gray matter" "viral eye infection" + "gray matter" "Otophysi" - "cardiovascular neoplasm" "germ cell" "jaw cancer" + "cardiovascular neoplasm" "layer of muscle tissue" "intestinal neuroendocrine neoplasm" "periderm" @@ -1721,6 +1699,7 @@ "immaterial entity"@en "cranial placode" "sleep disorder" + "role" "protein transport" "head and neck cancer" "tendon" @@ -1737,8 +1716,8 @@ "heart tube" "midgut" "brain" - "bladder organ" "sensory neuron" + "bladder organ" "respiratory tract infectious disorder" "collagen trimer" "neuron associated cell" @@ -1751,15 +1730,15 @@ "myocyte of atrioventricular node" "bile acid secretion" "reproductive organ" - "bone element" "capillary" + "bone element" "alcohol-related disorders" "intracellular membrane-bounded organelle" "type I hypersensitivity" "polychromatophilic" "malignant tumor of neck" - "anxiety" "extrinsic cardiomyopathy" + "anxiety" "detoxification" "carbohydrate homeostasis" "aromatic compound" @@ -1801,6 +1780,7 @@ "renal pelvis/ureter" "bone remodeling" "immune system process" + "metabolite" "midbrain neural tube" "parenchyma" "thyroid gland squamous cell carcinoma" @@ -1831,9 +1811,9 @@ "carbon oxoacid" "Glires" "carbamic acid" - "ommatidium" "autoimmune retinopathy" "superelliptic" + "ommatidium" "entire embryonic mesenchyme" "blindness (disorder)" "arterial disorder" @@ -1846,9 +1826,9 @@ "pharyngeal arch system" "hereditary endocrine growth disease" "cervical adenocarcinoma" + "microcirculatory vessel" "external ectoderm" "skeletal muscle disorder" - "microcirculatory vessel" "Herpesvirales" "cardiac muscle tissue of atrium" "ecto-epithelial cell" @@ -1859,8 +1839,8 @@ "Annelida" "Ecdysozoa" "Headache" - "motor neuron disorder" "monosaccharide metabolic process" + "motor neuron disorder" "anxiety disorder" "morphogenesis of embryonic epithelium" "sensory receptor cell" @@ -1874,6 +1854,7 @@ "Eremoneura" "detection of chemical stimulus involved in sensory perception of smell" "irregular connective tissue" + "p-block molecular entity" "pancreas dorsal primordium" "Herviviricetes" "lip and oral cavity squamous cell carcinoma" @@ -1885,8 +1866,8 @@ "monovalent inorganic cation" "monoatomic ion transmembrane transport" "spinal cord cancer" - "colorectal neuroendocrine tumor G1" "gastrin secreting cell" + "colorectal neuroendocrine tumor G1" "eyelid carcinoma" "corneal disorder" "alkali metal molecular entity" @@ -1894,6 +1875,7 @@ "squamous cell carcinoma of the small intestine" "cardiac muscle tissue" "ureter adenocarcinoma" + "anion" "autoimmune disorder of peripheral nervous system" "bile acid metabolic process" "Mendelian inheritance" @@ -1902,10 +1884,10 @@ "alcoholic hepatitis" "Clinical modifier" "kidney rudiment" - "contractile cell" - "exocrine pancreas" "extrahepatic bile duct" "portal vein" + "exocrine pancreas" + "contractile cell" "inherited thyroid metabolism disease" "cellular response to organonitrogen compound" "chronic salpingo-oophoritis" @@ -1924,6 +1906,7 @@ "intracellular glucose homeostasis" "foregut-midgut junction" "reflex" + "Saccharomyces cerevisiae metabolite" "muscle tissue disorder" "polycystic ovary syndrome" "lipid biosynthetic process" @@ -1958,14 +1941,15 @@ "acinar cell" "body part movement" "mesonephros" + "carbon group molecular entity" "response to radiation" "metal atom" "hydrides" "ampulla of vater cancer" "pigment cell" "mononuclear parent hydride" - "cervix epithelium" "trachea neoplasm" + "cervix epithelium" "vaginal squamous tumor" "eye epithelium" "trunk blood vessel" @@ -1985,6 +1969,7 @@ "glucagon secretion" "kidney" "inflammatory response to antigenic stimulus" + "material entity"@en "chewing" "mucus secretion" "dicarboxylic acid" @@ -2005,9 +1990,11 @@ "bacterial sexually transmitted disease" "cell projection assembly" "infective vaginitis" + "biochemical role" "psychiatric disorder" "squamous cell carcinoma of colon" "exocrine gland" + "multicellular organismal process" "mesothelial cell" "iron molecular entity" "secretory granule" @@ -2025,9 +2012,9 @@ "cell of skeletal muscle" "Sleep abnormality" "thyroid tumor" - "camera-type eye" "embryo development" "gallbladder adenocarcinoma" + "camera-type eye" "gastric neuroendocrine neoplasm" "articulation" "Dinosauria" @@ -2038,19 +2025,20 @@ "multicellular organism" "obstetric disorder" "presumptive blood" - "bilirubin IXalpha" "atrioventricular node disorder" + "bilirubin IXalpha" "anus neoplasm" "nose" "immune system disorder" "colonic neoplasm" "striated" - "pelvic complex" "alimentary part of gastrointestinal system" - "serositis" "cervix disorder" + "independent continuant"@en "head and neck neoplasm" + "serositis" "Abnormal glucose homeostasis" + "pelvic complex" "peptide hormone secretion" "gastric neoplasm" "pancreatic endocrine carcinoma" @@ -2058,10 +2046,10 @@ "monoatomic cation homeostasis" "Abnormality of metabolism/homeostasis" "carbohydrate transport" - "fully formed stage" "disorder of development or morphogenesis" "mesoderm morphogenesis" "chromosome condensation" + "fully formed stage" "Autosomal recessive inheritance" "lentivirus infection" "musculature" @@ -2071,13 +2059,14 @@ "digestive tract" "Lepidosauria" "autoimmune myocarditis" + "organic anion" "contractile fiber" "neural tube marginal layer" "Struthionidae" "Chromadorea" "mesonephric duct" - "bone development" "small molecule metabolic process" + "bone development" "response to light stimulus" "inherited lipid metabolism disorder" "ganglion" @@ -2116,14 +2105,15 @@ "process quality" "gallbladder carcinoma" "ciliated epithelium" - "grade III glioma" "gastric body carcinoma" + "grade III glioma" "oral cavity squamous cell carcinoma" "Neurofibrillary tangles" "amino acid zwitterion" "gastrointestinal system mucosa" "hypertensive nephropathy" "organelle lumen" + "fundamental particle" "Catarrhini" "multipotent" "respiratory system disorder" @@ -2133,9 +2123,10 @@ "secondary carcinoma" "regulation of heart contraction" "mineral metabolism disease" + "disease" "Rhabditida" "migratory neural crest cell" - "disease" + "fermion" "brain stem glioma" "cancer-associated retinopathy" "animal organ development" @@ -2167,8 +2158,8 @@ "ovarian neuroendocrine neoplasm" "central nervous system vasculitis" "hypertensive retinopathy" - "duodenum cancer" "collection of collagen fibrils" + "duodenum cancer" "Abnormal cerebral morphology" "type 2 diabetes mellitus" "future spinal cord" @@ -2201,8 +2192,8 @@ "anal carcinoma" "genitourinary system" "foregut" - "perceptual disorders" "retinal rod cell" + "perceptual disorders" "cell projection organization" "peptide transport" "embryonic head" @@ -2218,8 +2209,8 @@ "cystic duct" "germ layer" "regulation of membrane potential" - "thyroid gland disorder" "cellularity" + "thyroid gland disorder" "immunoglobulin mediated immune response" "kidney disorder" "wall of intestine" @@ -2256,6 +2247,7 @@ "digestive system carcinoma" "Abnormality of the endocrine system" "Visual impairment" + "neurotoxin" "heart cancer" "Orthoretrovirinae" "Rattus" @@ -2340,8 +2332,8 @@ "pre-chordal neural plate" "glucan biosynthetic process" "exposure to personal behavior" - "alcohol-induced disorders" "surface structure" + "alcohol-induced disorders" "reproductive system neoplasm" "collagen network" "intestinal neuroendocrine tumor G1" @@ -2363,6 +2355,7 @@ "mucosa of stomach" "Ortervirales" "Metazoa" + "s-block element atom" "nasal cavity carcinoma" "tumor of uterus" "osteogenesis imperfecta" @@ -2395,6 +2388,8 @@ "epithelial bud" "transport" "eye neoplasm" + "molecular_function" + "gene product or complex activity"@en "somatic stem cell division" "lens vesicle" "hereditary nephritis" @@ -2410,6 +2405,7 @@ "body proper" "conceptus" "infectious disorder of the nervous system" + "human metabolite" "primary amide" "immune system cancer" "nasal cavity neoplasm" @@ -2443,6 +2439,7 @@ "Cough" "chordate embryonic development" "adenocarcinoma of gallbladder and extrahepatic biliary tract" + "process"@en "small intestine carcinoma" "acid secretion" "catabolic process" @@ -2452,12 +2449,14 @@ "reproductive process" "malignant cardiac germ cell tumor" "muscle structure" + "main group molecular entity" "upper respiratory conduit" "Hypertension" "cardiogenetic disease" "skeletal muscle tissue" "cardiac muscle tissue of interatrial septum" "bile duct" + "physical object quality" "skin disease caused by bacterial infection" "neuroblast (sensu Vertebrata)" "allergic disease" @@ -2473,6 +2472,7 @@ "spinal cord glioma" "globin" "hypodermis" + "poison" "female reproductive organ" "neural tube formation" "connective tissue disorder" @@ -2496,8 +2496,8 @@ "response to glucose" "endothelial cell of vascular tree" "cell condensation" - "atopic conjunctivitis" "eye photoreceptor cell" + "atopic conjunctivitis" "anterior uvea" "midbrain hindbrain boundary neural plate" "syndromic dyslipidemia" @@ -2508,6 +2508,8 @@ "iron coordination entity" "Danio rerio" "central nervous system neuron" + "atom" + "uncharged atom" "organ" "inherited primary ovarian failure" "hematopoietic stem cell" @@ -2571,8 +2573,8 @@ "branched" "embryonic tissue" "respiratory tract epithelium" - "pancreatic duct" "cardiocyte" + "pancreatic duct" "central nervous system cancer" "appendage" "biliary bud" @@ -2585,15 +2587,16 @@ "acute inflammatory response to antigenic stimulus" "inorganic ion" "stomodeum" + "carbon group element atom" "autoimmune disorder of the nervous system" "dicarboxylic acid anion" "ectoderm development" "post-embryonic development" + "mesonephric neoplasm" "renal tubular secretion" "malignant gastric germ cell tumor" - "mesonephric neoplasm" - "carbohydrate transmembrane transport" "Alphaherpesvirinae" + "carbohydrate transmembrane transport" "neurectodermal cell" "serous acinus" "germinal neuroepithelium" @@ -2627,6 +2630,7 @@ "iron protein" "mesenchyme derived from neural crest" "Abnormality of the integument" + "nutrient" "fibroblast" "Diptera" "digestion" @@ -2644,6 +2648,7 @@ "conjunctivitis" "thyroid hormone metabolic process" "Increased inflammatory response" + "nonmetal atom" "EC 3.* (hydrolase) inhibitor" "aponeurosis" "oral cavity neoplasm" @@ -2694,6 +2699,7 @@ "body of stomach" "organism substance" "cell periphery" + "kinase activity" "extrahepatic bile duct neoplasm" "metallotetrapyrrole" "Reduced visual acuity" @@ -2709,6 +2715,7 @@ "large intestine" "lens of camera-type eye" "extracellular exosome biogenesis" + "quality of a substance" "Eukaryota" "hereditary neuromuscular disease" "Abnormal heart morphology" @@ -2736,12 +2743,13 @@ "regional part of brain" "neuronal receptor cell" "cholanoid" + "nuclear particle" "lower respiratory tract" "lung cancer" "uterus" "abdominal viscera" - "idiopathic vs non-idiopathic" "digestive tract diverticulum" + "idiopathic vs non-idiopathic" "cellular developmental process" "secretion by cell" "embryonic structure" @@ -2757,11 +2765,12 @@ "intestinal disorder" "non-neoplastic bile duct disorder" "chordate pharynx" + "organic molecular entity" "Acoelomorpha" "organic cyclic compound" "gallbladder primordium" - "Mullerian duct" "retina" + "Mullerian duct" "porphyrins" "stomach glandular region mucosa" "nucleus" @@ -2791,8 +2800,8 @@ "autoimmune disorder of gastrointestinal tract" "Pancreatitis" "dicarboxylic acids and O-substituted derivatives" - "bile acid biosynthetic process" "hereditary gallbladder disorder" + "bile acid biosynthetic process" "viral respiratory tract infection" "uterine ligament adenocarcinoma" "Caenorhabditis elegans" @@ -2809,9 +2818,9 @@ "intralobular duct" "myeloid cell homeostasis" "Abnormality of the skin" + "pancreatic acinus" "primitive urogenital sinus" "heterochromatin" - "pancreatic acinus" "blood island" "Opisthokonta" "infectious anterior uveitis" @@ -2838,13 +2847,13 @@ "endoderm of foregut-midgut junction" "epithelial sac" "kidney mesenchyme" - "blastula stage" "eye degenerative disorder" - "transparent" + "blastula stage" "Abnormality of the pancreatic islet cells" "extracellular matrix" "regulation of respiratory gaseous exchange" "duodenitis" + "transparent" "ectodermal cell" "squamous cell bile duct carcinoma" "abdomen" @@ -2888,8 +2897,8 @@ "hollow" "hepatitis" "multi-organism reproductive process" - "intra-ocular muscle" "small intestine neoplasm" + "intra-ocular muscle" "skin cancer" "Growth abnormality" "organic hydroxy compound biosynthetic process" @@ -2912,8 +2921,8 @@ "bone inflammation disease" "allergic rhinitis" "unilaminar epithelium" - "lung carcinoid tumor" "extracellular exosome assembly" + "lung carcinoid tumor" "neural tissue" "Bloody diarrhea"@en "hindbrain" @@ -2923,6 +2932,7 @@ "malignant glioma" "chemosensory system" "carbamate" + "hydrogen molecular entity" "nitrogen hydride" "mood disorder" "Pararnavirae" @@ -2951,6 +2961,7 @@ "inborn disorder of energy metabolism" "gallbladder cancer" "cardiogenic plate" + "cellular_component" "coronary artery disorder" "non-striated muscle cell" "endophthalmitis" @@ -2994,6 +3005,7 @@ "entire extraembryonic component" "alpha-amino acid" "pigment epithelium of eye" + "transferase activity" "pyloric canal" "Primate lentivirus group" "digestive system infectious disorder" @@ -3006,6 +3018,7 @@ "Bilateria" "response to insulin" "Abnormal respiratory system morphology" + "ion" "regulation of system process" "duodenal neuroendocrine neoplasm" "cognitive process" @@ -3017,6 +3030,7 @@ "anatomical structure homeostasis" "tissue remodeling" "ovarian squamous cell carcinoma" + "behavior process" "inherited" "cardiovascular system" "myocardial endocrine cell" @@ -3029,15 +3043,16 @@ "nervous system cancer" "Sauropsida" "artery" + "hydrogen atom" "squamous cell carcinoma of gallbladder and extrahepatic biliary tract" "pelvic region of trunk" - "dense connective tissue" "heart layer" "Insecta" "hematopoietic oligopotent progenitor cell" "dorsal pancreas" "internal female genitalia" "urethra adenocarcinoma" + "dense connective tissue" "presumptive hindbrain" "autoimmune pancreatitis" "macromolecule catabolic process" @@ -3052,8 +3067,8 @@ "idiopathic inflammatory myopathy" "gas molecular entity" "neoplastic, malignant" - "obstructive lung disease" "enkephalin secreting cell" + "obstructive lung disease" "smooth muscle tissue" "hereditary skin disorder" "endocrine gland" @@ -3067,69 +3082,54 @@ "glucan metabolic process" "organ subunit" "erythroid progenitor cell" - "general symptom" - "congestion" - "sore eyes" - "memory loss" - "hypoesthesia" - "feces and droppings symptom" - "bloodshot eye" - "alteration of consciousness" - "disturbances of sensation of smell and taste" - "wheezing" - "arrhythmia" - "extreme fatigue" - "fever" - "cyanosis" - "obsolete myalgia"@en - "ear symptom" - "head and neck symptom" - "diaphoresis" - "rash" - "mouth symptom" - "neurological and physiological symptom" - "shakes" - "fatigue" - "nausea" - "ageusia" - "loss of balance" - "nutrition, metabolism, and development symptom" - "cough" - "symptom" - "abdominal pain" - "sweaty" - "seizure" - "diarrhea" - "throat pain" - "slurred speech" - "cardiovascular system symptom" - "balance symptom"@en - "nervous system symptom" - "sensation perception" - "inability to think clearly" - "concentration difficulty" - "decreased appetite" - "eye symptom" - "loss of appetite" - "nose symptom" - "confusion" - "abnormal chest sound" - "alteration of appetite" - "pain" - "inability to concentrate" - "vomiting" - "respiratory abnormality" - "respiratory system and chest symptom" - "dyspnea" - "head symptom" - "skin and integumentary tissue symptom" - "headache" - "memory impairment" - "rhinorrhea" - "digestive system symptom" - "deafness" "time" "age" + "molecular entity"@en + "ethanol" + "central nervous system depressant" + "tobacco smoking behavior"@en + "antagonist" + "food" + "food consumption" + "teratogenic agent" + "drug" + "complex of molecular entities" + "agonist" + "feeding behavior" + "protein kinase C agonist" + "ethanols" + "regulation of drinking behavior" + "antiinfective agent" + "antiseptic drug" + "gene product" + "smoking behavior"@en + "consumption behavior"@en + "central nervous system drug" + "regulation of behavior"@en + "primary alcohol" + "atom"@en + "pharmacological role" + "ethoxide" + "tobacco consumption"@en + "antimicrobial agent" + "pharmaceutical" + "polar solvent" + "organic hydroxy compound" + "alkyl alcohol" + "protein kinase agonist" + "regulation of eating behavior" + "NMDA receptor antagonist" + "liquid consumption" + "regulation of alcohol consumption"@en + "regulation of consumption behavior"@en + "aliphatic alcohol" + "excitatory amino acid antagonist" + "alcohol consumption" + "disinfectant" + "alcohol" + "solvent" + "volatile organic compound" + "regulation of feeding behavior"@en "Education Level" "Fatigue data element" "Cancer data element" @@ -3401,8 +3401,7 @@ "Research or Clinical Assessment Tool" "Occupation or Discipline" "Sign or Symptom" - "single-organism process" - "single organism process" + "fluctuation of heart rate" "USCC" "GINET" "transient cerebral ischemia" @@ -3463,13 +3462,13 @@ "liver cancer" "Viral myocarditis" "Viral Myocarditis" + "neuroendocrine tumour of the rectum" + "neuroendocrine tumor of the rectum" "neuroendocrine tumor of pancreas" "neuroendocrine tumour of pancreas" "pancreatic endocrine tumor" "pancreatic endocrine tumour" "PANET" - "neuroendocrine tumour of the rectum" - "neuroendocrine tumor of the rectum" "nutrition disease" "calcium metabolism disorder" "calcium metabolism disease" @@ -3488,6 +3487,8 @@ "Proctosigmoiditis" "Rectosigmoiditis" "rectosigmoiditis" + "single-organism process" + "single organism process" "disorder of heart muscle" "CSCC" "haemoglobin disorder" @@ -4203,9 +4204,6 @@ "UAD" "lymphoplasmocytic sclerosing pancreatitis" "ovarian germ cell cancer" - "fluctuation of heart rate" - "monadic quality of continuant" - "monadic quality of an object" "malignant gastrointestinal neuroendocrine tumour" "malignant gastrointestinal neuroendocrine tumor" "malignant endocrine tumor" @@ -4352,6 +4350,8 @@ "generalized multiple sclerosis" "clinical infection" "alcoholic liver damage" + "monadic quality of continuant" + "monadic quality of an object" "malignant hematopoietic neoplasm (morphologic abnormality)" "malignant haematopoietic neoplasm (morphologic abnormality)" "hematopoietic cancer" @@ -4407,7 +4407,6 @@ "localised malignant gallbladder neoplasm" "localized malignant gallbladder neoplasm" "coronary arteriosclerosis" - "ingest" "digestive system neuroendocrine tumour" "gastrointestinal NET" "digestive system well differentiated neuroendocrine tumour" @@ -4722,23 +4721,53 @@ "tumour of the nervous system" "tumor of the nervous system" "neural neoplasm" - "enzyme activity" - "relational physical quality" - "physiological process" - "biological process" - "feeding behaviour" - "drinking behaviour" - "behaviour" - "behavior" - "eating behaviour" - "quality of a single physical entity" - "quality of continuant" - "multiply inhering quality of a physical entity" - "quality of a continuant" - "monadic quality of a continuant" - "quality of an object" - "molecular function" - "phosphokinase activity" + "ingest" + "blocked nose" + "stuffy nose" + "nasal obstruction" + "stuffed up nose" + "nasal blockage" + "numbness" + "fecal" + "redness of eye" + "red eye" + "taste alteration" + "abnormal heart rhythm" + "heart rhythm symptom" + "abnormal heart beat" + "irregular heartbeat" + "dysrhythmia" + "pyrexia" + "profuse perspiration" + "skin rash" + "rubor" + "skin eruption" + "skin redness" + "erythema" + "trembling" + "loss of taste" + "perspire" + "incontinence of feces" + "loose bowel" + "fecal incontinence" + "bacterial gastroenteritis" + "the runs" + "loose bowels" + "diarrhoea" + "sore throat" + "decreased sensorium" + "clouded sensorium" + "poor appetite" + "lack of appetite" + "inappetence" + "emesis" + "breathing difficulty" + "labored respiration" + "difficulty breathing" + "shortness of breath" + "breathlessness" + "cephalalgia" + "runny nose" "neuroendocrine tumor of esophagus" "esophagus NET" "esophageal neuroendocrine tumor" @@ -4793,8 +4822,8 @@ "colorectum inflammation" "proctocolitis" "ischaemic attack, transient" - "ischemic attack, transient" "transient ischaemic attack (disease)" + "ischemic attack, transient" "transient ischemic attacks" "transient ischemic attack (disease)" "transient cerebral ischaemia" @@ -4950,9 +4979,9 @@ "vascular tissue tumor" "tumour of vascular tissue" "tumor of vascular tissue" - "vascular system tumor" "vascular system neoplasm" "tumors, vascular" + "vascular system tumor" "vascular neoplasm" "vascular tissue neoplasm" "HSVE" @@ -4977,6 +5006,7 @@ "anemia hemolytic" "anaemia hemolytic" "hemolytic anemia" + "enzyme activity" "adenocarcinoma of the renal pelvis" "kidney renal pelvis adenocarcinoma" "kidney pelvis adenocarcinoma" @@ -5153,6 +5183,8 @@ "carcinoma of liver cells" "carcinoma of liver" "viral myocarditis" + "rectal neuroendocrine tumor" + "rectal neuroendocrine tumour" "well-differentiated pancreatic neuroendocrine neoplasm" "islet cell tumours - pancreas" "islet cell tumors of the pancreas" @@ -5168,8 +5200,6 @@ "islet cell tumors - pancreas" "pancreatic neuroendocrine tumor" "islet cell tumours of the pancreas" - "rectal neuroendocrine tumor" - "rectal neuroendocrine tumour" "nutritional disorder" "disorder of calcium metabolism" "malignant neoplasm of muscle structure" @@ -5335,6 +5365,8 @@ "disorder" "diseases and disorders" "diseases" + "physiological process" + "biological process" "myocardium disease or disorder" "myocardium disease" "myocardial disease" @@ -5892,6 +5924,7 @@ "malignant tumour of the small intestine" "malignant small intestine neoplasm" "malignant tumour of small bowel" + "relational physical quality" "familial fallopian tube carcinoma" "hereditary fallopian tube carcinoma" "hereditary fallopian tube cancer" @@ -6173,8 +6206,8 @@ "tumor of CNS" "central nervous system neoplasm" "brain/spinal cord tumor" - "tumor of the central nervous system" "neoplasm of the central nervous system" + "tumor of the central nervous system" "CNS tumor" "tumour of the CNS" "CNS neoplasm" @@ -6298,13 +6331,13 @@ "viral conjunctivitis" "Viruses conjunctivitis (disease)" "Viruses caused conjunctivitis (disease)" - "bronchial disorder" "bronchus disease" "disorder of bronchus" "bronchus disease or disorder" "disease of bronchus" "disease or disorder of bronchus" "bronchospasm" + "bronchial disorder" "ovary carcinoma" "ovarian carcinoma" "carcinoma of ovary" @@ -6962,10 +6995,10 @@ "smooth muscle neoplasm" "tumor of the smooth muscle" "tumour of smooth muscle" + "muscle tissue inflammation" "inflammatory disorder of muscle" "inflammation of muscle tissue" "inflammatory disorder of muscle (disorder)" - "muscle tissue inflammation" "intestine inflammation" "cholera morbus" "inflammation of intestine" @@ -7535,8 +7568,8 @@ "malignant neoplasm of cornea" "cornea cancer" "malignant tumor of cornea" - "malignant tumor of the cornea" "malignant tumour of cornea" + "malignant tumor of the cornea" "malignant corneal tumour" "cancer of cornea" "malignant neoplasm of the cornea" @@ -7640,19 +7673,19 @@ "hypnic headache (disease)" "hypnic headache" "viral eye infection" + "cancer of jaw skeleton" + "jaw skeleton cancer" + "malignant jaw skeleton neoplasm" + "malignant neoplasm of jaw skeleton" "cardiovascular system tumor" "cardiovascular system neoplasm" - "cardiovascular system tumour" "cardiovascular tumour" + "cardiovascular system tumour" "tumor of cardiovascular system" "cardiovascular tumor" "neoplasm of cardiovascular system" "tumour of cardiovascular system" "cardiovascular neoplasm" - "cancer of jaw skeleton" - "jaw skeleton cancer" - "malignant jaw skeleton neoplasm" - "malignant neoplasm of jaw skeleton" "neuroendocrine tumor of intestine" "neuroendocrine neoplasm of intestine" "intestine neuroendocrine tumour" @@ -7745,9 +7778,9 @@ "malignant neck tumor" "malignant neck tumour" "malignant tumor of the neck" + "secondary cardiomyopathy" "anxiety" "anxiety-related personality traits" - "secondary cardiomyopathy" "PID" "pelvic inflammatory disease" "airway allergy" @@ -8356,9 +8389,6 @@ "colonic tumor" "tumour of colon" "colonic neoplasm" - "inflammation of serous membrane" - "serous membrane inflammation" - "serositis" "cervical disorder" "uterine cervix disease or disorder" "uterine cervix disease" @@ -8382,6 +8412,9 @@ "neoplasm of craniocervical region" "tumor of craniocervical region" "craniocervical region tumor" + "inflammation of serous membrane" + "serous membrane inflammation" + "serositis" "tumour of the stomach" "stomach neoplasm (disease)" "stomach tumor" @@ -8518,8 +8551,6 @@ "carcinoma of gall bladder" "Gall bladder carcinoma (adeno)" "cancer of the gallbladder" - "anaplastic glioma" - "WHO grade III glioma" "carcinoma of the gastric body" "cancer of gastric body" "gastric body (stomach) cancer" @@ -8532,6 +8563,8 @@ "carcinoma of body of stomach" "gastric body carcinoma" "carcinoma of gastric body" + "anaplastic glioma" + "WHO grade III glioma" "oral cavity scc" "squamous cell carcinoma of the mouth" "mouth squamous cell carcinoma" @@ -8565,8 +8598,8 @@ "brainstem neuroglial tumour" "glioma of brain stem" "brain stem neuroglial tumour" - "malignant glioma of brainstem" "diffuse brainstem glioma" + "malignant glioma of brainstem" "glioma of the brainstem" "brainstem glioma" "brain stem neuroglial neoplasm" @@ -8771,7 +8804,6 @@ "disease of thyroid gland" "thyroid gland disease" "disorder of thyroid gland" - "disorder of kidney" "disease or disorder of kidney" "disease of kidney" "kidney disease or disorder" @@ -8779,6 +8811,7 @@ "kidney disease" "renal disorder" "kidney disorder" + "disorder of kidney" "hereditary neurodegenerative disease" "hereditary neurodegenerative disorder" "genetic neurodegenerative disease" @@ -9011,8 +9044,8 @@ "tumour of respiratory tract" "tumor of respiratory tract" "neoplasm of respiratory tract" - "tumour of the respiratory tract" "tract neoplasm, respiratory" + "tumour of the respiratory tract" "tract neoplasms, respiratory" "neoplasms, respiratory tract" "neoplasm of the respiratory tract" @@ -9061,6 +9094,7 @@ "carcinoma of nasal cavity" "carcinoma of the nasal cavity" "nasal cavity carcinoma" + "uterine tumor" "uterus tumour" "uterus tumor" "uterine neoplasm" @@ -9073,7 +9107,6 @@ "uterus neoplasm" "uterine neoplasms" "neoplasm of uterus" - "uterine tumor" "brittle bone disease" "Vrolik's disease" "Lobstein disease" @@ -9126,6 +9159,7 @@ "eye tumour" "ocular neoplasm" "tumour of the eye" + "molecular function" "hereditary nephritis" "central nervous system infectious disease" "infectious disease of central nervous system" @@ -9229,6 +9263,12 @@ "malignant heart germ cell tumor" "malignant germ cell tumor of the heart" "hereditary heart disease" + "quality of a single physical entity" + "quality of continuant" + "multiply inhering quality of a physical entity" + "quality of a continuant" + "monadic quality of a continuant" + "quality of an object" "Bacteria skin disease caused by infection" "Bacteria caused skin disease caused by infection" "type I hypersensitivity disease" @@ -9295,15 +9335,15 @@ "complex dyslipidemia" "syndrome associated with inherited lipid metabolism disorder" "complex dyslipidaemia" - "inflammation of nasal cavity mucosa" "nasal cavity mucosa inflammation" + "inflammation of nasal cavity mucosa" "inherited premature ovarian failure" "hereditary primary ovarian failure" + "migraine disorder" "migraine" "migraine with or without aura" "migraine variant" "migraine headache" - "migraine disorder" "hematopoietic system tumor" "neoplasm of blood" "haematopoietic system tumour" @@ -9341,8 +9381,8 @@ "notochord neoplasm" "tumour of notochord" "neoplasm of notochord" - "malignant notochord neoplasm" "notochord tumour" + "malignant notochord neoplasm" "tumor of notochord" "notochordal tumor" "notochord cancer" @@ -9473,20 +9513,10 @@ "diseases, neurologic autoimmune" "autoimmune disease of nervous system" "autoimmune disease, neurologic" - "malignant germ cell neoplasm of the stomach" - "malignant germ cell neoplasm of stomach" - "malignant germ cell tumor of stomach" - "malignant gastric germ cell tumor" - "malignant germ cell tumor of the stomach" - "malignant gastric germ cell neoplasm" - "malignant germ cell tumour of the stomach" - "malignant germ cell tumour of stomach" - "germ cell tumour of the stomach" - "germ cell tumor of the stomach" "tumor of mesonephric duct" "neoplasm of mesonephric duct" - "mesonephric tumor" "mesonephric duct neoplasm" + "mesonephric tumor" "Wolffian duct tumour" "mesonephric duct tumour" "tumour of mesonephric duct" @@ -9496,6 +9526,16 @@ "Wolffian duct neoplasm" "mesonephric duct tumor" "mesonephroma" + "malignant germ cell neoplasm of the stomach" + "malignant germ cell neoplasm of stomach" + "malignant germ cell tumor of stomach" + "malignant gastric germ cell tumor" + "malignant germ cell tumor of the stomach" + "malignant gastric germ cell neoplasm" + "malignant germ cell tumour of the stomach" + "malignant germ cell tumour of stomach" + "germ cell tumour of the stomach" + "germ cell tumor of the stomach" "optic choroid cancer" "malignant neoplasm of choroid" "malignant tumour of the choroid" @@ -9589,9 +9629,9 @@ "malignant neoplasm of kidney" "kidney cancer" "malignant tumor of the kidney" - "malignant tumour of the kidney" "malignant renal tumour" "malignant tumour of kidney" + "malignant tumour of the kidney" "malignant renal tumor" "malignant renal neoplasm" "malignant kidney neoplasm" @@ -9706,6 +9746,7 @@ "sickle-cell thalassemia with crisis" "sickle-cell thalassemia without crisis" "thalassemia Hb-S disease without crisis" + "phosphokinase activity" "tumour of extrahepatic bile duct" "neoplasm of extrahepatic bile duct" "extrahepatic bile duct neoplasm" @@ -9723,8 +9764,8 @@ "Ca body of pancreas" "pancreas cancer" "malignant neoplasm of the pancreas" - "malignant neoplasm of head of pancreas" "Ca tail of pancreas" + "malignant neoplasm of head of pancreas" "malignant neoplasm of body of pancreas" "pancreatic cancer" "malignant neoplasm of tail of pancreas" @@ -10126,18 +10167,18 @@ "lung carcinoid tumor" "carcinoid tumor of lung" "pulmonary carcinoid tumor" - "malignant neuroglial neoplasm" "glial cell tumour" "glioma, malignant" "malignant glial tumor" "malignant glioma" + "malignant glial neoplasm" "high-grade glioma" "glial cell tumor" - "malignant glial neoplasm" "malignant neuroglial tumour" "malignant glial tumour" "high grade glioma" "malignant neuroglial tumor" + "malignant neuroglial neoplasm" "grade 1/2" "squamous cell carcinoma of stomach" "gastric squamous cell carcinoma" @@ -10358,6 +10399,8 @@ "ovarian squamous cell carcinoma" "ovarian squamous cell cancer" "ovary squamous cell carcinoma" + "behaviour" + "behavior" "mesenchymal cell tumor" "mesenchymal neoplasm" "benign miscellaneous mesenchymal tumor" @@ -10423,52 +10466,9 @@ "DM" "digestive tract diverticulum inflammation" "inflammation of digestive tract diverticulum" - "blocked nose" - "stuffy nose" - "nasal obstruction" - "stuffed up nose" - "nasal blockage" - "numbness" - "fecal" - "redness of eye" - "red eye" - "taste alteration" - "abnormal heart rhythm" - "heart rhythm symptom" - "abnormal heart beat" - "irregular heartbeat" - "dysrhythmia" - "pyrexia" - "profuse perspiration" - "skin rash" - "rubor" - "skin eruption" - "skin redness" - "erythema" - "trembling" - "loss of taste" - "perspire" - "incontinence of feces" - "loose bowel" - "fecal incontinence" - "bacterial gastroenteritis" - "the runs" - "loose bowels" - "diarrhoea" - "sore throat" - "decreased sensorium" - "clouded sensorium" - "poor appetite" - "lack of appetite" - "inappetence" - "emesis" - "breathing difficulty" - "labored respiration" - "difficulty breathing" - "shortness of breath" - "breathlessness" - "cephalalgia" - "runny nose" + "feeding behaviour" + "drinking behaviour" + "eating behaviour" "Educational Level" "Education Level Completed" "Level of Education Attained" diff --git a/src/ontology/reports/xrefs.tsv b/src/ontology/reports/xrefs.tsv index 32b42c5..592a8c3 100644 --- a/src/ontology/reports/xrefs.tsv +++ b/src/ontology/reports/xrefs.tsv @@ -1,16 +1,77 @@ ?cls ?xref - "Wikipedia:Enzyme" - "Wikipedia:Physical_property" - "Wikipedia:Biological_process" - "EC:2.7.-.-" - "Reactome:R-HSA-8868783" - "EC:2.-.-.-" - "Reactome:R-HSA-5668414" - "Reactome:R-HSA-1483186" - "Reactome:R-HSA-1483089" - "snap:Quality" - "Reactome:R-HSA-6788855" - "Reactome:R-HSA-6788867" + "UMLS_ICD9CM_2005_AUI:A0284119" + "UMLS_CUI:C0159028" + "ICD9CM_2005:780" + "UMLS_ICD9CM_2005_AUI:A2797424" + "UMLS_CUI:C0751295" + "ICD9CM_2005:780.93" + "UMLS_ICD9CM_2005_AUI:A0389211" + "UMLS_CUI:C0234428" + "ICD9CM_2005:780.0" + "UMLS_ICD9CM_2005_AUI:A0243765" + "UMLS_CUI:C0495689" + "ICD9CM_2005:781.1" + "UMLS_ICD9CM_2005_AUI:A0133941" + "UMLS_CUI:C0043144" + "ICD9CM_2005:786.07" + "UMLS_ICD9CM_2005_AUI:A0058972" + "ICD9CM_2005:780.6" + "UMLS_CUI:C0015967" + "UMLS_ICD9CM_2005_AUI:A0044296" + "UMLS_CUI:C0010520" + "ICD9CM_2005:782.5" + "UMLS_ICD9CM_2005_AUI:A0284173" + "UMLS_CUI:C0476247" + "ICD9CM_2005:784" + "UMLS_CUI:C0015230" + "UMLS_ICD9CM_2005_AUI:A0243780" + "ICD9CM_2005:782.1" + "UMLS_ICD9CM_2005_AUI:A0750850" + "UMLS_CUI:C0375548" + "ICD9CM_2005:787.02" + "UMLS_ICD9CM_2005_AUI:A0284163" + "UMLS_CUI:C0159041" + "ICD9CM_2005:783" + "UMLS_ICD9CM_2005_AUI:A0043303" + "UMLS_CUI:C0010200" + "ICD9CM_2005:786.2" + "ICD9CM_2005:789.0" + "UMLS_ICD9CM_2005_AUI:A0387333" + "ICD9CM_2005:789.00" + "UMLS_ICD9CM_2005_AUI:A0637138" + "UMLS_CUI:C0000737" + "UMLS_ICD9CM_2005_AUI:A0048148" + "UMLS_CUI:C0011991" + "ICD9CM_2005:787.91" + "UMLS_CUI:C0242429" + "ICD9CM_2005:784.1" + "UMLS_ICD9CM_2005_AUI:A0284175" + "UMLS_ICD9CM_2005_AUI:A0284192" + "UMLS_CUI:C0159049" + "ICD9CM_2005:785" + "UMLS_ICD9CM_2005_AUI:A0284131" + "UMLS_CUI:C0159033" + "ICD9CM_2005:781" + "UMLS_ICD9CM_2005_AUI:A0284219" + "UMLS_CUI:C0159056" + "ICD9CM_2005:786.7" + "UMLS_ICD9CM_2005_AUI:A0284202" + "UMLS_CUI:C0159053" + "ICD9CM_2005:786.0" + "UMLS_ICD9CM_2005_AUI:A0284200" + "UMLS_CUI:C0476271" + "ICD9CM_2005:786" + "UMLS_ICD9CM_2005_AUI:A0284161" + "ICD9CM_2005:782.9" + "UMLS_CUI:C0159037" + "UMLS_ICD9CM_2005_AUI:A0284146" + "ICD9CM_2005:782" + "UMLS_CUI:C0018681" + "ICD9CM_2005:784.0" + "UMLS_ICD9CM_2005_AUI:A0065994" + "UMLS_ICD9CM_2005_AUI:A0284224" + "UMLS_CUI:C0159058" + "ICD9CM_2005:787" "Orphanet:506136" "DOID:5784" "NCIT:C95616" @@ -122,8 +183,6 @@ "DOID:734" "GARD:19900" "Orphanet:139009" - "MESH:C538274" - "UMLS:C0878654" "NCIT:C4349" "ONCOTREE:COAD" "UMLS:C0338106" @@ -140,6 +199,8 @@ "NCIT:C26722" "MESH:D029481" "ICD9:491.8" + "MESH:C538274" + "UMLS:C0878654" "NCIT:C5803" "DOID:4434" "GARD:21765" @@ -185,6 +246,7 @@ "ICD10CM:D55-D59" "MESH:D000743" "DOID:583" + "Wikipedia:Enzyme" "UMLS:C1335748" "DOID:4918" "NCIT:C6143" @@ -295,14 +357,14 @@ "UMLS:C0276138" "SCTID:89141000" "NCIT:C128381" + "UMLS:CN197361" + "NCIT:C135213" "NCIT:C27720" "EFO:1000045" "Orphanet:97253" "ICDO:8150/1" "ONCOTREE:PANET" "GARD:13034" - "UMLS:CN197361" - "NCIT:C135213" "EFO:0001069" "MESH:D009748" "ICD9:783.9" @@ -431,6 +493,7 @@ "ICD9:799.9" "EFO:0000408" "NCIT:C2991" + "Wikipedia:Biological_process" "NCIT:C35544" "SCTID:57809008" "NCIT:C5497" @@ -442,8 +505,8 @@ "UMLS:C0008311" "ICD9:576.1" "NCIT:C26718" - "MESH:D002761" "ICD10CM:K83.0" + "MESH:D002761" "DOID:9446" "SCTID:82403002" "NCIT:C3325" @@ -603,8 +666,8 @@ "DOID:5844" "SCTID:22298006" "EFO:0000612" - "NCIT:C27996" "ICD10CM:I21" + "NCIT:C27996" "MESH:D009203" "MESH:D006453" "ICD10CM:D58.1" @@ -860,6 +923,7 @@ "UMLS:C0153425" "ICD9:152.9" "DOID:10154" + "Wikipedia:Physical_property" "UMLS:C1512418" "DOID:7266" "NCIT:C40455" @@ -914,6 +978,7 @@ "NCIT:C3200" "ONCOTREE:LUNG" "MESH:D008175" + "EC:2.7.-.-" "SCTID:231504006" "ICD9:379.19" "MESH:D015422" @@ -1646,9 +1711,9 @@ "NCIT:C27605" "SCTID:443265004" "NCIT:C92196" - "MESH:D019965" "DOID:1561" "EFO:1001457" + "MESH:D019965" "ICD9:294.9" "DOID:0080832" "ICD9:731.8" @@ -1882,9 +1947,9 @@ "ICD9:428.9" "ICD9:404.13" "ICD9:404.01" + "SCTID:42343007" "NCIT:C3080" "ICD9:428" - "SCTID:42343007" "EFO:0000373" "DOID:6000" "ICD9:428.0" @@ -2319,8 +2384,8 @@ "NCIT:C2889" "UMLS:C0004364" "OMIM:109100" - "ICD9:279.49" "EFO:0005140" + "ICD9:279.49" "ICD9:279.4" "DOID:417" "ICD9:720" @@ -2391,13 +2456,13 @@ "MESH:D015828" "UMLS:C0015407" "SCTID:312132001" - "NCIT:C4784" - "SCTID:721573003" - "UMLS:C0497243" "EFO:0007333" "SCTID:126634001" "DOID:1862" "MESH:D007573" + "NCIT:C4784" + "SCTID:721573003" + "UMLS:C0497243" "DOID:4119" "NCIT:C5695" "UMLS:C1334231" @@ -2446,11 +2511,11 @@ "NCIT:C4940" "UMLS:C0746787" "SCTID:363489000" - "OMIM:607834" - "MESH:D001007" "ICD9:425.8" "SCTID:195029002" "DOID:3978" + "OMIM:607834" + "MESH:D001007" "ICD9:614.8" "EFO:1001388" "ICD10CM:N70-N77" @@ -2825,9 +2890,9 @@ "MedDRA:10071569" "UMLS:C3203653" "Orphanet:284264" + "SCTID:446022000" "EFO:0002919" "UMLS:C2960452" - "SCTID:446022000" "DOID:688" "DOID:2994" "UMLS:C0205851" @@ -2938,9 +3003,6 @@ "EFO:0004288" "NCIT:C2953" "MESH:D003110" - "NCIT:C70428" - "MESH:D012700" - "SCTID:370469003" "SCTID:63339007" "UMLS:C0007867" "MESH:D002577" @@ -2952,6 +3014,9 @@ "NCIT:C3077" "UMLS:C0018671" "ICD9:239.89" + "NCIT:C70428" + "MESH:D012700" + "SCTID:370469003" "NCIT:C3387" "EFO:0003897" "MESH:D013274" @@ -3050,12 +3115,12 @@ "NCIT:C3844" "DOID:4948" "SCTID:372140005" - "UMLS:C4287997" - "NCIT:C127816" "SCTID:254557000" "NCIT:C8399" "DOID:6705" "UMLS:C0345804" + "UMLS:C4287997" + "NCIT:C127816" "GARD:17932" "UMLS:C0585362" "SCTID:307502000" @@ -3437,11 +3502,11 @@ "ICD9:333.99" "ICD9:333.94" "SCTID:32914008" - "NCIT:C3867" "EFO:1000251" "DOID:1963" "UMLS:C0238122" "SCTID:276870001" + "NCIT:C3867" "ICD9:153.8" "NCIT:C9242" "ICD9:153" @@ -3638,6 +3703,7 @@ "DOID:14535" "UMLS:C1334566" "NCIT:C5371" + "snap:Quality" "MESH:D017192" "DOID:1205" "UMLS:C0020517" @@ -3796,11 +3862,11 @@ "DOID:438" "MESH:D020274" "UMLS:C0751872" + "ICDO:9110/1" + "NCIT:C4295" "UMLS:C1334584" "NCIT:C5486" "DOID:4716" - "ICDO:9110/1" - "NCIT:C4295" "DOID:12759" "EFO:1000866" "MESH:D002830" @@ -3945,6 +4011,8 @@ "SCTID:40108008" "UMLS:C0039730" "MESH:D013789" + "Reactome:R-HSA-6788855" + "Reactome:R-HSA-6788867" "SCTID:126855001" "UMLS:C0345913" "NCIT:C4441" @@ -4458,6 +4526,11 @@ "MESH:D013272" "NCIT:C4364" "UMLS:C0339349" + "Reactome:R-HSA-8868783" + "EC:2.-.-.-" + "Reactome:R-HSA-5668414" + "Reactome:R-HSA-1483186" + "Reactome:R-HSA-1483089" "NCIT:C35503" "SCTID:715852004" "UMLS:C1412036" @@ -4560,79 +4633,6 @@ "NCIT:C26752" "DOID:7475" "MESH:D004238" - "UMLS_ICD9CM_2005_AUI:A0284119" - "UMLS_CUI:C0159028" - "ICD9CM_2005:780" - "UMLS_ICD9CM_2005_AUI:A2797424" - "UMLS_CUI:C0751295" - "ICD9CM_2005:780.93" - "UMLS_ICD9CM_2005_AUI:A0389211" - "UMLS_CUI:C0234428" - "ICD9CM_2005:780.0" - "UMLS_ICD9CM_2005_AUI:A0243765" - "UMLS_CUI:C0495689" - "ICD9CM_2005:781.1" - "UMLS_ICD9CM_2005_AUI:A0133941" - "UMLS_CUI:C0043144" - "ICD9CM_2005:786.07" - "UMLS_ICD9CM_2005_AUI:A0058972" - "ICD9CM_2005:780.6" - "UMLS_CUI:C0015967" - "UMLS_ICD9CM_2005_AUI:A0044296" - "UMLS_CUI:C0010520" - "ICD9CM_2005:782.5" - "UMLS_ICD9CM_2005_AUI:A0284173" - "UMLS_CUI:C0476247" - "ICD9CM_2005:784" - "UMLS_CUI:C0015230" - "UMLS_ICD9CM_2005_AUI:A0243780" - "ICD9CM_2005:782.1" - "UMLS_ICD9CM_2005_AUI:A0750850" - "UMLS_CUI:C0375548" - "ICD9CM_2005:787.02" - "UMLS_ICD9CM_2005_AUI:A0284163" - "UMLS_CUI:C0159041" - "ICD9CM_2005:783" - "UMLS_ICD9CM_2005_AUI:A0043303" - "UMLS_CUI:C0010200" - "ICD9CM_2005:786.2" - "ICD9CM_2005:789.0" - "UMLS_ICD9CM_2005_AUI:A0387333" - "ICD9CM_2005:789.00" - "UMLS_ICD9CM_2005_AUI:A0637138" - "UMLS_CUI:C0000737" - "UMLS_ICD9CM_2005_AUI:A0048148" - "UMLS_CUI:C0011991" - "ICD9CM_2005:787.91" - "UMLS_CUI:C0242429" - "ICD9CM_2005:784.1" - "UMLS_ICD9CM_2005_AUI:A0284175" - "UMLS_ICD9CM_2005_AUI:A0284192" - "UMLS_CUI:C0159049" - "ICD9CM_2005:785" - "UMLS_ICD9CM_2005_AUI:A0284131" - "UMLS_CUI:C0159033" - "ICD9CM_2005:781" - "UMLS_ICD9CM_2005_AUI:A0284219" - "UMLS_CUI:C0159056" - "ICD9CM_2005:786.7" - "UMLS_ICD9CM_2005_AUI:A0284202" - "UMLS_CUI:C0159053" - "ICD9CM_2005:786.0" - "UMLS_ICD9CM_2005_AUI:A0284200" - "UMLS_CUI:C0476271" - "ICD9CM_2005:786" - "UMLS_ICD9CM_2005_AUI:A0284161" - "ICD9CM_2005:782.9" - "UMLS_CUI:C0159037" - "UMLS_ICD9CM_2005_AUI:A0284146" - "ICD9CM_2005:782" - "UMLS_CUI:C0018681" - "ICD9CM_2005:784.0" - "UMLS_ICD9CM_2005_AUI:A0065994" - "UMLS_ICD9CM_2005_AUI:A0284224" - "UMLS_CUI:C0159058" - "ICD9CM_2005:787" "IMDRF:E1801" "IMDRF:F1201" "IMDRF:E0109" diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 5262871..221bf65 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -1,4 +1,4 @@ -Prefix(:=) +Prefix(:=) Prefix(owl:=) Prefix(rdf:=) Prefix(xml:=) @@ -6,9 +6,9 @@ Prefix(xsd:=) Prefix(rdfs:=) -Ontology( - -Annotation(owl:versionInfo "2024-04-30") +Ontology( + +Annotation(owl:versionInfo "2024-05-01") Declaration(Class()) Declaration(Class()) diff --git a/src/sparql/dc-properties-violation.sparql b/src/sparql/dc-properties-violation.sparql index 7cb4594..633b702 100644 --- a/src/sparql/dc-properties-violation.sparql +++ b/src/sparql/dc-properties-violation.sparql @@ -6,6 +6,6 @@ SELECT ?term ?predicate WHERE { ?term ?predicate ?value . FILTER(STRSTARTS(STR(?predicate), "http://purl.org/dc/elements/1.1/")) - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/gbco/GCBO_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/GCBO_"))) } diff --git a/src/sparql/gcbo_terms.sparql b/src/sparql/gcbo_terms.sparql index d996533..f2262bb 100644 --- a/src/sparql/gcbo_terms.sparql +++ b/src/sparql/gcbo_terms.sparql @@ -3,5 +3,5 @@ WHERE { { ?s1 ?p1 ?term . } UNION { ?term ?p2 ?o2 . } - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/gbco/GCBO_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/GCBO_"))) } diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru index 579d886..b02316e 100644 --- a/src/sparql/inject-subset-declaration.ru +++ b/src/sparql/inject-subset-declaration.ru @@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf ?y . FILTER(isIRI(?y)) - FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(https://github.com/bmir-radx/gbco)")) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(https://github.com/bmir-radx)")) } \ No newline at end of file diff --git a/src/sparql/inject-synonymtype-declaration.ru b/src/sparql/inject-synonymtype-declaration.ru index 1a475ec..8ccc272 100644 --- a/src/sparql/inject-synonymtype-declaration.ru +++ b/src/sparql/inject-synonymtype-declaration.ru @@ -7,5 +7,5 @@ INSERT { ?y rdfs:subPropertyOf ?y . FILTER(isIRI(?y)) - FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(https://github.com/bmir-radx/gbco)")) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(https://github.com/bmir-radx)")) } \ No newline at end of file diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql index 435381e..c5ab06d 100644 --- a/src/sparql/iri-range-violation.sparql +++ b/src/sparql/iri-range-violation.sparql @@ -13,7 +13,7 @@ WHERE { oboInOwl:inSubset dcterms:contributor } ?term ?property ?value . - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/gbco/GCBO_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/GCBO_"))) FILTER (!isIRI(?value)) } diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql index c09531c..3a2bcac 100644 --- a/src/sparql/label-with-iri-violation.sparql +++ b/src/sparql/label-with-iri-violation.sparql @@ -4,6 +4,6 @@ SELECT ?term ?value WHERE { ?term rdfs:label ?value . FILTER (REGEX(?value, "http[s]?[:]")) - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/gbco/GCBO_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/GCBO_"))) } diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql index 9ef7690..e5df8bf 100644 --- a/src/sparql/owldef-self-reference-violation.sparql +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -7,6 +7,6 @@ SELECT ?term WHERE { { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] } UNION { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] } - FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/gbco/GCBO_"))) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://github.com/bmir-radx/GCBO_"))) }