From 1c83293e996b74701baa6d376dae15c224fbe3e3 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Wed, 12 Feb 2025 15:49:59 +0000 Subject: [PATCH 1/4] Add heel bone density term If applied, this commit will fix #355. --- src/patterns/data/default/entity_attribute.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/src/patterns/data/default/entity_attribute.tsv b/src/patterns/data/default/entity_attribute.tsv index 35d51aab..ca517128 100644 --- a/src/patterns/data/default/entity_attribute.tsv +++ b/src/patterns/data/default/entity_attribute.tsv @@ -4387,3 +4387,4 @@ OBA:VT1000472 subcutaneous adipose mass UBERON:0002190 subcutaneous adipose tiss OBA:VT0010482 body fat mass UBERON:0001013 adipose tissue PATO:0000125 mass https://orcid.org/0000-0001-8314-2140 OBA:2050418 voice quality trait UBERON:0034681 vocal organ PATO:0001519 sound quality PMID:37294764 https://orcid.org/0000-0001-6757-4744 OBA:2045460 body extent UBERON:0000468 multicellular organism PATO:0001708 1-D extent https://orcid.org/0000-0001-6757-4744 +OBA:2045558 heel bone density UBERON:0001450 PATO:0001019 mass density https://orcid.org/0000-0001-8314-2140 From 3b4333bb5a97f08fd5538d2314ed8ed94045a168 Mon Sep 17 00:00:00 2001 From: rays22 Date: Wed, 12 Feb 2025 16:04:38 +0000 Subject: [PATCH 2/4] Update dosdp patterns file --- src/patterns/definitions.owl | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 2cbe31fa..c9b2adf2 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2025-01-28") + +Annotation(owl:versionInfo "2025-02-12") Declaration(Class()) Declaration(Class()) @@ -12261,6 +12261,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -109468,6 +109469,14 @@ AnnotationAssertion( "response to environmental contaminant characteristics") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))))) +# Class: (heel bone density) + +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The mass density of a calcaneus.") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "mass density of calcaneus") +AnnotationAssertion(rdfs:label "heel bone density") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (ascending aorta diameter) AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The diameter of a ascending aorta.") @@ -180833,6 +180842,7 @@ SubClassOf(ObjectIntersectionOf( Ob SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) From 53e6945971c371e7f9f68d4f6364e98c715037c9 Mon Sep 17 00:00:00 2001 From: Ray Stefancsik Date: Wed, 12 Feb 2025 17:57:16 +0000 Subject: [PATCH 3/4] Fix labels to better reflect meaning of terms Also, move OBA:VT0005007 from entity-attribute to entity-attribute-location table to better reflect the original VT text definition of the term. --- src/patterns/data/default/entity_attribute.tsv | 6 +++--- src/patterns/data/default/entity_attribute_location.tsv | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/patterns/data/default/entity_attribute.tsv b/src/patterns/data/default/entity_attribute.tsv index ca517128..f193c60a 100644 --- a/src/patterns/data/default/entity_attribute.tsv +++ b/src/patterns/data/default/entity_attribute.tsv @@ -117,7 +117,7 @@ OBA:1000105 tissue composition UBERON:0000479 tissue PATO:0000025 composition OBA:1000106 skeletal tissue composition UBERON:0004755 skeletal tissue PATO:0000025 composition OBA:1000107 testis position UBERON:0000473 testis PATO:0000140 position OBA:1000109 anatomical pigmentation UBERON:0000061 anatomical structure PATO:0002247 degree of pigmentation -OBA:1000110 bone density UBERON:0002481 bone tissue PATO:0001019 mass density +OBA:1000110 bone tissue density UBERON:0002481 bone tissue PATO:0001019 mass density https://orcid.org/0000-0001-8314-2140 OBA:1000111 adrenal gland size UBERON:0002369 adrenal gland PATO:0000117 size OBA:1000112 tooth size UBERON:0001091 calcareous tooth PATO:0000117 size OBA:1000113 incisor size UBERON:0001098 incisor tooth PATO:0000117 size @@ -571,7 +571,6 @@ OBA:VT0004954 thymus mass UBERON:0002370 thymus PATO:0000125 mass OBA:VT0004972 regulatory T cell quantity CL:0000815 regulatory T cell PATO:0001555 has number of OBA:VT0004976 B-1 B cell quantity CL:0000819 B-1 B cell PATO:0001555 has number of OBA:VT0005006 osteoblast physiology trait CL:0000062 osteoblast PATO:0001509 functionality -OBA:VT0005007 bone mineral mass UBERON:0001474 bone element PATO:0001019 mass density OBA:VT0005045 thymus cortex area UBERON:0002123 cortex of thymus PATO:0001323 area OBA:VT0005069 NK cell physiology trait CL:0000623 natural killer cell PATO:0001509 functionality OBA:VT0005078 cytotoxic T cell physiology trait CL:0000910 cytotoxic T cell PATO:0001509 functionality @@ -4387,4 +4386,5 @@ OBA:VT1000472 subcutaneous adipose mass UBERON:0002190 subcutaneous adipose tiss OBA:VT0010482 body fat mass UBERON:0001013 adipose tissue PATO:0000125 mass https://orcid.org/0000-0001-8314-2140 OBA:2050418 voice quality trait UBERON:0034681 vocal organ PATO:0001519 sound quality PMID:37294764 https://orcid.org/0000-0001-6757-4744 OBA:2045460 body extent UBERON:0000468 multicellular organism PATO:0001708 1-D extent https://orcid.org/0000-0001-6757-4744 -OBA:2045558 heel bone density UBERON:0001450 PATO:0001019 mass density https://orcid.org/0000-0001-8314-2140 +OBA:2045558 heel bone density UBERON:0001450 calcaneus PATO:0001019 mass density https://orcid.org/0000-0001-8314-2140 +OBA:2045559 bone density UBERON:0001474 bone element PATO:0001019 mass density https://orcid.org/0000-0001-8314-2140 diff --git a/src/patterns/data/default/entity_attribute_location.tsv b/src/patterns/data/default/entity_attribute_location.tsv index 345dc4b6..5fb44ce2 100644 --- a/src/patterns/data/default/entity_attribute_location.tsv +++ b/src/patterns/data/default/entity_attribute_location.tsv @@ -8052,3 +8052,4 @@ OBA:2052957 PR:Q96J42 PATO:0000070 amount UBERON:0000178 blood PMID:3841286 OBA:2052958 PR:O75356 PATO:0000070 amount UBERON:0000178 blood PMID:38412862 https://orcid.org/0000-0001-6757-4744 OBA:2052959 PR:P51531 PATO:0000070 amount UBERON:0000178 blood PMID:38412862 https://orcid.org/0000-0001-6757-4744 OBA:2052960 PR:P00441 PATO:0000070 amount UBERON:0000178 blood PMID:38412862 https://orcid.org/0000-0001-6757-4744 +OBA:VT0005007 bone mineral amount CHEBI:46662 mineral PATO:0000070 amount UBERON:0001474 bone element bone mineral mass https://orcid.org/0000-0001-8314-2140 From b8bc198e3ec54e890733e3498a621febc41b7f88 Mon Sep 17 00:00:00 2001 From: rays22 Date: Wed, 12 Feb 2025 18:09:37 +0000 Subject: [PATCH 4/4] Update dosdp patterns file --- src/patterns/definitions.owl | 26 +++++++++++++++++++------- 1 file changed, 19 insertions(+), 7 deletions(-) diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index c9b2adf2..1fce7e6e 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -12262,6 +12262,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -59399,11 +59400,12 @@ AnnotationAssertion(Annotation( "anatomical pigmentation") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (bone density) +# Class: (bone tissue density) AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The mass density of a bone tissue.") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "mass density of bone tissue") -AnnotationAssertion(rdfs:label "bone density") +AnnotationAssertion(rdfs:label "bone tissue density") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) # Class: (adrenal gland size) @@ -109477,6 +109479,14 @@ AnnotationAssertion(Annotation( "heel bone density") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +# Class: (bone density) + +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The mass density of a bone element.") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "mass density of bone element") +AnnotationAssertion(rdfs:label "bone density") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) + # Class: (ascending aorta diameter) AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The diameter of a ascending aorta.") @@ -171070,12 +171080,14 @@ AnnotationAssertion(Annotation( "osteoblast physiology trait") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -# Class: (bone mineral mass) +# Class: (bone mineral amount) -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "The mass density of a bone element.") -AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute") "mass density of bone element") -AnnotationAssertion(rdfs:label "bone mineral mass") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute_location") "The amount of a mineral when measured in bone element.") +AnnotationAssertion( "https://orcid.org/0000-0001-8314-2140") +AnnotationAssertion(Annotation( "AUTO:patterns/patterns/entity_attribute_location") "bone element mineral amount") +AnnotationAssertion( "bone mineral mass") +AnnotationAssertion(rdfs:label "bone mineral amount") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) # Class: (osteoblast development trait)