From a6dc32b6cf98a144d8ea2313cd2681325d510268 Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Wed, 7 Feb 2024 11:15:41 -0500 Subject: [PATCH 1/4] working on #3912 Adding collapsedAnatomicalEntity.yaml perforateAnatomicalEntity.yaml exsertedAnatomicalEntity.yaml patterns and data --- .../default/collapsedAnatomicalEntity.tsv | 3 + .../data/default/exsertedAnatomicalEntity.tsv | 8 +++ .../default/perforateAnatomicalEntity.tsv | 9 +++ .../collapsedAnatomicalEntity.yaml | 55 ++++++++++++++ .../exsertedAnatomicalEntity.yaml | 72 +++++++++++++++++++ src/patterns/dosdp-patterns/external.txt | 3 + .../perforateAnatomicalEntity.yaml | 63 ++++++++++++++++ 7 files changed, 213 insertions(+) create mode 100644 src/patterns/data/default/collapsedAnatomicalEntity.tsv create mode 100644 src/patterns/data/default/exsertedAnatomicalEntity.tsv create mode 100644 src/patterns/data/default/perforateAnatomicalEntity.tsv create mode 100644 src/patterns/dosdp-patterns/collapsedAnatomicalEntity.yaml create mode 100644 src/patterns/dosdp-patterns/exsertedAnatomicalEntity.yaml create mode 100644 src/patterns/dosdp-patterns/perforateAnatomicalEntity.yaml diff --git a/src/patterns/data/default/collapsedAnatomicalEntity.tsv b/src/patterns/data/default/collapsedAnatomicalEntity.tsv new file mode 100644 index 00000000..6dc9a652 --- /dev/null +++ b/src/patterns/data/default/collapsedAnatomicalEntity.tsv @@ -0,0 +1,3 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0006024 collapsed Reissner membrane http://purl.obolibrary.org/obo/UBERON_0002281 vestibular membrane of cochlear duct +http://purl.obolibrary.org/obo/MP_0012681 collapsed brain ventricles http://purl.obolibrary.org/obo/UBERON_0004086 brain ventricle diff --git a/src/patterns/data/default/exsertedAnatomicalEntity.tsv b/src/patterns/data/default/exsertedAnatomicalEntity.tsv new file mode 100644 index 00000000..7b741dda --- /dev/null +++ b/src/patterns/data/default/exsertedAnatomicalEntity.tsv @@ -0,0 +1,8 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0009105 penis prolapse http://purl.obolibrary.org/obo/UBERON_0000989 penis +http://purl.obolibrary.org/obo/MP_0000493 rectal prolapse http://purl.obolibrary.org/obo/UBERON_0001052 rectum +http://purl.obolibrary.org/obo/MP_0000385 distended hair follicles http://purl.obolibrary.org/obo/UBERON_0002073 hair follicle +http://purl.obolibrary.org/obo/MP_0002750 exophthalmos http://purl.obolibrary.org/obo/UBERON_0010230 eyeball of camera-type eye +http://purl.obolibrary.org/obo/MP_0001343 pronounced eyelids http://purl.obolibrary.org/obo/UBERON_0001711 eyelid +http://purl.obolibrary.org/obo/MP_0003681 protruding ear lobes http://purl.obolibrary.org/obo/UBERON_0001847 lobule of pinna +http://purl.obolibrary.org/obo/MP_0009908 protruding tongue http://purl.obolibrary.org/obo/UBERON_0001723 tongue diff --git a/src/patterns/data/default/perforateAnatomicalEntity.tsv b/src/patterns/data/default/perforateAnatomicalEntity.tsv new file mode 100644 index 00000000..15db5065 --- /dev/null +++ b/src/patterns/data/default/perforateAnatomicalEntity.tsv @@ -0,0 +1,9 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0031432 cornea perforation http://purl.obolibrary.org/obo/UBERON_0000964 cornea +http://purl.obolibrary.org/obo/MP_0030414 tympanic membrane perforation http://purl.obolibrary.org/obo/UBERON_0002364 tympanic membrane +http://purl.obolibrary.org/obo/MP_0004463 basisphenoid bone foramen http://purl.obolibrary.org/obo/UBERON_0006428 basisphenoid bone +http://purl.obolibrary.org/obo/MP_0004378 frontal bone foramen http://purl.obolibrary.org/obo/UBERON_0000209 tetrapod frontal bone +http://purl.obolibrary.org/obo/MP_0004442 occipital bone foramen http://purl.obolibrary.org/obo/UBERON_0001676 occipital bone +http://purl.obolibrary.org/obo/MP_0004342 scapular bone foramen http://purl.obolibrary.org/obo/UBERON_0006849 scapula +http://purl.obolibrary.org/obo/MP_0004679 xiphoid process foramen http://purl.obolibrary.org/obo/UBERON_0006430 xiphoid cartilage +http://purl.obolibrary.org/obo/MP_0004225 patent cardiac foramen ovale http://purl.obolibrary.org/obo/UBERON_0002085 interatrial septum diff --git a/src/patterns/dosdp-patterns/collapsedAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/collapsedAnatomicalEntity.yaml new file mode 100644 index 00000000..e843616e --- /dev/null +++ b/src/patterns/dosdp-patterns/collapsedAnatomicalEntity.yaml @@ -0,0 +1,55 @@ +--- +pattern_name: collapsedAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/collapsedAnatomicalEntity.yaml + +description: 'Use this phenotype pattern when an anatomical entity has + collapsed and loses its normal structure by becoming flat or caved in.' + +# examples: +# - http://purl.obolibrary.org/obo/MP_0006024 # collapsed Reissner membrane +# - http://purl.obolibrary.org/obo/MP_0012681 # collapsed brain ventricles +# - http://purl.obolibrary.org/obo/ZP_0000118 # forebrain ventricle collapsed, abnormal +# - http://purl.obolibrary.org/obo/ZP_0131104 # atrioventricular canal collapsed, abnormal + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0002-9900-7880 # Yvonne M. Bradford [ybradford] + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + +classes: + collapsed: PATO:0001478 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "collapsed %s" + vars: + - anatomical_entity + +def: + text: "A structural failure that affects %s so that it becomes flat or caved + in." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'collapsed' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... diff --git a/src/patterns/dosdp-patterns/exsertedAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/exsertedAnatomicalEntity.yaml new file mode 100644 index 00000000..34cffa86 --- /dev/null +++ b/src/patterns/dosdp-patterns/exsertedAnatomicalEntity.yaml @@ -0,0 +1,72 @@ +--- +pattern_name: exsertedAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/exsertedAnatomicalEntity.yaml + +description: 'Use this phenotype pattern when an anatomical entity is + abnormally protruding or projecting from the body. These anatomical + entities may be described as being prolapsed, protuberant or sticking out.' + +# examples: +# - http://purl.obolibrary.org/obo/ZP_0016742 # pectoral fin exserted, abnormal +# - http://purl.obolibrary.org/obo/HP_0002035 # Rectal prolapse +# - http://purl.obolibrary.org/obo/MP_0000493 # rectal prolapse + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + +classes: + exserted: PATO:0000623 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + narrow_synonym: oio:hasNarrowSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "exserted %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "protuberant %s" + vars: + - anatomical_entity + + - annotationProperty: narrow_synonym + text: "%s prolapse" + vars: + - anatomical_entity + + - annotationProperty: narrow_synonym + text: "prolapsed %s" + vars: + - anatomical_entity + +def: + text: "An exserted %s is protruding or projecting from the body abnormally." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'exserted' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... diff --git a/src/patterns/dosdp-patterns/external.txt b/src/patterns/dosdp-patterns/external.txt index 1b0db200..c92abd89 100644 --- a/src/patterns/dosdp-patterns/external.txt +++ b/src/patterns/dosdp-patterns/external.txt @@ -17,4 +17,7 @@ http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalMorphologyOfPartOfAna http://purl.obolibrary.org/obo/upheno/patterns-dev/necroticAnatomicalEntity.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/fibroticAnatomicalEntity.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalConstrictionOfAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/exsertedAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/perforateAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/collapsedAnatomicalEntity.yaml diff --git a/src/patterns/dosdp-patterns/perforateAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/perforateAnatomicalEntity.yaml new file mode 100644 index 00000000..9fe86955 --- /dev/null +++ b/src/patterns/dosdp-patterns/perforateAnatomicalEntity.yaml @@ -0,0 +1,63 @@ +--- +pattern_name: perforateAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/perforateAnatomicalEntity.yaml + +description: "Use this pattern for phenotypes when an anatomical entity has an + abnormal hole or a series of holes. Consider the alternative 'PATO:0000609 + closure incomplete' pattern for anatomical entities where a hole is present + normally at one developmental period but it remains open." + +# examples: +# - http://purl.obolibrary.org/obo/ZP_0002341 # retina perforate, abnormal +# - http://purl.obolibrary.org/obo/HP_0100583 # Corneal perforation +# - http://purl.obolibrary.org/obo/MP_0030414 # tympanic membrane perforation + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + +classes: + perforate: PATO:0002112 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "%s perforation" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "perforated %s" + vars: + - anatomical_entity + +def: + text: "The presence of one or more abnormal holes in %s." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'perforate' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... From 9d9871858f178ecf22bd70bd30a7adfce804e1d7 Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Wed, 7 Feb 2024 11:34:14 -0500 Subject: [PATCH 2/4] working on #3912 Adding obstructedAnatomicalEntity abnormallyFusedAnatomicalEntities abnormallyProtrudingAnatomicalEntity --- .../abnormallyFusedAnatomicalEntities.tsv | 50 ++++++++++++ .../abnormallyProtrudingAnatomicalEntity.tsv | 8 ++ .../default/obstructedAnatomicalEntity.tsv | 15 ++++ .../abnormallyFusedAnatomicalEntities.yaml | 48 ++++++++++++ .../abnormallyProtrudingAnatomicalEntity.yaml | 69 +++++++++++++++++ src/patterns/dosdp-patterns/external.txt | 4 + .../obstructedAnatomicalEntity.yaml | 77 +++++++++++++++++++ 7 files changed, 271 insertions(+) create mode 100644 src/patterns/data/default/abnormallyFusedAnatomicalEntities.tsv create mode 100644 src/patterns/data/default/abnormallyProtrudingAnatomicalEntity.tsv create mode 100644 src/patterns/data/default/obstructedAnatomicalEntity.tsv create mode 100644 src/patterns/dosdp-patterns/abnormallyFusedAnatomicalEntities.yaml create mode 100644 src/patterns/dosdp-patterns/abnormallyProtrudingAnatomicalEntity.yaml create mode 100644 src/patterns/dosdp-patterns/obstructedAnatomicalEntity.yaml diff --git a/src/patterns/data/default/abnormallyFusedAnatomicalEntities.tsv b/src/patterns/data/default/abnormallyFusedAnatomicalEntities.tsv new file mode 100644 index 00000000..09c66d65 --- /dev/null +++ b/src/patterns/data/default/abnormallyFusedAnatomicalEntities.tsv @@ -0,0 +1,50 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label anatomical_entity_fused_with anatomical_entity_fused_with_label +http://purl.obolibrary.org/obo/MP_0009437 arytenoid and cricoid cartilage fusion http://purl.obolibrary.org/obo/UBERON_0001740 arytenoid cartilage http://purl.obolibrary.org/obo/UBERON_0002375 cricoid cartilage +http://purl.obolibrary.org/obo/MP_0030086 bony syngnathia http://purl.obolibrary.org/obo/UBERON_0011597 bone of upper jaw http://purl.obolibrary.org/obo/UBERON_0004768 bone of lower jaw +http://purl.obolibrary.org/obo/MP_0004619 caudal vertebral fusion http://purl.obolibrary.org/obo/UBERON_0001095 caudal vertebra http://purl.obolibrary.org/obo/UBERON_0001095 caudal vertebra +http://purl.obolibrary.org/obo/MP_0004620 cervical vertebral fusion http://purl.obolibrary.org/obo/UBERON_0002413 cervical vertebra http://purl.obolibrary.org/obo/UBERON_0002413 cervical vertebra +http://purl.obolibrary.org/obo/MP_0009438 cricoid and tracheal cartilage fusion http://purl.obolibrary.org/obo/UBERON_0002375 cricoid cartilage http://purl.obolibrary.org/obo/UBERON_0003604 trachea cartilage +http://purl.obolibrary.org/obo/MP_0030087 fibrous syngnathia http://purl.obolibrary.org/obo/UBERON_0004103 alveolar ridge http://purl.obolibrary.org/obo/UBERON_0004103 alveolar ridge +http://purl.obolibrary.org/obo/MP_0010989 fused bronchial cartilage rings http://purl.obolibrary.org/obo/UBERON_0001956 cartilage of bronchus http://purl.obolibrary.org/obo/UBERON_0001956 cartilage of bronchus +http://purl.obolibrary.org/obo/MP_0001307 fused cornea and lens http://purl.obolibrary.org/obo/UBERON_0000964 cornea http://purl.obolibrary.org/obo/UBERON_0000965 lens of camera-type eye +http://purl.obolibrary.org/obo/MP_0000963 fused dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_0000044 dorsal root ganglion http://purl.obolibrary.org/obo/UBERON_0000044 dorsal root ganglion +http://purl.obolibrary.org/obo/MP_0030474 fused incisors http://purl.obolibrary.org/obo/UBERON_0001098 incisor tooth http://purl.obolibrary.org/obo/UBERON_0001098 incisor tooth +http://purl.obolibrary.org/obo/MP_0003189 fused joints http://purl.obolibrary.org/obo/UBERON_0000982 skeletal joint http://purl.obolibrary.org/obo/UBERON_0000982 skeletal joint +http://purl.obolibrary.org/obo/MP_0003605 fused kidneys http://purl.obolibrary.org/obo/UBERON_0002113 kidney http://purl.obolibrary.org/obo/UBERON_0002113 kidney +http://purl.obolibrary.org/obo/MP_0009553 fused lips http://purl.obolibrary.org/obo/UBERON_0001834 upper lip http://purl.obolibrary.org/obo/UBERON_0001835 lower lip +http://purl.obolibrary.org/obo/MP_0030475 fused lower incisors http://purl.obolibrary.org/obo/UBERON_0003451 lower jaw incisor http://purl.obolibrary.org/obo/UBERON_0003451 lower jaw incisor +http://purl.obolibrary.org/obo/MP_0004639 fused metacarpal bones http://purl.obolibrary.org/obo/UBERON_0002374 metacarpal bone http://purl.obolibrary.org/obo/UBERON_0002374 metacarpal bone +http://purl.obolibrary.org/obo/MP_0004642 fused metatarsal bones http://purl.obolibrary.org/obo/UBERON_0001448 metatarsal bone http://purl.obolibrary.org/obo/UBERON_0001448 metatarsal bone +http://purl.obolibrary.org/obo/MP_0030473 fused molars http://purl.obolibrary.org/obo/UBERON_0003655 molar tooth http://purl.obolibrary.org/obo/UBERON_0003655 molar tooth +http://purl.obolibrary.org/obo/MP_0008730 fused phalanges http://purl.obolibrary.org/obo/UBERON_0003221 phalanx http://purl.obolibrary.org/obo/UBERON_0003221 phalanx +http://purl.obolibrary.org/obo/MP_0020350 fused pharyngeal arches http://purl.obolibrary.org/obo/UBERON_0002539 pharyngeal arch http://purl.obolibrary.org/obo/UBERON_0002539 pharyngeal arch +http://purl.obolibrary.org/obo/MP_0011530 fused radius and ulna http://purl.obolibrary.org/obo/UBERON_0001423 radius bone http://purl.obolibrary.org/obo/UBERON_0001424 ulna +http://purl.obolibrary.org/obo/MP_0014080 fused small intestinal villi http://purl.obolibrary.org/obo/UBERON_0001213 intestinal villus http://purl.obolibrary.org/obo/UBERON_0001213 intestinal villus +http://purl.obolibrary.org/obo/MP_0011733 fused somites http://purl.obolibrary.org/obo/UBERON_0002329 somite http://purl.obolibrary.org/obo/UBERON_0002329 somite +http://purl.obolibrary.org/obo/MP_0008919 fused tarsal bones http://purl.obolibrary.org/obo/UBERON_0001447 tarsal bone http://purl.obolibrary.org/obo/UBERON_0001447 tarsal bone +http://purl.obolibrary.org/obo/MP_0030472 fused teeth http://purl.obolibrary.org/obo/UBERON_0001091 calcareous tooth http://purl.obolibrary.org/obo/UBERON_0001091 calcareous tooth +http://purl.obolibrary.org/obo/MP_0004552 fused tracheal cartilage rings http://purl.obolibrary.org/obo/UBERON_0003604 trachea cartilage http://purl.obolibrary.org/obo/UBERON_0003604 trachea cartilage +http://purl.obolibrary.org/obo/MP_0030476 fused upper incisors http://purl.obolibrary.org/obo/UBERON_0003450 upper jaw incisor http://purl.obolibrary.org/obo/UBERON_0003450 upper jaw incisor +http://purl.obolibrary.org/obo/MP_0013911 fused vestibular saccule and utricle http://purl.obolibrary.org/obo/UBERON_0001854 saccule of membranous labyrinth http://purl.obolibrary.org/obo/UBERON_0001853 utricle of membranous labyrinth +http://purl.obolibrary.org/obo/MP_0010728 fusion of atlas and occipital bones http://purl.obolibrary.org/obo/UBERON_0001092 vertebral bone 1 http://purl.obolibrary.org/obo/UBERON_0001676 occipital bone +http://purl.obolibrary.org/obo/MP_0010701 fusion of atlas and odontoid process http://purl.obolibrary.org/obo/UBERON_0001092 vertebral bone 1 http://purl.obolibrary.org/obo/UBERON_0004096 odontoid process of cervical vertebra 2 +http://purl.obolibrary.org/obo/MP_0004572 fusion of basioccipital and basisphenoid bone http://purl.obolibrary.org/obo/UBERON_0001692 basioccipital bone http://purl.obolibrary.org/obo/UBERON_0006428 basisphenoid bone +http://purl.obolibrary.org/obo/MP_0004568 fusion of glossopharyngeal and vagus nerve http://purl.obolibrary.org/obo/UBERON_0001649 glossopharyngeal nerve http://purl.obolibrary.org/obo/UBERON_0001759 vagus nerve +http://purl.obolibrary.org/obo/MP_0004613 fusion of vertebral arches http://purl.obolibrary.org/obo/UBERON_0003861 neural arch http://purl.obolibrary.org/obo/UBERON_0003861 neural arch +http://purl.obolibrary.org/obo/MP_0004612 fusion of vertebral bodies http://purl.obolibrary.org/obo/UBERON_0001075 bony vertebral centrum http://purl.obolibrary.org/obo/UBERON_0001075 bony vertebral centrum +http://purl.obolibrary.org/obo/MP_0030110 incudomalleolar fusion http://purl.obolibrary.org/obo/UBERON_0001688 incus bone http://purl.obolibrary.org/obo/UBERON_0001689 malleus bone +http://purl.obolibrary.org/obo/MP_0004621 lumbar vertebral fusion http://purl.obolibrary.org/obo/UBERON_0002414 lumbar vertebra http://purl.obolibrary.org/obo/UBERON_0002414 lumbar vertebra +http://purl.obolibrary.org/obo/MP_0009487 rectourethral fusion http://purl.obolibrary.org/obo/UBERON_0001052 rectum http://purl.obolibrary.org/obo/UBERON_0000057 urethra +http://purl.obolibrary.org/obo/MP_0009486 rectovaginal fusion http://purl.obolibrary.org/obo/UBERON_0001052 rectum http://purl.obolibrary.org/obo/UBERON_0000996 vagina +http://purl.obolibrary.org/obo/MP_0012817 rhombomere fusion http://purl.obolibrary.org/obo/UBERON_0001892 rhombomere http://purl.obolibrary.org/obo/UBERON_0001892 rhombomere +http://purl.obolibrary.org/obo/MP_0000154 rib fusion http://purl.obolibrary.org/obo/UBERON_0002228 rib http://purl.obolibrary.org/obo/UBERON_0002228 rib +http://purl.obolibrary.org/obo/MP_0004622 sacral vertebral fusion http://purl.obolibrary.org/obo/UBERON_0001094 sacral vertebra http://purl.obolibrary.org/obo/UBERON_0001094 sacral vertebra +http://purl.obolibrary.org/obo/MP_0003445 sirenomelia http://purl.obolibrary.org/obo/UBERON_0002103 hindlimb http://purl.obolibrary.org/obo/UBERON_0002103 hindlimb +http://purl.obolibrary.org/obo/MP_0010082 sternebra fusion http://purl.obolibrary.org/obo/UBERON_0002208 sternebra http://purl.obolibrary.org/obo/UBERON_0002208 sternebra +http://purl.obolibrary.org/obo/MP_0013393 symblepharon http://purl.obolibrary.org/obo/UBERON_0001812 palpebral conjunctiva http://purl.obolibrary.org/obo/UBERON_0010306 bulbar conjunctiva +http://purl.obolibrary.org/obo/MP_0000564 syndactyly http://purl.obolibrary.org/obo/UBERON_0002544 digit http://purl.obolibrary.org/obo/UBERON_0002544 digit +http://purl.obolibrary.org/obo/MP_0030085 syngnathia http://purl.obolibrary.org/obo/UBERON_0001709 upper jaw region http://purl.obolibrary.org/obo/UBERON_0001710 lower jaw region +http://purl.obolibrary.org/obo/MP_0004623 thoracic vertebral fusion http://purl.obolibrary.org/obo/UBERON_0002347 thoracic vertebra http://purl.obolibrary.org/obo/UBERON_0002347 thoracic vertebra +http://purl.obolibrary.org/obo/MP_0013264 tongue ankylosis http://purl.obolibrary.org/obo/UBERON_0001723 tongue http://purl.obolibrary.org/obo/UBERON_0003679 mouth floor +http://purl.obolibrary.org/obo/MP_0030449 tooth ankylosis http://purl.obolibrary.org/obo/UBERON_0001753 cementum http://purl.obolibrary.org/obo/UBERON_0004103 alveolar ridge +http://purl.obolibrary.org/obo/MP_0004609 vertebral fusion http://purl.obolibrary.org/obo/UBERON_0002412 vertebra http://purl.obolibrary.org/obo/UBERON_0002412 vertebra diff --git a/src/patterns/data/default/abnormallyProtrudingAnatomicalEntity.tsv b/src/patterns/data/default/abnormallyProtrudingAnatomicalEntity.tsv new file mode 100644 index 00000000..abd9ce93 --- /dev/null +++ b/src/patterns/data/default/abnormallyProtrudingAnatomicalEntity.tsv @@ -0,0 +1,8 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label reviewed comment +http://purl.obolibrary.org/obo/MP_0009079 prolapsed intervertebral disk http://purl.obolibrary.org/obo/UBERON_0001066 intervertebral disk ok should use protruding +http://purl.obolibrary.org/obo/MP_0005577 uterus prolapse http://purl.obolibrary.org/obo/UBERON_0000995 uterus ok should use protruding +http://purl.obolibrary.org/obo/MP_0000500 small intestinal prolapse http://purl.obolibrary.org/obo/UBERON_0002108 small intestine ok should use protruding +http://purl.obolibrary.org/obo/MP_0006120 mitral valve prolapse http://purl.obolibrary.org/obo/UBERON_0002135 mitral valve ok see HPO textual definition Mitral valve prolapse HP:0001634 (uses exserted in EQ) +http://purl.obolibrary.org/obo/MP_0006118 aortic valve prolapse http://purl.obolibrary.org/obo/UBERON_0002137 aortic valve ok see HPO textual definition Aortic valve prolapse HP:0025578 (uses exserted in EQ) +http://purl.obolibrary.org/obo/MP_0006129 pulmonary valve prolapse http://purl.obolibrary.org/obo/UBERON_0002146 pulmonary valve ok no HPO term +http://purl.obolibrary.org/obo/MP_0006125 tricuspid valve prolapse http://purl.obolibrary.org/obo/UBERON_0002134 tricuspid valve ok \ No newline at end of file diff --git a/src/patterns/data/default/obstructedAnatomicalEntity.tsv b/src/patterns/data/default/obstructedAnatomicalEntity.tsv new file mode 100644 index 00000000..9fa4785d --- /dev/null +++ b/src/patterns/data/default/obstructedAnatomicalEntity.tsv @@ -0,0 +1,15 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0011676 aortic arch obstruction http://purl.obolibrary.org/obo/UBERON_0001508 arch of aorta +http://purl.obolibrary.org/obo/MP_0006134 artery occlusion http://purl.obolibrary.org/obo/UBERON_0001637 artery +http://purl.obolibrary.org/obo/MP_0003270 intestinal obstruction http://purl.obolibrary.org/obo/UBERON_0000160 intestine +http://purl.obolibrary.org/obo/MP_0031101 nasal obstruction http://purl.obolibrary.org/obo/UBERON_0001707 nasal cavity +http://purl.obolibrary.org/obo/MP_0013451 nasolacrimal duct obstruction http://purl.obolibrary.org/obo/UBERON_0002392 nasolacrimal duct +http://purl.obolibrary.org/obo/MP_0006417 rete testis obstruction http://purl.obolibrary.org/obo/UBERON_0003959 rete testis +http://purl.obolibrary.org/obo/MP_0031143 retina artery occlusion http://purl.obolibrary.org/obo/UBERON_0001620 central retinal artery +http://purl.obolibrary.org/obo/MP_0013497 trachea occlusion http://purl.obolibrary.org/obo/UBERON_0003126 trachea +http://purl.obolibrary.org/obo/MP_0003587 ureter obstruction http://purl.obolibrary.org/obo/UBERON_0000056 ureter +http://purl.obolibrary.org/obo/MP_0011491 ureteropelvic junction obstruction http://purl.obolibrary.org/obo/UBERON_0009972 ureteropelvic junction +http://purl.obolibrary.org/obo/MP_0011492 ureterovesical junction obstruction http://purl.obolibrary.org/obo/UBERON_0009973 ureterovesical junction +http://purl.obolibrary.org/obo/MP_0011801 urethra obstruction http://purl.obolibrary.org/obo/UBERON_0000057 urethra +http://purl.obolibrary.org/obo/MP_0009552 urinary bladder obstruction http://purl.obolibrary.org/obo/UBERON_0001255 urinary bladder +http://purl.obolibrary.org/obo/MP_0006137 venoocculsion http://purl.obolibrary.org/obo/UBERON_0001638 vein diff --git a/src/patterns/dosdp-patterns/abnormallyFusedAnatomicalEntities.yaml b/src/patterns/dosdp-patterns/abnormallyFusedAnatomicalEntities.yaml new file mode 100644 index 00000000..392ed91c --- /dev/null +++ b/src/patterns/dosdp-patterns/abnormallyFusedAnatomicalEntities.yaml @@ -0,0 +1,48 @@ +pattern_name: abnormallyFusedAnatomicalEntities +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyFusedAnatomicalEntities.yaml +description: "An anatomical entity that is abnormally fused with another anatomical entity." + +classes: + fused: PATO:0000642 + abnormal: PATO:0000460 + anatomical entity: UBERON:0001062 + +relations: + inheres_in: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + towards: RO:0002503 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + anatomical_entity: "'anatomical entity'" + anatomical_entity_fused_with: "'anatomical entity'" + +name: + text: "abnormally fused %s and %s" + vars: + - anatomical_entity + - anatomical_entity_fused_with + +annotations: +- annotationProperty: exact_synonym + text: "abnormal fusion of %s and %s" + vars: + - anatomical_entity + - anatomical_entity_fused_with + +def: + text: "Any abnormal fusion of the %s and the %s." + vars: + - anatomical_entity + - anatomical_entity_fused_with + +equivalentTo: + text: "'has_part' some ('fused' and ('inheres_in' some %s) and ('towards' some %s) and ('has_modifier' some 'abnormal'))" + vars: + - anatomical_entity + - anatomical_entity_fused_with +contributors: +- https://orcid.org/0000-0002-3528-5267 diff --git a/src/patterns/dosdp-patterns/abnormallyProtrudingAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/abnormallyProtrudingAnatomicalEntity.yaml new file mode 100644 index 00000000..ebeb9f21 --- /dev/null +++ b/src/patterns/dosdp-patterns/abnormallyProtrudingAnatomicalEntity.yaml @@ -0,0 +1,69 @@ +--- +pattern_name: abnormallyProtrudingAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyProtrudingAnatomicalEntity.yaml + +description: 'Use this phenotype pattern template, when an anatomical entity is + protruding or projecting out or beyond a surface or boundary. When an + anatomical entity is abnormally protruding or projecting from the body, use + the more specific pattern of "exsertedAnatomicalEntity" instead of the + pattern defined below.' + +# examples: +# - http://purl.obolibrary.org/obo/ZP_0002287 # forebrain protruding, abnormal +# - http://purl.obolibrary.org/obo/HP_0010808 # Protruding tongue +# - http://purl.obolibrary.org/obo/MP_0009908 # protruding tongue +# - http://purl.obolibrary.org/obo/XPO_0115495 # abnormally protruding proctodeum + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + +classes: + protruding: PATO:0001598 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "abnormally protruding %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "abnormal %s protrusion" + vars: + - anatomical_entity + - annotationProperty: exact_synonym + text: "protruding %s" + vars: + - anatomical_entity + +def: + text: "An abnormally protruding %s that extends out above or beyond an + anatomical surface or boundary." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'protruding' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... diff --git a/src/patterns/dosdp-patterns/external.txt b/src/patterns/dosdp-patterns/external.txt index c92abd89..f2b516c8 100644 --- a/src/patterns/dosdp-patterns/external.txt +++ b/src/patterns/dosdp-patterns/external.txt @@ -20,4 +20,8 @@ http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalConstrictionOfAnatomi http://purl.obolibrary.org/obo/upheno/patterns-dev/exsertedAnatomicalEntity.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/perforateAnatomicalEntity.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/collapsedAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/obstructedAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyFusedAnatomicalEntities.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyProtrudingAnatomicalEntity.yaml + diff --git a/src/patterns/dosdp-patterns/obstructedAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/obstructedAnatomicalEntity.yaml new file mode 100644 index 00000000..4a522d9d --- /dev/null +++ b/src/patterns/dosdp-patterns/obstructedAnatomicalEntity.yaml @@ -0,0 +1,77 @@ +--- +pattern_name: obstructedAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/obstructedAnatomicalEntity.yaml + +description: 'Use this phenotype pattern when an anatomical space of an + anatomical entity is blocked or filled with filled with one or more + obstacles. Typically, this results in some impediment, blockage, or reversal + of the normal flow of the contents of the entity or space. The use of an + anatomical space class would be preferred to material anatomical entities for + this phenotype pattern, but the logical pattern definition is kept permissive + for now.' + +# examples: +# - http://purl.obolibrary.org/obo/HP_0005214 # Intestinal obstruction +# - http://purl.obolibrary.org/obo/MP_0003270 # intestinal obstruction +# - http://purl.obolibrary.org/obo/MP_0006134 # artery occlusion +# - http://purl.obolibrary.org/obo/HP_0006000 # Ureteral obstruction +# - http://purl.obolibrary.org/obo/MP_0031101 # nasal obstruction +# - http://purl.obolibrary.org/obo/ZP_0021087 # bile canaliculus obstructed, abnormal + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + - https://orcid.org/0000-0002-7073-9172 # David Osumi-Sutherland + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + +classes: + obstructed: PATO:0000648 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 # anatomical_space: UBERON:0000464 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym + xref: oio:hasDbXref + +vars: + anatomical_space: "'anatomical_entity'" + +name: + text: "%s obstruction" + vars: + - anatomical_space + +annotations: + - annotationProperty: exact_synonym + text: "obstruction of %s" + vars: + - anatomical_space + + - annotationProperty: exact_synonym + text: "obstructed %s" + vars: + - anatomical_space + +def: + text: "Obstructed %s due to it being blocked or filled with one or more + obstacles." + vars: + - anatomical_space + +equivalentTo: + text: "'has_part' some ( + 'obstructed' + and ('characteristic_of' some %s) + and ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_space +... From cd772f173d1f456a474a51480785218a199c8cc2 Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Wed, 7 Feb 2024 12:04:13 -0500 Subject: [PATCH 3/4] working on #3912 Adding abnormalSizeOfAnatomicalEntity foldedAnatomicalEntity wrinkledAnatomicalEntity --- .../abnormalSizeOfAnatomicalEntity.tsv | 67 +++++++++++++++++++ .../data/default/foldedAnatomicalEntity.tsv | 2 + .../data/default/wrinkledAnatomicalEntity.tsv | 4 ++ .../abnormalSizeOfAnatomicalEntity.yaml | 50 ++++++++++++++ src/patterns/dosdp-patterns/external.txt | 3 + .../foldedAnatomicalEntity.yaml | 64 ++++++++++++++++++ .../wrinkledAnatomicalEntity.yaml | 67 +++++++++++++++++++ 7 files changed, 257 insertions(+) create mode 100644 src/patterns/data/default/abnormalSizeOfAnatomicalEntity.tsv create mode 100644 src/patterns/data/default/foldedAnatomicalEntity.tsv create mode 100644 src/patterns/data/default/wrinkledAnatomicalEntity.tsv create mode 100644 src/patterns/dosdp-patterns/abnormalSizeOfAnatomicalEntity.yaml create mode 100644 src/patterns/dosdp-patterns/foldedAnatomicalEntity.yaml create mode 100644 src/patterns/dosdp-patterns/wrinkledAnatomicalEntity.yaml diff --git a/src/patterns/data/default/abnormalSizeOfAnatomicalEntity.tsv b/src/patterns/data/default/abnormalSizeOfAnatomicalEntity.tsv new file mode 100644 index 00000000..b9825b13 --- /dev/null +++ b/src/patterns/data/default/abnormalSizeOfAnatomicalEntity.tsv @@ -0,0 +1,67 @@ +defined_class defined_class_label entity entity_label +http://purl.obolibrary.org/obo/MP_0013442 abnormal Harderian gland size http://purl.obolibrary.org/obo/UBERON_0004187 Harderian gland +http://purl.obolibrary.org/obo/MP_0008134 abnormal Peyer's patch size http://purl.obolibrary.org/obo/UBERON_0001211 Peyer's patch +http://purl.obolibrary.org/obo/MP_0020143 abnormal adrenal gland x-zone size http://purl.obolibrary.org/obo/UBERON_0009024 adrenal gland X zone +http://purl.obolibrary.org/obo/MP_0003956 abnormal body size http://purl.obolibrary.org/obo/UBERON_0000468 multicellular organism +http://purl.obolibrary.org/obo/MP_0000771 abnormal brain size http://purl.obolibrary.org/obo/UBERON_0000955 brain +http://purl.obolibrary.org/obo/MP_0013229 abnormal brain ventricle size http://purl.obolibrary.org/obo/UBERON_0004086 brain ventricle +http://purl.obolibrary.org/obo/MP_0020538 abnormal cerebellum fastigial nucleus size http://purl.obolibrary.org/obo/UBERON_0002153 fastigial nucleus +http://purl.obolibrary.org/obo/MP_0009100 abnormal clitoris size http://purl.obolibrary.org/obo/UBERON_0002411 clitoris +http://purl.obolibrary.org/obo/MP_0020573 abnormal corpus callosum size http://purl.obolibrary.org/obo/UBERON_0002336 corpus callosum +http://purl.obolibrary.org/obo/MP_0010031 abnormal cranium size http://purl.obolibrary.org/obo/UBERON_0003128 cranium +http://purl.obolibrary.org/obo/MP_0010866 abnormal prenatal body size http://purl.obolibrary.org/obo/UBERON_0000922 embryo +http://purl.obolibrary.org/obo/MP_0004926 abnormal epididymis size http://purl.obolibrary.org/obo/UBERON_0001301 epididymis +http://purl.obolibrary.org/obo/MP_0002697 abnormal eye size http://purl.obolibrary.org/obo/UBERON_0000019 camera-type eye +http://purl.obolibrary.org/obo/MP_0003671 abnormal eyelid aperture http://purl.obolibrary.org/obo/UBERON_0001819 palpebral fissure +http://purl.obolibrary.org/obo/MP_0030063 abnormal face size http://purl.obolibrary.org/obo/UBERON_0001456 face +http://purl.obolibrary.org/obo/MP_0004198 abnormal fetal size http://purl.obolibrary.org/obo/UBERON_0000323 late embryo +http://purl.obolibrary.org/obo/MP_0012137 abnormal forebrain size http://purl.obolibrary.org/obo/UBERON_0001890 forebrain +http://purl.obolibrary.org/obo/MP_0030041 abnormal forehead size http://purl.obolibrary.org/obo/UBERON_0008200 forehead +http://purl.obolibrary.org/obo/MP_0020134 abnormal gallbladder size http://purl.obolibrary.org/obo/UBERON_0002110 gall bladder +http://purl.obolibrary.org/obo/MP_0011496 abnormal head size http://purl.obolibrary.org/obo/UBERON_0000033 head +http://purl.obolibrary.org/obo/MP_0020323 abnormal heart apex size http://purl.obolibrary.org/obo/UBERON_0002098 apex of heart +http://purl.obolibrary.org/obo/MP_0010578 abnormal heart left ventricle size http://purl.obolibrary.org/obo/UBERON_0002084 heart left ventricle +http://purl.obolibrary.org/obo/MP_0010577 abnormal heart right ventricle size http://purl.obolibrary.org/obo/UBERON_0002080 heart right ventricle +http://purl.obolibrary.org/obo/MP_0005406 abnormal heart size http://purl.obolibrary.org/obo/UBERON_0000948 heart +http://purl.obolibrary.org/obo/MP_0012262 abnormal hindbrain size http://purl.obolibrary.org/obo/UBERON_0002028 hindbrain +http://purl.obolibrary.org/obo/MP_0020544 abnormal hippocampal fornix size http://purl.obolibrary.org/obo/UBERON_0000052 fornix of brain +http://purl.obolibrary.org/obo/MP_0008281 abnormal hippocampus size http://purl.obolibrary.org/obo/UBERON_0002421 hippocampal formation +http://purl.obolibrary.org/obo/MP_0002706 abnormal kidney size http://purl.obolibrary.org/obo/UBERON_0002113 kidney +http://purl.obolibrary.org/obo/MP_0004848 abnormal liver size http://purl.obolibrary.org/obo/UBERON_0002107 liver +http://purl.obolibrary.org/obo/MP_0004881 abnormal lung size http://purl.obolibrary.org/obo/UBERON_0002048 lung +http://purl.obolibrary.org/obo/MP_0000701 abnormal lymph node size http://purl.obolibrary.org/obo/UBERON_0000029 lymph node +http://purl.obolibrary.org/obo/MP_0012088 abnormal midbrain size http://purl.obolibrary.org/obo/UBERON_0001891 midbrain +http://purl.obolibrary.org/obo/MP_0020066 abnormal neocortex size http://purl.obolibrary.org/obo/UBERON_0001950 neocortex +http://purl.obolibrary.org/obo/MP_0020547 abnormal optic chiasm size http://purl.obolibrary.org/obo/UBERON_0000959 optic chiasma +http://purl.obolibrary.org/obo/MP_0006216 abnormal optic disk size http://purl.obolibrary.org/obo/UBERON_0001783 optic disc +http://purl.obolibrary.org/obo/MP_0006210 abnormal orbit size http://purl.obolibrary.org/obo/UBERON_0001697 orbit of skull +http://purl.obolibrary.org/obo/MP_0004853 abnormal ovary size http://purl.obolibrary.org/obo/UBERON_0000992 ovary +http://purl.obolibrary.org/obo/MP_0009063 abnormal oviduct size http://purl.obolibrary.org/obo/UBERON_0003889 fallopian tube +http://purl.obolibrary.org/obo/MP_0009106 abnormal pancreas size http://purl.obolibrary.org/obo/UBERON_0001264 pancreas +http://purl.obolibrary.org/obo/MP_0009170 abnormal pancreatic islet size http://purl.obolibrary.org/obo/UBERON_0000006 islet of Langerhans +http://purl.obolibrary.org/obo/MP_0008936 abnormal pituitary gland size http://purl.obolibrary.org/obo/UBERON_0000007 pituitary gland +http://purl.obolibrary.org/obo/MP_0011519 abnormal placenta labyrinth size http://purl.obolibrary.org/obo/UBERON_0003946 placenta labyrinth +http://purl.obolibrary.org/obo/MP_0004258 abnormal placenta size http://purl.obolibrary.org/obo/UBERON_0001987 placenta +http://purl.obolibrary.org/obo/MP_0020532 abnormal pons size http://purl.obolibrary.org/obo/UBERON_0000988 pons +http://purl.obolibrary.org/obo/MP_0020561 abnormal pontine nuclei size http://purl.obolibrary.org/obo/UBERON_0002151 pontine nuclear group +http://purl.obolibrary.org/obo/MP_0020565 abnormal pontocerebellar fibers size http://purl.obolibrary.org/obo/UBERON_0022421 pontocerebellar tract +http://purl.obolibrary.org/obo/MP_0020569 abnormal premotor cortex size http://purl.obolibrary.org/obo/UBERON_0016634 premotor cortex +http://purl.obolibrary.org/obo/MP_0004959 abnormal prostate gland size http://purl.obolibrary.org/obo/UBERON_0002367 prostate gland +http://purl.obolibrary.org/obo/MP_0004907 abnormal seminal vesicle size http://purl.obolibrary.org/obo/UBERON_0000998 seminal vesicle +http://purl.obolibrary.org/obo/MP_0006307 abnormal seminiferous tubule size http://purl.obolibrary.org/obo/UBERON_0001343 seminiferous tubule of testis +http://purl.obolibrary.org/obo/MP_0012005 abnormal septum pellucidum size http://purl.obolibrary.org/obo/UBERON_0004714 septum pellucidum +http://purl.obolibrary.org/obo/MP_0009458 abnormal skeletal muscle size http://purl.obolibrary.org/obo/UBERON_0001134 skeletal muscle tissue +http://purl.obolibrary.org/obo/MP_0005222 abnormal somite size http://purl.obolibrary.org/obo/UBERON_0002329 somite +http://purl.obolibrary.org/obo/MP_0002224 abnormal spleen size http://purl.obolibrary.org/obo/UBERON_0002106 spleen +http://purl.obolibrary.org/obo/MP_0012097 abnormal spongiotrophoblast size http://purl.obolibrary.org/obo/UBERON_0004021 spongiotrophoblast layer +http://purl.obolibrary.org/obo/MP_0012280 abnormal sternebra size http://purl.obolibrary.org/obo/UBERON_0002208 sternebra +http://purl.obolibrary.org/obo/MP_0020553 abnormal stria medullaris size http://purl.obolibrary.org/obo/UBERON_0006086 stria medullaris +http://purl.obolibrary.org/obo/MP_0020535 abnormal subiculum size http://purl.obolibrary.org/obo/UBERON_0002191 subiculum +http://purl.obolibrary.org/obo/MP_0020541 abnormal substantia nigra size http://purl.obolibrary.org/obo/UBERON_0002038 substantia nigra +http://purl.obolibrary.org/obo/MP_0004849 abnormal testis size http://purl.obolibrary.org/obo/UBERON_0000473 testis +http://purl.obolibrary.org/obo/MP_0020525 abnormal thalamus size http://purl.obolibrary.org/obo/UBERON_0001897 dorsal plus ventral thalamus +http://purl.obolibrary.org/obo/MP_0002364 abnormal thymus size http://purl.obolibrary.org/obo/UBERON_0002370 thymus +http://purl.obolibrary.org/obo/MP_0009225 abnormal uterine cervix size http://purl.obolibrary.org/obo/UBERON_0000002 uterine cervix +http://purl.obolibrary.org/obo/MP_0004902 abnormal uterus size http://purl.obolibrary.org/obo/UBERON_0000995 uterus +http://purl.obolibrary.org/obo/MP_0008977 abnormal vagina size http://purl.obolibrary.org/obo/UBERON_0000996 vagina +http://purl.obolibrary.org/obo/MP_0020557 abnormal ventromedial hypothalamic nucleus size http://purl.obolibrary.org/obo/UBERON_0001935 ventromedial nucleus of hypothalamus diff --git a/src/patterns/data/default/foldedAnatomicalEntity.tsv b/src/patterns/data/default/foldedAnatomicalEntity.tsv new file mode 100644 index 00000000..3c6ca63f --- /dev/null +++ b/src/patterns/data/default/foldedAnatomicalEntity.tsv @@ -0,0 +1,2 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0003736 folded helix http://purl.obolibrary.org/obo/UBERON_0002488 helix of outer ear diff --git a/src/patterns/data/default/wrinkledAnatomicalEntity.tsv b/src/patterns/data/default/wrinkledAnatomicalEntity.tsv new file mode 100644 index 00000000..0359ef9b --- /dev/null +++ b/src/patterns/data/default/wrinkledAnatomicalEntity.tsv @@ -0,0 +1,4 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0021107 retina fold http://purl.obolibrary.org/obo/UBERON_0000966 retina +http://purl.obolibrary.org/obo/MP_0011205 excessive folding of visceral yolk sac http://purl.obolibrary.org/obo/UBERON_0008852 visceral yolk sac +http://purl.obolibrary.org/obo/MP_0001211 wrinkled skin http://purl.obolibrary.org/obo/UBERON_0000014 zone of skin diff --git a/src/patterns/dosdp-patterns/abnormalSizeOfAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/abnormalSizeOfAnatomicalEntity.yaml new file mode 100644 index 00000000..abeadb16 --- /dev/null +++ b/src/patterns/dosdp-patterns/abnormalSizeOfAnatomicalEntity.yaml @@ -0,0 +1,50 @@ +pattern_name: abnormalSizeOfAnatomicalEntity +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalSizeOfAnatomicalEntity.yaml +description: "An abnormal size (the relative extent of something) of an anatomical entity, such as HP_0012504 'Abnormal size of pituitary gland'." + +contributors: +- https://orcid.org/0000-0002-9900-7880 +- https://orcid.org/0000-0001-9076-6015 +- https://orcid.org/0000-0002-9611-1279 +- https://orcid.org/0000-0002-3528-5267 +- https://orcid.org/0000-0001-5208-3432 +- https://orcid.org/0000-0002-1373-1705 +- https://orcid.org/0000-0003-4148-4606 +- https://orcid.org/0000-0002-7356-1779 +- https://orcid.org/0000-0001-7941-2961 +classes: + size: PATO:0000117 + abnormal: PATO:0000460 + anatomical entity: UBERON:0001062 + +relations: + inheres_in: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + entity: "'anatomical entity'" + +name: + text: "abnormal size of %s" + vars: + - entity + +annotations: +- annotationProperty: exact_synonym + text: "abnormal size of the %s" + vars: + - entity + +def: + text: "A deviation from the normal size of the %s." + vars: + - entity + +equivalentTo: + text: "'has_part' some ('size' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" + vars: + - entity diff --git a/src/patterns/dosdp-patterns/external.txt b/src/patterns/dosdp-patterns/external.txt index f2b516c8..48520e31 100644 --- a/src/patterns/dosdp-patterns/external.txt +++ b/src/patterns/dosdp-patterns/external.txt @@ -23,5 +23,8 @@ http://purl.obolibrary.org/obo/upheno/patterns-dev/collapsedAnatomicalEntity.yam http://purl.obolibrary.org/obo/upheno/patterns-dev/obstructedAnatomicalEntity.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyFusedAnatomicalEntities.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyProtrudingAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/wrinkledAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/foldedAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalSizeOfAnatomicalEntity.yaml diff --git a/src/patterns/dosdp-patterns/foldedAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/foldedAnatomicalEntity.yaml new file mode 100644 index 00000000..c2aa288e --- /dev/null +++ b/src/patterns/dosdp-patterns/foldedAnatomicalEntity.yaml @@ -0,0 +1,64 @@ +--- +pattern_name: foldedAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/foldedAnatomicalEntity.yaml + +description: "Use this phenotype pattern when an anatomical entity has + morphological abnormalities involving folding all or any part of it + over another connected part. Consider the related 'PATO:0001810 + wrinkled' anatomical entity pattern where the abnormal anatomical + entity is marked by one or more creases in a normally smooth surface." + +# examples: +# - http://purl.obolibrary.org/obo/ZP_0011575 # caudal fin folded, abnormal +# - http://purl.obolibrary.org/obo/MP_0003736 # folded helix +# - http://purl.obolibrary.org/obo/HP_0008544 # Abnormally folded helix + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-9900-7880 # Yvonne M. Bradford + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + +classes: + folded: PATO:0001910 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "folded %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "abnormally folded %s" + vars: + - anatomical_entity + +def: + text: "A morphological anomaly that involves folding all or any part + of %s over another connected part." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'folded' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... diff --git a/src/patterns/dosdp-patterns/wrinkledAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/wrinkledAnatomicalEntity.yaml new file mode 100644 index 00000000..c0d58136 --- /dev/null +++ b/src/patterns/dosdp-patterns/wrinkledAnatomicalEntity.yaml @@ -0,0 +1,67 @@ +--- +pattern_name: wrinkledAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/wrinkledAnatomicalEntity.yaml + +description: "Use this phenotype pattern when anatomical entity is + marked by one or more creases in a normally smooth surface. Consider + the 'foldedAnatomicalEntity.yaml' phenotype pattern when the + anatomical when an anatomical entity has morphological abnormalities + involving folding all or any part of it over another connected part." + +# examples: +# - http://purl.obolibrary.org/obo/MP_0021107 # retina fold +# - http://purl.obolibrary.org/obo/MP_0011205 # excessive folding of visceral yolk sac +# - http://purl.obolibrary.org/obo/HP_0008052 # Retinal fold +# - http://purl.obolibrary.org/obo/MP_0001211 # wrinkled skin +# - http://purl.obolibrary.org/obo/ZP_0015987 # nuclear envelope cell wrinkled, abnormal + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-9900-7880 # Yvonne M. Bradford + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + +classes: + wrinkled: PATO:0001810 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "wrinkled %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "abnormally wrinkled %s" + vars: + - anatomical_entity + +def: + text: "Wrinkled %s displaying one or more creases in a normally smooth + surface." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'wrinkled' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... From 7fa504af69a0674c5eeb8958933ac0971c76bf64 Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Wed, 7 Feb 2024 12:23:04 -0500 Subject: [PATCH 4/4] working on #3912 Adding abnormallyDecreasedWetnessOfAnatomicalEntity abnormallyGlisteningAnatomicalEntity abnormallyOpaqueAnatomicalEntity --- ...allyDecreasedWetnessOfAnatomicalEntity.tsv | 5 ++ .../abnormallyGlisteningAnatomicalEntity.tsv | 3 + .../abnormallyOpaqueAnatomicalEntity.tsv | 3 + ...llyDecreasedWetnessOfAnatomicalEntity.yaml | 87 +++++++++++++++++++ .../abnormallyGlisteningAnatomicalEntity.yaml | 62 +++++++++++++ .../abnormallyOpaqueAnatomicalEntity.yaml | 67 ++++++++++++++ src/patterns/dosdp-patterns/external.txt | 4 + 7 files changed, 231 insertions(+) create mode 100644 src/patterns/data/default/abnormallyDecreasedWetnessOfAnatomicalEntity.tsv create mode 100644 src/patterns/data/default/abnormallyGlisteningAnatomicalEntity.tsv create mode 100644 src/patterns/data/default/abnormallyOpaqueAnatomicalEntity.tsv create mode 100644 src/patterns/dosdp-patterns/abnormallyDecreasedWetnessOfAnatomicalEntity.yaml create mode 100644 src/patterns/dosdp-patterns/abnormallyGlisteningAnatomicalEntity.yaml create mode 100644 src/patterns/dosdp-patterns/abnormallyOpaqueAnatomicalEntity.yaml diff --git a/src/patterns/data/default/abnormallyDecreasedWetnessOfAnatomicalEntity.tsv b/src/patterns/data/default/abnormallyDecreasedWetnessOfAnatomicalEntity.tsv new file mode 100644 index 00000000..8f24acdb --- /dev/null +++ b/src/patterns/data/default/abnormallyDecreasedWetnessOfAnatomicalEntity.tsv @@ -0,0 +1,5 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0000624 xerostomia http://purl.obolibrary.org/obo/UBERON_0000165 mouth +http://purl.obolibrary.org/obo/MP_0001337 dry eyes http://purl.obolibrary.org/obo/UBERON_0000019 camera-type eye +http://purl.obolibrary.org/obo/MP_0003536 vagina dryness http://purl.obolibrary.org/obo/UBERON_0000996 vagina +http://purl.obolibrary.org/obo/MP_0014053 dry hair http://purl.obolibrary.org/obo/UBERON_0001037 strand of hair diff --git a/src/patterns/data/default/abnormallyGlisteningAnatomicalEntity.tsv b/src/patterns/data/default/abnormallyGlisteningAnatomicalEntity.tsv new file mode 100644 index 00000000..c7f38b1b --- /dev/null +++ b/src/patterns/data/default/abnormallyGlisteningAnatomicalEntity.tsv @@ -0,0 +1,3 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0000411 shiny fur http://purl.obolibrary.org/obo/UBERON_0010166 coat of hair +http://purl.obolibrary.org/obo/MP_0001196 shiny skin http://purl.obolibrary.org/obo/UBERON_0000014 zone of skin diff --git a/src/patterns/data/default/abnormallyOpaqueAnatomicalEntity.tsv b/src/patterns/data/default/abnormallyOpaqueAnatomicalEntity.tsv new file mode 100644 index 00000000..03bddadb --- /dev/null +++ b/src/patterns/data/default/abnormallyOpaqueAnatomicalEntity.tsv @@ -0,0 +1,3 @@ +defined_class defined_class_label anatomical_entity anatomical_entity_label +http://purl.obolibrary.org/obo/MP_0001304 cataract http://purl.obolibrary.org/obo/UBERON_0000965 lens of camera-type eye +http://purl.obolibrary.org/obo/MP_0002700 opacity of vitreous body http://purl.obolibrary.org/obo/UBERON_0001798 vitreous body diff --git a/src/patterns/dosdp-patterns/abnormallyDecreasedWetnessOfAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/abnormallyDecreasedWetnessOfAnatomicalEntity.yaml new file mode 100644 index 00000000..25e7eef8 --- /dev/null +++ b/src/patterns/dosdp-patterns/abnormallyDecreasedWetnessOfAnatomicalEntity.yaml @@ -0,0 +1,87 @@ +--- +pattern_name: abnormallyDecreasedWetnessOfAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedWetnessOfAnatomicalEntity.yaml + +description: "Use this phenotype pattern when an anatomical entity exhibits + decreased liquid coverage, for example, when the aqueous or oily layer on its + surface is reduced. Consider the alternative 'PATO:0001801 decreased water + composition' phenotype pattern when the water contained in an entity is + reduced as opposed to a reduced amount of liquid on its surface." + +# examples: +# - http://purl.obolibrary.org/obo/PATO_0001824 # http://purl.obolibrary.org/obo/HP_0000217 Xerostomia +# - http://purl.obolibrary.org/obo/PATO_0001824 # http://purl.obolibrary.org/obo/HP_0011359 Dry hair +# - http://purl.obolibrary.org/obo/PATO_0001824 # http://purl.obolibrary.org/obo/MP_0000624 xerostomia +# - http://purl.obolibrary.org/obo/PATO_0001824 # http://purl.obolibrary.org/obo/MP_0001337 dry eyes +# - http://purl.obolibrary.org/obo/MP_0003536 # vagina dryness + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + - https://orcid.org/0000-0002-4142-7153 # Sabrina Toro + - https://orcid.org/0000-0001-7941-2961 # Leigh Carmody + +classes: + decreased_surface_wetness: PATO:0001826 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + related_synonym: oio:hasRelatedSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "decreased surface wetness of %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "decreased wetness of %s" + vars: + - anatomical_entity + + - annotationProperty: exact_synonym + text: "decreased %s surface wetness" + vars: + - anatomical_entity + + - annotationProperty: exact_synonym + text: "decreased %s wetness" + vars: + - anatomical_entity + + - annotationProperty: related_synonym + text: "%s dryness" + vars: + - anatomical_entity + + - annotationProperty: related_synonym + text: "dry %s" + vars: + - anatomical_entity + +def: + text: "A relatively low wetness on the surface of %s." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'decreased_surface_wetness' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... diff --git a/src/patterns/dosdp-patterns/abnormallyGlisteningAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/abnormallyGlisteningAnatomicalEntity.yaml new file mode 100644 index 00000000..ebc1de70 --- /dev/null +++ b/src/patterns/dosdp-patterns/abnormallyGlisteningAnatomicalEntity.yaml @@ -0,0 +1,62 @@ +--- +pattern_name: abnormallyGlisteningAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyGlisteningAnatomicalEntity.yaml + +description: 'Use this phenotype pattern when an anatomical entity reflects + more light than it does normally.' + +# examples: +# - http://purl.obolibrary.org/obo/MP_0000411 # shiny fur +# - http://purl.obolibrary.org/obo/MP_0001196 # shiny skin + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0002-1373-1705 # Clare Pilgrim + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + - https://orcid.org/0000-0002-7073-9172 # David Osumi-Sutherland + - https://orcid.org/0000-0002-9900-7880 # Yvonne M. Bradford + - https://orcid.org/0000-0003-2699-3066 # Meghan A. Balk + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + +classes: + glistening: PATO:0001373 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "glistening %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "shiny %s" + vars: + - anatomical_entity + +def: + text: "Abnormally shiny, glossy or glistening appearance of %s." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'glistening' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... diff --git a/src/patterns/dosdp-patterns/abnormallyOpaqueAnatomicalEntity.yaml b/src/patterns/dosdp-patterns/abnormallyOpaqueAnatomicalEntity.yaml new file mode 100644 index 00000000..2d9aa966 --- /dev/null +++ b/src/patterns/dosdp-patterns/abnormallyOpaqueAnatomicalEntity.yaml @@ -0,0 +1,67 @@ +--- +pattern_name: abnormallyOpaqueAnatomicalEntity + +pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyOpaqueAnatomicalEntity.yaml + +description: 'Use this phenotype pattern in case of reduced clarity of an + anatomical entity, for example, when it is cloudy or shows decreased + transparency.' + +# examples: +# - http://purl.obolibrary.org/obo/HP_0000518 # Cataract +# - http://purl.obolibrary.org/obo/HP_0007787 # Posterior subcapsular cataract +# - http://purl.obolibrary.org/obo/MP_0001304 # cataract +# - http://purl.obolibrary.org/obo/MP_0002700 # opacity of vitreous body +# - http://purl.obolibrary.org/obo/ZP_0002198 # yolk opaque, abnormal + +contributors: + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0003-4606-0597 # Susan Bello + - https://orcid.org/0000-0002-6490-7723 # Anna V. Anagnostopoulos + +classes: + opaque: PATO:0000963 + abnormal: PATO:0000460 + anatomical_entity: UBERON:0001062 + +relations: + characteristic_of: RO:0000052 + has_modifier: RO:0002573 + has_part: BFO:0000051 + +annotationProperties: + exact_synonym: oio:hasExactSynonym + +vars: + anatomical_entity: "'anatomical_entity'" + +name: + text: "opaque %s" + vars: + - anatomical_entity + +annotations: + - annotationProperty: exact_synonym + text: "opacity of %s" + vars: + - anatomical_entity + + - annotationProperty: exact_synonym + text: "cloudy %s" + vars: + - anatomical_entity + +def: + text: "Impaired ability or inability of light to pass through %s." + vars: + - anatomical_entity + +equivalentTo: + text: "'has_part' some ( + 'opaque' and + ('characteristic_of' some %s) and + ('has_modifier' some 'abnormal') + )" + vars: + - anatomical_entity +... diff --git a/src/patterns/dosdp-patterns/external.txt b/src/patterns/dosdp-patterns/external.txt index 48520e31..200219ee 100644 --- a/src/patterns/dosdp-patterns/external.txt +++ b/src/patterns/dosdp-patterns/external.txt @@ -26,5 +26,9 @@ http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyProtrudingAnatomica http://purl.obolibrary.org/obo/upheno/patterns-dev/wrinkledAnatomicalEntity.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/foldedAnatomicalEntity.yaml http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormalSizeOfAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyOpaqueAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyGlisteningAnatomicalEntity.yaml +http://purl.obolibrary.org/obo/upheno/patterns-dev/abnormallyDecreasedWetnessOfAnatomicalEntity.yaml +