From cd772f173d1f456a474a51480785218a199c8cc2 Mon Sep 17 00:00:00 2001 From: Sue Bello Date: Wed, 7 Feb 2024 12:04:13 -0500 Subject: [PATCH] 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 +...