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src/patterns/data/default/abnormalSizeOfAnatomicalEntity.tsv
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| 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 |
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| 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 |
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| 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 |
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src/patterns/dosdp-patterns/abnormalSizeOfAnatomicalEntity.yaml
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| 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'." | ||
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| 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 | ||
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| relations: | ||
| inheres_in: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
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| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
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| vars: | ||
| entity: "'anatomical entity'" | ||
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| name: | ||
| text: "abnormal size of %s" | ||
| vars: | ||
| - entity | ||
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| annotations: | ||
| - annotationProperty: exact_synonym | ||
| text: "abnormal size of the %s" | ||
| vars: | ||
| - entity | ||
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| def: | ||
| text: "A deviation from the normal size of the %s." | ||
| vars: | ||
| - entity | ||
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| equivalentTo: | ||
| text: "'has_part' some ('size' and ('inheres_in' some %s) and ('has_modifier' some 'abnormal'))" | ||
| vars: | ||
| - entity |
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| --- | ||
| pattern_name: foldedAnatomicalEntity | ||
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| pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/foldedAnatomicalEntity.yaml | ||
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| 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." | ||
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| # 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 | ||
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| 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 | ||
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| classes: | ||
| folded: PATO:0001910 | ||
| abnormal: PATO:0000460 | ||
| anatomical_entity: UBERON:0001062 | ||
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| relations: | ||
| characteristic_of: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
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| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
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| vars: | ||
| anatomical_entity: "'anatomical_entity'" | ||
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| name: | ||
| text: "folded %s" | ||
| vars: | ||
| - anatomical_entity | ||
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| annotations: | ||
| - annotationProperty: exact_synonym | ||
| text: "abnormally folded %s" | ||
| vars: | ||
| - anatomical_entity | ||
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| def: | ||
| text: "A morphological anomaly that involves folding all or any part | ||
| of %s over another connected part." | ||
| vars: | ||
| - anatomical_entity | ||
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| equivalentTo: | ||
| text: "'has_part' some ( | ||
| 'folded' and | ||
| ('characteristic_of' some %s) and | ||
| ('has_modifier' some 'abnormal') | ||
| )" | ||
| vars: | ||
| - anatomical_entity | ||
| ... |
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| --- | ||
| pattern_name: wrinkledAnatomicalEntity | ||
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| pattern_iri: http://purl.obolibrary.org/obo/upheno/patterns-dev/wrinkledAnatomicalEntity.yaml | ||
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| 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." | ||
|
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| # 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 | ||
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| 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 | ||
|
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| classes: | ||
| wrinkled: PATO:0001810 | ||
| abnormal: PATO:0000460 | ||
| anatomical_entity: UBERON:0001062 | ||
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| relations: | ||
| characteristic_of: RO:0000052 | ||
| has_modifier: RO:0002573 | ||
| has_part: BFO:0000051 | ||
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| annotationProperties: | ||
| exact_synonym: oio:hasExactSynonym | ||
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| vars: | ||
| anatomical_entity: "'anatomical_entity'" | ||
|
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| name: | ||
| text: "wrinkled %s" | ||
| vars: | ||
| - anatomical_entity | ||
|
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| annotations: | ||
| - annotationProperty: exact_synonym | ||
| text: "abnormally wrinkled %s" | ||
| vars: | ||
| - anatomical_entity | ||
|
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| def: | ||
| text: "Wrinkled %s displaying one or more creases in a normally smooth | ||
| surface." | ||
| vars: | ||
| - anatomical_entity | ||
|
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||
| equivalentTo: | ||
| text: "'has_part' some ( | ||
| 'wrinkled' and | ||
| ('characteristic_of' some %s) and | ||
| ('has_modifier' some 'abnormal') | ||
| )" | ||
| vars: | ||
| - anatomical_entity | ||
| ... |