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Align abnormal morphology of anatomical entity EQs with HPO #3692

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rays22 opened this issue Nov 10, 2022 · 0 comments
Open

Align abnormal morphology of anatomical entity EQs with HPO #3692

rays22 opened this issue Nov 10, 2022 · 0 comments
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HPO mapping mapping of MP to HP terms KidsFirst patterns usage of and data for Upheno patterns

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@rays22
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rays22 commented Nov 10, 2022

There are matching MP-HPO terms where only the HPO term has an EQ, but the MP term of the pair does not have any.
See uPheno issue: obophenotype/upheno#898 (comment) .

I have created the table below with 37 of these pairs.
After your review, I can add these EQs to the appropriate MP terms in one go.
There are two patterns used for these in HPO:

  1. abnormalMorphologyOfAnatomicalEntity
  2. abnormalMorphologyOfPartOfAnatomicalEntity
pattern HP EQ MP ID MP LABEL HP ID HP LABEL
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'arch of aorta') and ('has modifier' some abnormal)) MP:0004113 abnormal aortic arch morphology HP:0012303 Abnormal aortic arch morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'cortex of kidney') and ('has modifier' some abnormal)) MP:0000521 abnormal kidney cortex morphology HP:0011035 Abnormal renal cortex morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'fused sacrum') and ('has modifier' some abnormal)) MP:0010113 abnormal sacrum morphology HP:0005107 Abnormal sacrum morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'heart left ventricle') and ('has modifier' some abnormal)) MP:0003921 abnormal heart left ventricle morphology HP:0001711 Abnormal left ventricle morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'heart right ventricle') and ('has modifier' some abnormal)) MP:0003920 abnormal heart right ventricle morphology HP:0001707 Abnormal right ventricle morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'interatrial septum') and ('has modifier' some abnormal)) MP:0000282 abnormal interatrial septum morphology HP:0011994 Abnormal atrial septum morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'internal ear') and ('has modifier' some abnormal)) MP:0000026 abnormal inner ear morphology HP:0011390 Morphological abnormality of the inner ear
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'interventricular septum') and ('has modifier' some abnormal)) MP:0000281 abnormal interventricular septum morphology HP:0010438 Abnormal ventricular septum morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'left cardiac atrium') and ('has modifier' some abnormal)) MP:0003923 abnormal heart left atrium morphology HP:0025579 Abnormal left atrium morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'metatarsal bone') and ('has modifier' some abnormal)) MP:0003072 abnormal metatarsal bone morphology HP:0001832 Abnormal metatarsal morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'postcranial axial skeleton') and ('has modifier' some abnormal)) MP:0002114 abnormal axial skeleton morphology HP:0009121 Abnormal axial skeleton morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'pulmonary vein') and ('has modifier' some abnormal)) MP:0002726 abnormal pulmonary vein morphology HP:0030968 Abnormal pulmonary vein morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'right cardiac atrium') and ('has modifier' some abnormal)) MP:0003922 abnormal heart right atrium morphology HP:0025580 Abnormal right atrium morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some 'trabecular network of bone') and ('has modifier' some abnormal)) MP:0000130 abnormal trabecular bone morphology HP:0100671 Abnormal trabecular bone morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some liver) and ('has modifier' some abnormal)) MP:0000598 abnormal liver morphology HP:0410042 Abnormal liver morphology
abnormalMorphologyOfAnatomicalEntity 'has part' some (morphology and ('characteristic of' some vein) and ('has modifier' some abnormal)) MP:0002725 abnormal vein morphology HP:0002624 Abnormal venous morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'aortic valve') and ('has modifier' some abnormal)) MP:0002747 abnormal aortic valve morphology HP:0001646 Abnormal aortic valve morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'appendicular skeleton') and ('has modifier' some abnormal)) MP:0009250 abnormal appendicular skeleton morphology HP:0011844 Abnormal appendicular skeleton morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'bony vertebral centrum') and ('has modifier' some abnormal)) MP:0000141 abnormal vertebral body morphology HP:0003312 Abnormal form of the vertebral bodies
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'cerebral hemisphere white matter') and ('has modifier' some abnormal)) MP:0008026 abnormal brain white matter morphology HP:0002500 Abnormal cerebral white matter morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'clavicle bone') and ('has modifier' some abnormal)) MP:0005298 abnormal clavicle morphology HP:0000889 Abnormal clavicle morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'common carotid artery plus branches') and ('has modifier' some abnormal)) MP:0004181 abnormal carotid artery morphology HP:0005344 Abnormal carotid artery morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'coronary artery') and ('has modifier' some abnormal)) MP:0004111 abnormal coronary artery morphology HP:0006704 Abnormal coronary artery morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'facial skeleton') and ('has modifier' some abnormal)) MP:0005274 abnormal viscerocranium morphology HP:0011821 Abnormality of facial skeleton
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'mitral valve') and ('has modifier' some abnormal)) MP:0000286 abnormal mitral valve morphology HP:0001633 Abnormal mitral valve morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'pulmonary artery') and ('has modifier' some abnormal)) MP:0000484 abnormal pulmonary artery morphology HP:0030966 Abnormal pulmonary artery morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'pulmonary valve') and ('has modifier' some abnormal)) MP:0002748 abnormal pulmonary valve morphology HP:0001641 Abnormal pulmonary valve morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'secondary palate') and ('has modifier' some abnormal)) MP:0003755 abnormal palate morphology HP:0000174 Abnormal palate morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some 'tricuspid valve') and ('has modifier' some abnormal)) MP:0002624 abnormal tricuspid valve morphology HP:0001702 Abnormal tricuspid valve morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some aorta) and ('has modifier' some abnormal)) MP:0000272 abnormal aorta morphology HP:0001679 Abnormal aortic morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some brain) and ('has modifier' some abnormal)) MP:0002152 abnormal brain morphology HP:0012443 Abnormality of brain morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some bronchus) and ('has modifier' some abnormal)) MP:0002264 abnormal bronchus morphology HP:0025426 Abnormal bronchus morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some ear) and ('has modifier' some abnormal)) MP:0002102 abnormal ear morphology HP:0031703 Abnormal ear morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some heart) and ('has modifier' some abnormal)) MP:0000266 abnormal heart morphology HP:0001627 Abnormal heart morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some skull) and ('has modifier' some abnormal)) MP:0000438 abnormal cranium morphology HP:0000929 Abnormal skull morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some sternum) and ('has modifier' some abnormal)) MP:0000157 abnormal sternum morphology HP:0000766 Abnormal sternum morphology
abnormalMorphologyOfPartOfAnatomicalEntity 'has part' some (morphology and ('characteristic of part of' some vertebra) and ('has modifier' some abnormal)) MP:0000137 abnormal vertebrae morphology HP:0003468 Abnormal vertebral morphology
@rays22 rays22 added HPO mapping mapping of MP to HP terms patterns usage of and data for Upheno patterns labels Nov 10, 2022
sbello added a commit that referenced this issue Dec 12, 2022
updated some MP patterns to use the HPO patterns for exact matches
added 1 new PATO term to imports
sbello added a commit that referenced this issue Apr 17, 2024
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Labels
HPO mapping mapping of MP to HP terms KidsFirst patterns usage of and data for Upheno patterns
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