Skip to content

Commit

Permalink
Merge pull request #40 from mapping-commons/addCongenitalHeartDisease
Browse files Browse the repository at this point in the history 
adding terms for CHD models
  • Loading branch information
@sbello
sbello authored Jan 25, 2024
2 parents 826c000 + a208e05 commit 23dbe53
Showing 1 changed file with 38 additions and 0 deletions.
38 changes: 38 additions & 0 deletions mappings/mp_hp_mgi_all.sssom.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1535,3 +1535,41 @@ HP:0020222 Hypohomocysteinemia skos:exactMatch 1 MP:0012334 decreased circulatin
HP:0100961 Enlarged hippocampus skos:broadMatch 1 MP:0020082 increased hippocampus volume semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2023-11-16 Down Syndrome
HP:0034011 Reduced progressive sperm motility skos:exactMatch 0.9 MP:0020451 decreased sperm progressive motility semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2023-10-13 Down Syndrome| possibility the the HP term is slightly broader based on the text definition but I think the intent is for these to describe the same phenotype
HP:0100961 Enlarged hippocampus skos:exactMatch 1 MP:0008282 enlarged hippocampus semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2023-11-16
HP:0000069 Abnormality of the ureter skos:broadMatch 1 MP:0000534 abnormal ureter morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0000069 Abnormality of the ureter skos:broadMatch 1 MP:0003589 abnormal ureter physiology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0001760 Abnormal foot morphology skos:narrowMatch 1 MP:0000572 abnormal autopod morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25 ask Leigh to check the HP definition as this specifies 'skeleton' of the foot
HP:0002101 Abnormal lung lobation skos:broadMatch 1 MP:0011011 impaired lung lobe morphogenesis semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25 "calling this broad as the MP term is defined as failure to form any of the lobes, we should review the MP definition and usage as it is unclear does this mean at least 1 lobe is affected or that all lobes are affected"
HP:0002245 Meckel diverticulum skos:narrowMatch 1 MP:0002581 abnormal ileum morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0002594 Pancreatic hypoplasia skos:broadMatch 1 MP:0009111 pancreas hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25 HP term is defined as 'hypoplasia' but has underdevelopment as a synonym so I went with broad
HP:0003115 Abnormal EKG skos:exactMatch 0.7 MP:0010508 abnormal heart electrocardiography waveform feature semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25 "check with Leigh, the HP definition is abnormal rhythm and that doesn't seem right"
HP:0004414 Abnormality of the pulmonary artery skos:broadMatch 1 MP:0000484 abnormal pulmonary artery morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25 the HP term has both morphology and physiology child terms but lives on the morphoogy branch
HP:0008771 Aplasia/Hypoplasia of the ear skos:broadMatch 1 MP:0003679 ear lobe hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0008771 Aplasia/Hypoplasia of the ear skos:broadMatch 1 MP:0006286 inner ear hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0010872 T-wave inversion skos:narrowMatch 1 MP:0010505 abnormal T wave semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0011603 Congenital malformation of the great arteries skos:narrowMatch 1 MP:0002191 abnormal artery morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0011615 Abnormal pulmonary situs morphology skos:narrowMatch 1 MP:0010853 abnormal lung position or orientation semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0012243 Abnormal reproductive system morphology skos:exactMatch 1 MP:0002160 abnormal reproductive system morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0010948 Abnormal fetal cardiovascular morphology skos:narrowMatch 1 MP:0000267 abnormal heart development semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0010948 Abnormal fetal cardiovascular morphology skos:broadMatch 0.9 MP:0000269 abnormal heart looping semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0003811 Neonatal death skos:narrowMatch 1 MP:0002081 perinatal lethality semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0006705 Abnormal atrioventricular valve morphology skos:exactMatch 0.8 MP:0002745 abnormal atrioventricular valve morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 the definition of the HPO term does not specify morphology but the term label and placement indicates this is supposed to be morphology so I called this an exact match
HP:0001646 Abnormal aortic valve morphology skos:narrowMatch 1 MP:0002746 abnormal semilunar valve morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 HPO lacks the grouping term so I mapped to the 2 specific valves
HP:0001641 Abnormal pulmonary valve morphology skos:narrowMatch 1 MP:0002746 abnormal semilunar valve morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0001696 Situs inversus totalis skos:narrowMatch 0.9 MP:0002766 situs inversus semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 "Placement of these terms is very different, in HPO these are under heart morphology while in the MP these are under heterotaxia, not sure why the HP terms are not under heterotaxy"
HP:0031592 Situs inversus with levocardia skos:narrowMatch 0.9 MP:0002766 situs inversus semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0005120 Abnormal cardiac atrium morphology skos:exactMatch 1 MP:0003105 abnormal heart atrium morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0001669 Transposition of the great arteries skos:exactMatch 1 MP:0004110 transposition of great arteries semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0001713 Abnormal cardiac ventricle morphology skos:exactMatch 0.8 MP:0005294 abnormal heart ventricle morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 the definition of the HPO term does not specify morphology but the term label and placement indicates this is supposed to be morphology so I called this an exact match
HP:0010883 Aortic valve atresia skos:exactMatch 0.9 MP:0006115 aortic valve atresia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 definitions are written differently but I think they are intended to be the same
HP:0006677 Prolonged QRS complex skos:exactMatch 0.9 MP:0010392 prolonged QRS complex duration semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 some uncertainty based on inclusion of 'duration' in the MP term but I think these are the same
HP:0004762 Hypoplasia of right ventricle skos:broadMatch 0.9 MP:0010422 heart right ventricle hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 "HP uses hypoplasia for 'reduced size' not just from decreased cell number, MP only uses hypoplasia for decreased size due to decreased cell number"
HP:0001711 Abnormal left ventricle morphology skos:broadMatch 1 MP:0010446 heart left ventricle hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24
HP:0030962 Abnormal morphology of the great vessels skos:broadMatch 0.8 MP:0010458 pulmonary trunk hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 does the trunk count as a great vessel? It seemed like the best fit and made sense since the trunk splits into the pulmonary arteries and these are great vessels
HP:0004971 Pulmonary artery hypoplasia skos:broadMatch 0.9 MP:0010460 pulmonary artery hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-24 HP defined as underdevelopment while MP is specifically reduced cell number
HP:0012304 Hypoplastic aortic arch skos:broadMatch 0.9 MP:0010485 aortic arch hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25 HP defined as underdevelopment while MP is specifically reduced cell number
HP:0001679 Abnormal aortic morphology skos:broadMatch 0.9 MP:0010541 aorta hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0001711 Abnormal left ventricle morphology skos:broadMatch 0.9 MP:0010580 decreased heart left ventricle size semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0003819 Death in childhood skos:closeMatch 1 MP:0011085 "postnatal lethality, complete penetrance" semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0011573 Hypoplastic tricuspid valve skos:broadMatch 0.9 MP:0011680 tricuspid valve hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25 HP defined as underdevelopment while MP is specifically reduced cell number
HP:0001627 Abnormal heart morphology skos:broadMatch 1 MP:0012515 abnormal heart apex morphology semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25
HP:0001633 Abnormal mitral valve morphology skos:broadMatch 1 MP:0031523 mitral valve hypoplasia semapv:ManualMappingCuration orcid:0000-0003-4606-0597 2024-01-25

0 comments on commit 23dbe53

Please sign in to comment.