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Add test curations #146

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Add test curations #146

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0523be1
Curated 1 mapping (sangeethavempati)
svempati21 Aug 14, 2023
5e56d00
Curated 2 mappings (sangeethavempati)
svempati21 Aug 14, 2023
2cda2c5
Curated 15 mappings (sangeethavempati)
svempati21 Aug 17, 2023
76968b7
Update provenance
cthoyt Aug 18, 2023
a4c34e7
Fix mappings
cthoyt Aug 24, 2023
a3ed312
Update provenance and tests
cthoyt Aug 31, 2023
09b2eed
Merge branch 'master' into sangeetha
cthoyt Aug 31, 2023
900e4f6
Update mappings.tsv
cthoyt Aug 31, 2023
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2 changes: 1 addition & 1 deletion src/biomappings/resources/__init__.py
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Expand Up @@ -183,7 +183,7 @@ def _load_table(fname) -> List[Dict[str, str]]:


def _clean(header, row):
d = dict(zip(header, row))
d = dict(itt.zip_longest(header, row, fillvalue=None))
return {k: v if v else None for k, v in d.items()}


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1 change: 1 addition & 0 deletions src/biomappings/resources/curators.tsv
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Expand Up @@ -6,3 +6,4 @@ ddomingof 0000-0002-2046-6145 Daniel Domingo-Fernandez
cmungall 0000-0002-6601-2165 Christopher Mungall
KrishnaTO 0000-0002-2627-0696 Krishna Udaiwal
sumir 0000-0002-1216-4761 Sumir Pandit
sangeethavempati 0009-0006-0654-7594 Sangeetha Vempati
11 changes: 11 additions & 0 deletions src/biomappings/resources/incorrect.tsv
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Expand Up @@ -608,16 +608,21 @@ mesh C477269 3 beta-hydroxy-delta 5-steroid dehydrogenase, rat skos:exactMatch g
mesh C509674 marinocine protein, Marinomonas mediterranea skos:exactMatch go GO:0033736 L-lysine 6-oxidase activity semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh C531673 Familial ependymoma skos:exactMatch doid DOID:5509 pediatric ependymoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C531763 Irritable heart skos:exactMatch doid DOID:0111154 postural orthostatic tachycardia syndrome semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh C535425 Congenital torticollis skos:exactMatch hp HP:0005988 Congenital muscular torticollis semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh C535442 Bile acid synthesis defect, congenital, 1 skos:exactMatch doid DOID:0050674 congenital bile acid synthesis defect semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C535536 Iridogoniodysgenesis, dominant type skos:exactMatch doid DOID:0050786 iridogoniodysgenesis syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C535568 Absent patella skos:exactMatch hp HP:0006443 Patellar aplasia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh C535837 Pancreatic carcinoma, familial skos:exactMatch doid DOID:4905 pancreatic carcinoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C535847 Hay-Wells syndrome skos:exactMatch doid DOID:0090119 ankyloblepharon-ectodermal defects-cleft lip/palate syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C535968 Hereditary macular coloboma skos:exactMatch hp HP:0001116 Macular coloboma semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh C536021 Achromatopsia 1 skos:exactMatch hp HP:0011516 Achromatopsia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh C536133 Meckel syndrome type 1 skos:exactMatch doid DOID:0050778 Meckel syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh C536192 Brittle cornea syndrome 1 skos:exactMatch doid DOID:14775 brittle cornea syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C536277 Idiopathic dilation cardiomyopathy skos:exactMatch doid DOID:0110429 dilated cardiomyopathy 1H semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C536300 Partington X-linked mental retardation syndrome skos:exactMatch doid DOID:14744 Partington syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C536439 Corneal endothelial dystrophy type 2 skos:exactMatch doid DOID:0110855 posterior polymorphous corneal dystrophy 1 semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C536645 Pemphigus vulgaris, familial skos:exactMatch doid DOID:0060851 pemphigus vulgaris semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C537068 Focal facial dermal dysplasia skos:exactMatch hp HP:0011336 Bitemporal forceps marks semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh C537137 Orstavik Lindemann Solberg syndrome skos:exactMatch doid DOID:0111591 congenital heart defects, hamartomas of tongue, and polysyndactyly semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C537519 Schwartz-Lelek syndrome skos:exactMatch doid DOID:0080033 craniometaphyseal dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C537996 Dysgnathia complex skos:exactMatch doid DOID:0060341 agnathia-otocephaly complex semapv:ManualMappingCuration orcid:0000-0003-1307-2508
Expand All @@ -641,11 +646,14 @@ mesh D000068256 Darbepoetin alfa skos:exactMatch hgnc 4392 GNAS semapv:ManualMap
mesh D000068437 Pemetrexed skos:exactMatch chebi CHEBI:17509 5'-S-methyl-5'-thioadenosine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000068800 Etanercept skos:exactMatch hgnc 11917 TNFRSF1B semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000070636 Rotator Cuff Injuries skos:exactMatch efo 1001250 rotator cuff tear semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000070636 Rotator Cuff Injuries skos:exactMatch hp HP:0032201 Rotator cuff tear semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9
mesh D000071636 Protein Phosphatase 2C skos:exactMatch hgnc 9279 PDP1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D000074767 Diapause skos:exactMatch go GO:0030431 sleep semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000075529 Solitary Kidney skos:exactMatch hp HP:0000122 Unilateral renal agenesis semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95
mesh D000077190 Interferon alpha-2 skos:exactMatch hgnc 5423 IFNA2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000077212 Ropivacaine skos:exactMatch chebi CHEBI:8890 (S)-ropivacaine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000077324 Crystalloid Solutions skos:exactMatch go GO:0044312 crystalloid semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000152 Acne Vulgaris skos:exactMatch hp HP:0001061 Acne semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9
mesh D000203 Activities of Daily Living skos:exactMatch efo 0008451 activities of daily living score measurement semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D000309 Adrenal Insufficiency skos:exactMatch doid DOID:10493 adrenal cortical hypofunction semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D000371 Agglutination skos:exactMatch go GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules semapv:ManualMappingCuration orcid:0000-0003-4423-4370
Expand All @@ -666,6 +674,7 @@ mesh D001661 Biliary Tract Neoplasms skos:exactMatch doid DOID:0050625 biliary t
mesh D001731 Bisphosphoglycerate Mutase skos:exactMatch go GO:0004619 phosphoglycerate mutase activity semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D001749 Urinary Bladder Neoplasms skos:exactMatch doid DOID:4007 bladder carcinoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D001761 Bleomycin skos:exactMatch chebi CHEBI:3139 bleomycin A2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D001766 Blindness skos:exactMatch hp HP:0000572 Visual loss semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95
mesh D001792 Blood Platelets skos:exactMatch efo 0009237 Estimated Platelets Measurement semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D001859 Bone Neoplasms skos:exactMatch efo 1000350 Malignant Bone Neoplasm semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D001907 Boutonneuse Fever skos:exactMatch doid DOID:0050035 African tick-bite fever semapv:ManualMappingCuration orcid:0000-0003-1307-2508
Expand All @@ -682,9 +691,11 @@ mesh D003884 Dermoid Cyst skos:exactMatch doid DOID:5117 dermoid cyst of ovary s
mesh D003924 Diabetes Mellitus, Type 2 skos:exactMatch doid DOID:0050524 maturity-onset diabetes of the young semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D003925 Diabetic Angiopathies skos:exactMatch doid DOID:10182 diabetic peripheral angiopathy semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D004407 Dysgerminoma skos:exactMatch doid DOID:5511 dysgerminoma of ovary semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D004408 Dysgeusia skos:exactMatch hp HP:0031249 Parageusia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh D004410 Dyslexia skos:exactMatch doid DOID:13365 reading disorder semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D004697 Endocarditis, Bacterial skos:exactMatch doid DOID:0060000 infective endocarditis semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D004932 Esophageal and Gastric Varices skos:exactMatch doid DOID:112 esophageal varix semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D005058 Eunuchism skos:exactMatch hp HP:0008720 Primary testicular failure semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh D005234 Fatty Liver skos:exactMatch efo 0008527 steatosis semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D005319 Fetal Hemoglobin skos:exactMatch efo 0004576 fetal hemoglobin measurement semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D005351 Fibromatosis, Gingival skos:exactMatch doid DOID:0060466 gingival fibromatosis semapv:ManualMappingCuration orcid:0000-0003-1307-2508
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