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Curated 5 mappings (sangeethavempati)
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@svempati21
svempati21 committed Aug 23, 2023
2 parents ad0cf85 + 76968b7 commit 93383c1
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Showing 6 changed files with 83 additions and 6 deletions.
5 changes: 4 additions & 1 deletion src/biomappings/resources/__init__.py
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Expand Up @@ -477,9 +477,12 @@ def _standardize_mapping(mapping):
return mapping


CURATORS_PATH = get_resource_file_path("curators.tsv")


def load_curators():
"""Load the curators table."""
return _load_table(get_resource_file_path("curators.tsv"))
return _load_table(CURATORS_PATH)


def filter_predictions(custom_filter: Mapping[str, Mapping[str, Mapping[str, str]]]) -> None:
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1 change: 1 addition & 0 deletions src/biomappings/resources/curators.tsv
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Expand Up @@ -5,3 +5,4 @@ hoytfamily 0000-0003-1307-2508 Amelia Hoyt
ddomingof 0000-0002-2046-6145 Daniel Domingo-Fernandez
cmungall 0000-0002-6601-2165 Christopher Mungall
KrishnaTO 0000-0002-2627-0696 Krishna Udaiwal
sangeethavempati 0009-0006-0654-7594 Sangeetha Vempati
26 changes: 26 additions & 0 deletions src/biomappings/resources/incorrect.tsv
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Expand Up @@ -599,6 +599,7 @@ 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
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mesh C535425 Congenital torticollis skos:exactMatch hp HP:0005988 Congenital muscular torticollis semapv:ManualMappingCuration web 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
Expand All @@ -607,6 +608,16 @@ mesh C535837 Pancreatic carcinoma, familial skos:exactMatch doid DOID:4905 pancr
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 web 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 web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
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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
>>>>>>> 76968b7c37964c296d08d4492b845e93d78de11c
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
Expand Down Expand Up @@ -637,6 +648,7 @@ 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
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mesh D000070636 Rotator Cuff Injuries skos:exactMatch hp HP:0032201 Rotator cuff tear semapv:ManualMappingCuration web 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
Expand All @@ -645,6 +657,16 @@ mesh D000077190 Interferon alpha-2 skos:exactMatch hgnc 5423 IFNA2 semapv:Manual
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 web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9
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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
>>>>>>> 76968b7c37964c296d08d4492b845e93d78de11c
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 @@ -665,7 +687,11 @@ 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
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mesh D001766 Blindness skos:exactMatch hp HP:0000572 Visual loss semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95
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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
>>>>>>> 76968b7c37964c296d08d4492b845e93d78de11c
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
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