diff --git a/src/biomappings/resources/__init__.py b/src/biomappings/resources/__init__.py index 24208a16..47665fc2 100644 --- a/src/biomappings/resources/__init__.py +++ b/src/biomappings/resources/__init__.py @@ -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: diff --git a/src/biomappings/resources/curators.tsv b/src/biomappings/resources/curators.tsv index c912c64b..16ec0ff0 100644 --- a/src/biomappings/resources/curators.tsv +++ b/src/biomappings/resources/curators.tsv @@ -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 diff --git a/src/biomappings/resources/incorrect.tsv b/src/biomappings/resources/incorrect.tsv index 4c72d001..f681255a 100644 --- a/src/biomappings/resources/incorrect.tsv +++ b/src/biomappings/resources/incorrect.tsv @@ -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 +<<<<<<< HEAD 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 @@ -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 +======= +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 @@ -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 +<<<<<<< HEAD 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 @@ -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 +======= +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 @@ -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 +<<<<<<< HEAD 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 +======= +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 diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index f8563968..30eb4507 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -4539,7 +4539,11 @@ mesh C486356 FGF12 protein, human skos:exactMatch uniprot P61328 FGF12 semapv:Ma mesh C486393 RAX protein, human skos:exactMatch uniprot Q9Y2V3 RAX semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C486593 PARVG protein, human skos:exactMatch uniprot Q9HBI0 PARVG semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C486655 BMF protein, human skos:exactMatch uniprot Q96LC9 BMF semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +<<<<<<< HEAD mesh C487483 ANNA-2 antibody, human skos:exactMatch hp HP:5000030 Anti-Ri antibody semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +======= +mesh C487483 ANNA-2 antibody, human skos:exactMatch hp HP:5000030 Anti-Ri antibody semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +>>>>>>> 76968b7c37964c296d08d4492b845e93d78de11c mesh C488098 NXNL1 protein, human skos:exactMatch uniprot Q96CM4 NXNL1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C488261 ZW10 protein, human skos:exactMatch uniprot O43264 ZW10 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C488760 RAET1E protein, human skos:exactMatch uniprot Q8TD07 RAET1E semapv:ManualMappingCuration orcid:0000-0001-9439-5346 @@ -4720,7 +4724,11 @@ mesh C535419 Charcot-Marie-Tooth disease, Type 4A skos:exactMatch doid DOID:0110 mesh C535420 Charcot-Marie-Tooth disease, Type 4B1 skos:exactMatch doid DOID:0110191 Charcot-Marie-Tooth disease type 4B1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535421 Charcot-Marie-Tooth disease, Type 4B2 skos:exactMatch doid DOID:0110190 Charcot-Marie-Tooth disease type 4B2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535436 Bethlem myopathy skos:exactMatch doid DOID:0050663 Bethlem myopathy semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +<<<<<<< HEAD mesh C535438 Bidirectional tachycardia skos:exactMatch hp HP:0034040 Bidirectional ventricular tachycardia semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +======= +mesh C535438 Bidirectional tachycardia skos:exactMatch hp HP:0034040 Bidirectional ventricular tachycardia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +>>>>>>> 76968b7c37964c296d08d4492b845e93d78de11c mesh C535440 Bietti Crystalline Dystrophy skos:exactMatch doid DOID:0050664 Bietti crystalline corneoretinal dystrophy semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535441 Bifid nose skos:exactMatch hp HP:0011803 Bifid nose semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535443 Bile acid synthesis defect, congenital, 2 skos:exactMatch doid DOID:0111069 congenital bile acid synthesis defect 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4754,16 +4762,27 @@ mesh C535566 Absent corpus callosum cataract immunodeficiency skos:exactMatch do mesh C535572 Cantu syndrome skos:exactMatch doid DOID:0060569 hypertrichotic osteochondrodysplasia Cantu type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535579 Cardiofaciocutaneous syndrome skos:exactMatch doid DOID:0060233 cardiofaciocutaneous syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535581 Cardiomyopathy dilated with Woolly hair and keratoderma skos:exactMatch doid DOID:0090128 Carvajal syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +<<<<<<< HEAD mesh C535584 Cardiomyopathy, infantile histiocytoid skos:exactMatch hp HP:0005152 Histiocytoid cardiomyopathy semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh C535584 Cardiomyopathy, infantile histiocytoid skos:exactMatch hp HP:0005152 Histiocytoid cardiomyopathy 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 C535588 Carnitine palmitoyl transferase 1A deficiency skos:exactMatch doid DOID:0090129 carnitine palmitoyltransferase I deficiency semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535600 dopamine beta hydroxylase deficiency skos:exactMatch doid DOID:0090145 dopamine beta-hydroxylase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535601 Dosage-sensitive sex reversal skos:exactMatch doid DOID:0111777 46,XY sex reversal 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535602 Doyne honeycomb retinal dystrophy skos:exactMatch doid DOID:0060745 Doyne honeycomb retinal dystrophy semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535607 Aicardi-Goutieres syndrome skos:exactMatch doid DOID:0050629 Aicardi-Goutieres syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +<<<<<<< HEAD mesh C535618 Hairy elbows skos:exactMatch hp HP:0004780 Elbow hypertrichosis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535627 Hand foot uterus syndrome skos:exactMatch doid DOID:0060739 hand-foot-genital syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535642 Growth retardation, Alopecia, Pseudoanodontia and Optic atrophy skos:exactMatch doid DOID:0112249 GAPO syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535648 Familial primary gastric lymphoma skos:exactMatch hp HP:0045038 Gastric lymphoma semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh C535618 Hairy elbows skos:exactMatch hp HP:0004780 Elbow hypertrichosis semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535627 Hand foot uterus syndrome skos:exactMatch doid DOID:0060739 hand-foot-genital syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C535642 Growth retardation, Alopecia, Pseudoanodontia and Optic atrophy skos:exactMatch doid DOID:0112249 GAPO syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +mesh C535648 Familial primary gastric lymphoma skos:exactMatch hp HP:0045038 Gastric lymphoma 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 C535658 Acromesomelic dysplasia skos:exactMatch doid DOID:0080049 acromesomelic dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535661 Acromesomelic dysplasia, Maroteaux type skos:exactMatch doid DOID:0080050 acromesomelic dysplasia, Maroteaux type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535662 Acromicric dysplasia skos:exactMatch doid DOID:0111243 acromicric dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4790,7 +4809,11 @@ mesh C535780 Spondylocarpotarsal synostosis skos:exactMatch doid DOID:0090116 sp mesh C535786 Spondyloepimetaphyseal dysplasia, sponastrime type skos:exactMatch doid DOID:5684 spondyloepimetaphyseal dysplasia, Sponastrime type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535788 Spondyloepiphyseal dysplasia, congenita skos:exactMatch doid DOID:14789 spondyloepiphyseal dysplasia congenita semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535789 Spondyloepiphyseal dysplasia, Omani type skos:exactMatch doid DOID:0050813 spondyloepiphyseal dysplasia with congenital joint dislocations semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +<<<<<<< HEAD mesh C535802 Sprengel deformity skos:exactMatch hp HP:0000912 Sprengel anomaly semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh C535802 Sprengel deformity skos:exactMatch hp HP:0000912 Sprengel anomaly 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 C535803 succinic semialdehyde dehydrogenase deficiency skos:exactMatch doid DOID:0060175 succinic semialdehyde dehydrogenase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535811 Molybdenum cofactor deficiency skos:exactMatch hp HP:0003570 Molybdenum cofactor deficiency semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535813 Neuropathy, hereditary motor and sensory, Russe type skos:exactMatch doid DOID:0110196 Charcot-Marie-Tooth disease type 4G semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4845,7 +4868,11 @@ mesh C536096 Myoclonic dystonia skos:exactMatch doid DOID:0090033 myoclonic dyst mesh C536102 Myopathy, congenital nonprogressive with Moebius and Robin sequences skos:exactMatch doid DOID:0080194 Carey-Fineman-Ziter syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536106 Myostatin-related muscle hypertrophy skos:exactMatch doid DOID:0111072 myostatin-related muscle hypertrophy semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536108 N syndrome skos:exactMatch doid DOID:0050769 N syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +<<<<<<< HEAD mesh C536111 Partial agenesis of corpus callosum skos:exactMatch hp HP:0001338 Partial agenesis of the corpus callosum semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh C536111 Partial agenesis of corpus callosum skos:exactMatch hp HP:0001338 Partial agenesis of the corpus callosum 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 C536123 Nivelon Nivelon Mabille syndrome skos:exactMatch doid DOID:0060644 chondrodysplasia-pseudohermaphroditism syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536129 Achromatopsia 3 skos:exactMatch doid DOID:0110008 achromatopsia 3 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536131 Meckel syndrome type 2 skos:exactMatch doid DOID:0070116 Meckel syndrome 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4922,7 +4949,11 @@ mesh C536494 Uveal melanoma skos:exactMatch hp HP:0007716 Uveal melanoma semapv: mesh C536495 VACTERL association skos:exactMatch doid DOID:14679 VACTERL association semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536510 Thiamine responsive megaloblastic anemia syndrome skos:exactMatch doid DOID:0090117 thiamine-responsive megaloblastic anemia syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536512 Thiopurine S methyltranferase deficiency skos:exactMatch doid DOID:0080172 thiopurine S-methyltransferase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +<<<<<<< HEAD mesh C536524 Valinemia skos:exactMatch hp HP:0010910 Hypervalinemia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh C536524 Valinemia skos:exactMatch hp HP:0010910 Hypervalinemia 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 C536525 Valproic acid antenatal infection skos:exactMatch doid DOID:0060471 fetal valproate syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536528 Van der Woude syndrome skos:exactMatch doid DOID:0060239 Van der Woude syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536530 Van Maldergem Wetzburger Verloes syndrome skos:exactMatch doid DOID:0060238 Van Maldergem syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -5242,7 +5273,11 @@ mesh C538344 Navajo neurohepatopathy skos:exactMatch doid DOID:0080125 mitochond mesh C538346 Naxos disease skos:exactMatch doid DOID:0080551 Naxos disease semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538348 Nemaline myopathy 1 skos:exactMatch doid DOID:0110926 nemaline myopathy 1 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538351 Nemaline myopathy 4 skos:exactMatch doid DOID:0110932 nemaline myopathy 4 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +<<<<<<< HEAD mesh C538354 Potato nose skos:exactMatch hp HP:0000414 Bulbous nose semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh C538354 Potato nose skos:exactMatch hp HP:0000414 Bulbous nose 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 C538355 Potocki-Lupski syndrome skos:exactMatch doid DOID:0060853 Potocki-Lupski syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538356 Potocki-Shaffer syndrome skos:exactMatch doid DOID:0111687 Potocki-Shaffer syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538361 Reticular dysgenesis skos:exactMatch doid DOID:0060020 reticular dysgenesis semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -5310,7 +5345,11 @@ mesh C562489 Lymphoid Interstitial Pneumonia skos:exactMatch doid DOID:0050159 l mesh C562509 Popliteal Pterygium Syndrome skos:exactMatch doid DOID:0060055 popliteal pterygium syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C562524 Fibrochondrogenesis skos:exactMatch doid DOID:0060465 fibrochondrogenesis semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C562538 Cerebrocostomandibular Syndrome skos:exactMatch doid DOID:0111248 cerebrocostomandibular syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +<<<<<<< HEAD mesh C562546 Megalodactyly skos:exactMatch hp HP:0004099 Macrodactyly semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh C562546 Megalodactyly skos:exactMatch hp HP:0004099 Macrodactyly 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 C562562 Colonic Atresia skos:exactMatch hp HP:0010448 Colonic atresia semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C562563 Microcolon skos:exactMatch hp HP:0004388 Microcolon semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C562568 Cerebellar Hypoplasia skos:exactMatch doid DOID:0070338 cerebellar hypoplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -6034,7 +6073,11 @@ mesh D000009 Abdominal Muscles skos:exactMatch ncit C32040 Abdominal Muscle sema mesh D000019 Abortifacient Agents skos:exactMatch chebi CHEBI:50691 abortifacient semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000022 Abortion, Spontaneous skos:exactMatch ncit C34336 Spontaneous Abortion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000038 Abscess skos:exactMatch hp HP:0025615 Abscess semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +<<<<<<< HEAD mesh D000058 Accidental Falls skos:exactMatch hp HP:0002527 Falls semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +======= +mesh D000058 Accidental Falls skos:exactMatch hp HP:0002527 Falls 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 D000066450 Mouse Embryonic Stem Cells skos:exactMatch efo 0004038 mouse embryonic stem cell semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000066530 Neurological Rehabilitation skos:exactMatch ncit C157934 Neurological Rehabilitation semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000067128 Extracellular Vesicles skos:exactMatch go GO:1903561 extracellular vesicle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 @@ -8791,7 +8834,7 @@ mesh D064794 Lorajmine skos:exactMatch chebi CHEBI:135646 lorajmine semapv:Manua mesh D064800 Prolyl-Hydroxylase Inhibitors skos:exactMatch chebi CHEBI:132365 EC 1.14.11.2 (procollagen-proline dioxygenase) inhibitor semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D064801 Phospholipase A2 Inhibitors skos:exactMatch chebi CHEBI:50469 EC 3.1.1.4 (phospholipase A2) inhibitor semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064847 Multimodal Imaging skos:exactMatch ncit C19341 Multimodal Imaging semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -mesh D064878 Web Browser skos:exactMatch ncit C142748 Web Browser semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +mesh D064878 orcid:0009-0006-0654-7594 Browser skos:exactMatch ncit C142748 orcid:0009-0006-0654-7594 Browser semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064886 Dataset skos:exactMatch ncit C47824 Data Set semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064888 Observational Study skos:exactMatch ncit C16084 Observational Study semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064890 Social Determinants of Health skos:exactMatch ncit C171586 Social Determinants of Health semapv:ManualMappingCuration orcid:0000-0001-9439-5346 diff --git a/src/biomappings/testing.py b/src/biomappings/testing.py index 42d08cad..6e86550d 100644 --- a/src/biomappings/testing.py +++ b/src/biomappings/testing.py @@ -9,6 +9,7 @@ import bioregistry from biomappings.resources import ( + CURATORS_PATH, Mappings, MappingTuple, PredictionTuple, @@ -126,7 +127,9 @@ def test_contributors(self): for mapping in itt.chain(self.mappings, self.incorrect, self.unsure): source = mapping["source"] if not source.startswith("orcid:"): - continue + self.assertTrue(source.startswith("web-")) + ss = source[len("web-") :] + self.fail(msg=f'Add an entry with "{ss}" and your ORCID to {CURATORS_PATH}') self.assertIn(source[len("orcid:") :], contributor_orcids) def test_cross_redundancy(self): diff --git a/src/biomappings/wsgi.py b/src/biomappings/wsgi.py index 306e409f..6e44fa65 100644 --- a/src/biomappings/wsgi.py +++ b/src/biomappings/wsgi.py @@ -132,11 +132,12 @@ def get_app( KNOWN_USERS = {record["user"]: record["orcid"] for record in load_curators()} -def _manual_source(): - known_user = KNOWN_USERS.get(getpass.getuser()) +def _manual_source() -> str: + usr = getpass.getuser() + known_user = KNOWN_USERS.get(usr) if known_user: return f"orcid:{known_user}" - return "web" + return f"web-{usr}" class Controller: