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Fix mappings
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@cthoyt
cthoyt committed Aug 24, 2023
1 parent 76968b7 commit a4c34e7
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Showing 4 changed files with 6 additions and 6 deletions.
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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3 changes: 3 additions & 0 deletions src/biomappings/resources/incorrect.tsv
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Expand Up @@ -613,6 +613,7 @@ mesh C536277 Idiopathic dilation cardiomyopathy skos:exactMatch doid DOID:011042
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 web 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 Down Expand Up @@ -681,9 +682,11 @@ 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 web 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 web 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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2 changes: 2 additions & 0 deletions src/biomappings/resources/mappings.tsv
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Expand Up @@ -5061,6 +5061,7 @@ mesh C537210 Knuckle pads, leuconychia and sensorineural deafness skos:exactMatc
mesh C537213 Kohlschutter Tonz syndrome skos:exactMatch doid DOID:0111668 Kohlschutter-Tonz syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C537218 Saccharopinuria skos:exactMatch hp HP:0034028 Saccharopinuria semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9
mesh C537227 Sakati syndrome skos:exactMatch doid DOID:0060359 Sakati-Nyhan syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C537236 Sarcosinemia skos:exactMatch hp HP:0010896 Hypersarcosinemia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh C537247 Hemochromatosis, type 2 skos:exactMatch doid DOID:0111034 hemochromatosis type 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C537248 Hemochromatosis, type 3 skos:exactMatch doid DOID:0111030 hemochromatosis type 3 semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh C537249 Hemochromatosis, type 4 skos:exactMatch doid DOID:0111028 hemochromatosis type 4 semapv:ManualMappingCuration orcid:0000-0003-1307-2508
Expand Down Expand Up @@ -7068,6 +7069,7 @@ mesh D005283 Fentanyl skos:exactMatch chebi CHEBI:119915 fentanyl semapv:ManualM
mesh D005285 Fermentation skos:exactMatch go GO:0006113 fermentation semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D005306 Fertilization skos:exactMatch go GO:0009566 fertilization semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D005316 Fetal Distress skos:exactMatch hp HP:0025116 Fetal distress semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D005330 Fetofetal Transfusion skos:exactMatch hp HP:0031110 Twin-to-twin transfusion semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9
mesh D005342 Fibrinolysis skos:exactMatch go GO:0042730 fibrinolysis semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D005348 Fibrocystic Breast Disease skos:exactMatch doid DOID:5998 microglandular adenosis semapv:ManualMappingCuration orcid:0000-0003-1307-2508
mesh D005350 Fibroma skos:exactMatch doid DOID:0050871 fibroma semapv:ManualMappingCuration orcid:0000-0001-9439-5346
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5 changes: 0 additions & 5 deletions src/biomappings/resources/predictions.tsv
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Expand Up @@ -24584,7 +24584,6 @@ mesh C536980 Transient erythroblastopenia of childhood skos:exactMatch ncit C131
mesh C537007 Kaposiform Hemangioendothelioma skos:exactMatch ncit C27510 Kaposiform Hemangioendothelioma semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537029 Lipomatous hemangiopericytoma skos:exactMatch ncit C27499 Lipomatous Hemangiopericytoma semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537048 Allanson Pantzar McLeod syndrome skos:exactMatch hp HP:0008660 Renotubular dysgenesis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537068 Focal facial dermal dysplasia skos:exactMatch hp HP:0011336 Bitemporal forceps marks semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537079 Bare lymphocyte syndrome 2 skos:exactMatch ncit C171268 Bare Lymphocyte Syndrome Type 2 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537080 Baritosis skos:exactMatch ncit C34410 Baritosis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537108 Chromosome 21 monosomy skos:exactMatch ncit C36469 Monosomy 21 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
Expand All @@ -24595,7 +24594,6 @@ mesh C537168 Papillorenal syndrome skos:exactMatch ncit C123230 Renal Coloboma S
mesh C537180 Familial paroxysmal dystonia skos:exactMatch doid DOID:0090053 episodic kinesigenic dyskinesia 1 semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py
mesh C537206 Spinocerebellar Ataxia 29 skos:exactMatch hp HP:0002335 Agenesis of cerebellar vermis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537234 Sandifer syndrome skos:exactMatch ncit C113397 Sandifer's Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537236 Sarcosinemia skos:exactMatch hp HP:0010896 Hypersarcosinemia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537256 Vascular purpura skos:exactMatch ncit C35499 Vascular Purpura semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537267 Langer mesomelic dysplasia skos:exactMatch ncit C126876 Langer Mesomelic Dysplasia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh C537297 Autosomal Dominant Lateral Temporal Lobe Epilepsy skos:exactMatch ncit C141441 Autosomal Dominant Lateral Temporal Lobe Epilepsy semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
Expand Down Expand Up @@ -29248,7 +29246,6 @@ mesh D004397 Fonofos skos:exactMatch ncit C163659 Fonofos semapv:LexicalMatching
mesh D004400 Dyphylline skos:exactMatch chebi CHEBI:4728 dyphylline semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D004402 Dysautonomia, Familial skos:exactMatch ncit C84706 Familial Dysautonomia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D004404 Dysentery, Amebic skos:exactMatch ncit C34558 Amebic Colitis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D004408 Dysgeusia skos:exactMatch hp HP:0031249 Parageusia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D004410 Dyslexia skos:exactMatch ncit C96410 Dyslexia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D004413 Dysostoses skos:exactMatch ncit C34560 Dysostosis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D004416 Dysplastic Nevus Syndrome skos:exactMatch ncit C7584 Dysplastic Nevus Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
Expand Down Expand Up @@ -29554,7 +29551,6 @@ mesh D005051 Eubacterium skos:exactMatch ncit C86383 Eubacterium semapv:LexicalM
mesh D005052 Eucalyptus skos:exactMatch ncit C72308 Eucalyptus globulus semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005054 Eugenol skos:exactMatch chebi CHEBI:4917 eugenol semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005057 Eukaryotic Cells skos:exactMatch ncit C12596 Eukaryotic Cells semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005058 Eunuchism skos:exactMatch hp HP:0008720 Primary testicular failure semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005060 Europe skos:exactMatch ncit C26274 Europe semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005062 European Union skos:exactMatch ncit C45252 European Union semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005063 Europium skos:exactMatch chebi CHEBI:32999 europium atom semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
Expand Down Expand Up @@ -29677,7 +29673,6 @@ mesh D005317 Fetal Growth Retardation skos:exactMatch ncit C114875 Fetus Small f
mesh D005318 Fetal Heart skos:exactMatch ncit C34167 Fetal Heart semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005320 Fetal Macrosomia skos:exactMatch hp HP:0001520 Large for gestational age semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py
mesh D005320 Fetal Macrosomia skos:exactMatch ncit C113486 Fetal Macrosomia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005330 Fetofetal Transfusion skos:exactMatch hp HP:0031110 Twin-to-twin transfusion semapv:LexicalMatching 0.9 generate_hp_mesh_mappings.py
mesh D005330 Fetofetal Transfusion skos:exactMatch ncit C113824 Twin-Twin Transfusion Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005331 Fetomaternal Transfusion skos:exactMatch ncit C113149 Fetal-Maternal Hemorrhage semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
mesh D005333 Fetus skos:exactMatch ncit C13235 Fetus semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py
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