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Merge pull request #360 from TranslatorSRI/add-manual-concords
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Some additional manual concords for Disease/Phenotype cliques and DrugChemical conflation.
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@gaurav
gaurav authored Nov 4, 2024
2 parents 321490a + abfdd64 commit 242c179
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Showing 2 changed files with 31 additions and 17 deletions.
13 changes: 13 additions & 0 deletions input_data/manual_concords/disease.txt
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Expand Up @@ -111,3 +111,16 @@ MONDO:0007079 oio:closeMatch UMLS:C4536264
# Not sure why MONDO:0005799 isn't connecting with MONDO:0005799, but we can connect it manually here.
# See https://github.com/NCATSTranslator/Tests/issues/92
MONDO:0005799 xref MESH:D006725

# These pairs were reported by Gwenlyn in https://github.com/TranslatorSRI/Babel/issues/333
MONDO:0007540 oio:closeMatch DOID:10017
HP:0003124 oio:closeMatch NCIT:C37967
EFO:1001393 oio:closeMatch UMLS:C0031094
EFO:0006911 oio:closeMatch UMLS:C0401160
EFO:1001404 oio:closeMatch UMLS:C0032805
MONDO:0017169 oio:closeMatch DOID:3125
EFO:1001390 oio:closeMatch UMLS:C2936258
HP:0040412 oio:closeMatch UMLS:C0587044
EFO:1001348 oio:closeMatch UMLS:C1136321
MONDO:0015517 oio:closeMatch DOID:12177
EFO:1001863 oio:closeMatch UMLS:C0042135
35 changes: 18 additions & 17 deletions input_data/manual_concords/drugchemical.tsv
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Expand Up @@ -12,20 +12,21 @@ MESH:D007252 skos:exactMatch CHEMBL.COMPOUND:CHEMBL2109042 "They should be combi
MESH:C415772 skos:exactMatch CHEMBL.COMPOUND:CHEMBL2108230 "They should be combined, but they’re not — we can temporarily fix it in DrugChemical conflation, but we should figure out a comprehensive solution to this." https://github.com/TranslatorSRI/NodeNormalization/issues/224
UNII:A1ED6W905I skos:exactMatch CHEMBL.COMPOUND:CHEMBL2108230 "They should be combined, but they’re not — we can temporarily fix it in DrugChemical conflation, but we should figure out a comprehensive solution to this." https://github.com/TranslatorSRI/NodeNormalization/issues/224
UNII:XX73205DH5 skos:exactMatch CHEMBL.COMPOUND:CHEMBL2367706 "They should be combined, but they’re not — we can temporarily fix it in DrugChemical conflation, but we should figure out a comprehensive solution to this." https://github.com/TranslatorSRI/Babel/issues/230
CHEBI:5931 skos:exactMatch PUBCHEM.COMPOUND:70678557 Both “Insulin” https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch DRUGBANK:DB00030 Insulin and “Insulin human” https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:GFX7QIS1II "Insulin and ""Insulin lispro""
" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:2ZM8CX04RZ "Insulin and ""Insulin glargine""
" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch DRUGBANK:DB18001 "Insulin and ""Neutral Protamine Hagedorn (NPH) insulin""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:D933668QVX "Insulin and ""Insulin aspart""
" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:AVT680JB39 "Insulin and ""Insulin pork""
" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:54Q18076QB "Insulin and “Insulin degludec""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:4FT78T86XV "Insulin and ""Insulin detemir""
" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:7XIY785AZD "Insulin and ""Insulin glulisine”" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch CHEBI:228608 "Insulin and ""Insulin beef”" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:54Q18076QB "Insulin and ""Insulin degludec""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch PUBCHEM.COMPOUND:70678557 Both “Insulin” https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch DRUGBANK:DB00030 Insulin and “Insulin human” https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:GFX7QIS1II "Insulin and ""Insulin lispro""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:2ZM8CX04RZ "Insulin and ""Insulin glargine""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:narrowMatch RXCUI:1736859 Insulin and “insulin glargine 100 UNT/ML [Basaglar]” https://github.com/TranslatorSRI/Babel/issues/356
CHEBI:5931 skos:exactMatch DRUGBANK:DB18001 "Insulin and ""Neutral Protamine Hagedorn (NPH) insulin""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:D933668QVX "Insulin and ""Insulin aspart""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:AVT680JB39 "Insulin and ""Insulin pork""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:54Q18076QB "Insulin and “Insulin degludec""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:4FT78T86XV "Insulin and ""Insulin detemir""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:7XIY785AZD "Insulin and ""Insulin glulisine”" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch CHEBI:228608 "Insulin and ""Insulin beef”" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:5931 skos:exactMatch UNII:54Q18076QB "Insulin and ""Insulin degludec""" https://github.com/TranslatorSRI/Babel/issues/327
CHEBI:4672 skos:relatedMatch CHEBI:59809 "CHEBI:4672 “Docetaxel” and CHEBI:59809 “Docetaxel trihydrate” are apparently medically similar, and we appear to have split clique issues" https://github.com/TranslatorSRI/NameResolution/issues/99
CHEBI:136034 skos:relatedMatch HMDB:HMDB0254418 "Not sure why these aren’t combining, or where the latter is even coming from really." https://github.com/TranslatorSRI/Babel/issues/358
CHEBI:59173 skos:relatedMatch PUBCHEM.COMPOUND:19797045 Conflating all the bivalirudin cliques into a single conflated clique https://github.com/TranslatorSRI/Babel/issues/346
CHEBI:59173 skos:relatedMatch PUBCHEM.COMPOUND:78357798 Conflating all the bivalirudin cliques into a single conflated clique https://github.com/TranslatorSRI/Babel/issues/346
MESH:D013668 skos:exactMatch CHEMBL.COMPOUND:CHEMBL1201522 Appears to be the same concept https://github.com/TranslatorSRI/NodeNormalization/issues/280

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