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fd2d161
Adds extract for wiki
bwalsh Mar 7, 2020
220e8ea
Drug enricher: remote database drift
bwalsh Mar 20, 2020
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4 changes: 4 additions & 0 deletions dev-requirements.txt
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Expand Up @@ -21,3 +21,7 @@ dictionaryutils==2.0.7
dvc>=0.50.1
# for allele normalization with maf2maf
cwltool==1.0.20191022103248
# for wiki transform
python-slugify==4.0.0
# for wiki export
gen3==2.2.3
2 changes: 2 additions & 0 deletions outputs/wiki/.gitignore
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@@ -0,0 +1,2 @@
*.gz
*.json
4 changes: 2 additions & 2 deletions tests/unit/enrichers/test_drug_enricher.py
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Expand Up @@ -27,7 +27,7 @@

EXPECTED = [
{'id': 'CID2244', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID2244', 'chebi_id': 'CHEBI:15365', 'chembl_id': 'CHEMBL25', 'drugbank_id': 'DB00945', 'synonym': 'ASPIRIN', 'inchi': 'InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)', 'inchi_key': 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N', 'taxonomy': {'class': 'Benzene and substituted derivatives', 'description': 'This compound belongs to the class of organic compounds known as acylsalicylic acids. These are o-acylated derivatives of salicylic acid.', 'direct-parent': 'Acylsalicylic acids', 'kingdom': 'Organic compounds', 'subclass': 'Benzoic acids and derivatives', 'superclass': 'Benzenoids'}, 'approved_countries': ['Canada', 'EU', 'US'], 'usan_stem_definition': None, 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"2244"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID3385', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID3385', 'chebi_id': 'CHEBI:46345', 'chembl_id': 'CHEMBL185', 'drugbank_id': 'DB00544', 'synonym': 'FLUOROURACIL', 'inchi': 'InChI=1S/C4H3FN2O2/c5-2-1-6-4(9)7-3(2)8/h1H,(H2,6,7,8,9)', 'inchi_key': 'GHASVSINZRGABV-UHFFFAOYSA-N', 'taxonomy': {'class': 'Diazines', 'description': 'This compound belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.', 'direct-parent': 'Halopyrimidines', 'kingdom': 'Organic compounds', 'subclass': 'Pyrimidines and pyrimidine derivatives', 'superclass': 'Organoheterocyclic compounds'}, 'approved_countries': ['Canada', 'US'], 'usan_stem_definition': 'uracil derivatives used as thyroid antagonists and as antineoplastics', 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"3385"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID3385', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID3385', 'chebi_id': 'CHEBI:46345', 'chembl_id': 'CHEMBL185', 'drugbank_id': 'DB00544', 'synonym': 'FLUOROURACIL', 'inchi': 'InChI=1S/C4H3FN2O2/c5-2-1-6-4(9)7-3(2)8/h1H,(H2,6,7,8,9)', 'inchi_key': 'GHASVSINZRGABV-UHFFFAOYSA-N', 'taxonomy': {'class': 'Diazines', 'description': 'This compound belongs to the class of organic compounds known as halopyrimidines. These are aromatic compounds containing a halogen atom linked to a pyrimidine ring. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.', 'direct-parent': 'Halopyrimidines', 'kingdom': 'Organic compounds', 'subclass': 'Pyrimidines and pyrimidine derivatives', 'superclass': 'Organoheterocyclic compounds'}, 'approved_countries': ['Canada', 'US'], 'usan_stem_definition': 'uracil type antineoplastics; uracil derivatives used as thyroid antagonists and as antineoplastics', 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"3385"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID9863776', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID9863776', 'chebi_id': 'CHEBI:67559', 'chembl_id': 'CHEMBL1077979', 'drugbank_id': None, 'synonym': '9863776', 'inchi': 'InChI=1S/C19H22O7/c1-11-5-3-7-14(20)18(23)15(21)8-4-6-12-9-13(25-2)10-16(22)17(12)19(24)26-11/h3-4,6-7,9-11,15,18,21-23H,5,8H2,1-2H3/b6-4+,7-3-/t11-,15-,18+/m0/s1', 'inchi_key': 'NEQZWEXWOFPKOT-BYRRXHGESA-N', 'taxonomy': None, 'approved_countries': [], 'usan_stem_definition': None, 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"9863776"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID10172943', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID10172943', 'chebi_id': 'CHEBI:91351', 'chembl_id': 'CHEMBL379300', 'drugbank_id': 'DB08073', 'synonym': '10172943', 'inchi': 'InChI=1S/C24H23N5O/c1-15-22-10-16(6-7-24(22)29-28-15)17-9-20(13-26-11-17)30-14-19(25)8-18-12-27-23-5-3-2-4-21(18)23/h2-7,9-13,19,27H,8,14,25H2,1H3,(H,28,29)/t19-/m0/s1', 'inchi_key': 'YWTBGJGMTBHQTM-IBGZPJMESA-N', 'taxonomy': {'class': 'Indoles and derivatives', 'description': 'This compound belongs to the class of organic compounds known as 3-alkylindoles. These are compounds containing an indole moiety that carries an alkyl chain at the 3-position.', 'direct-parent': '3-alkylindoles', 'kingdom': 'Organic compounds', 'subclass': 'Indoles', 'superclass': 'Organoheterocyclic compounds'}, 'approved_countries': [], 'usan_stem_definition': None, 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"10172943"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID9549184', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID9549184', 'chebi_id': 'CHEBI:91457', 'chembl_id': 'CHEMBL1970879', 'drugbank_id': None, 'synonym': '9549184', 'inchi': 'InChI=1S/C34H39N9O3/c1-21(44)41-14-16-42(17-15-41)24-9-11-25(12-10-24)43-33-30(32(35)36-20-37-33)31(39-43)23-8-13-26(29(19-23)46-3)38-34(45)28-18-22-6-4-5-7-27(22)40(28)2/h4-8,13,18-20,24-25H,9-12,14-17H2,1-3H3,(H,38,45)(H2,35,36,37)', 'inchi_key': 'ZMNWFTYYYCSSTF-UHFFFAOYSA-N', 'taxonomy': None, 'approved_countries': [], 'usan_stem_definition': None, 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"9549184"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
Expand All @@ -38,7 +38,7 @@
{'id': 'CID2244', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID2244', 'chebi_id': 'CHEBI:15365', 'chembl_id': 'CHEMBL25', 'drugbank_id': 'DB00945', 'synonym': 'ASPIRIN', 'inchi': 'InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)', 'inchi_key': 'BSYNRYMUTXBXSQ-UHFFFAOYSA-N', 'taxonomy': {'class': 'Benzene and substituted derivatives', 'description': 'This compound belongs to the class of organic compounds known as acylsalicylic acids. These are o-acylated derivatives of salicylic acid.', 'direct-parent': 'Acylsalicylic acids', 'kingdom': 'Organic compounds', 'subclass': 'Benzoic acids and derivatives', 'superclass': 'Benzenoids'}, 'approved_countries': ['Canada', 'EU', 'US'], 'usan_stem_definition': None, 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"2244"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID2733526', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID2733526', 'chebi_id': 'CHEBI:41774', 'chembl_id': 'CHEMBL83', 'drugbank_id': 'DB00675', 'synonym': 'Tamoxifen', 'inchi': 'InChI=1S/C26H29NO/c1-4-25(21-11-7-5-8-12-21)26(22-13-9-6-10-14-22)23-15-17-24(18-16-23)28-20-19-27(2)3/h5-18H,4,19-20H2,1-3H3/b26-25-', 'inchi_key': 'NKANXQFJJICGDU-QPLCGJKRSA-N', 'taxonomy': {'class': 'Stilbenes', 'description': 'This compound belongs to the class of organic compounds known as stilbenes. These are organic compounds containing a 1,2-diphenylethylene moiety. Stilbenes (C6-C2-C6 ) are derived from the common phenylpropene (C6-C3) skeleton building block. The introduction of one or more hydroxyl groups to a phenyl ring lead to stilbenoids.', 'direct-parent': 'Stilbenes', 'kingdom': 'Organic compounds', 'superclass': 'Phenylpropanoids and polyketides'}, 'approved_countries': ['Canada', 'US'], 'usan_stem_definition': None, 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"2733526"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID2733526', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID2733526', 'chebi_id': 'CHEBI:41774', 'chembl_id': 'CHEMBL83', 'drugbank_id': 'DB00675', 'synonym': 'Tamoxifen', 'inchi': 'InChI=1S/C26H29NO/c1-4-25(21-11-7-5-8-12-21)26(22-13-9-6-10-14-22)23-15-17-24(18-16-23)28-20-19-27(2)3/h5-18H,4,19-20H2,1-3H3/b26-25-', 'inchi_key': 'NKANXQFJJICGDU-QPLCGJKRSA-N', 'taxonomy': {'class': 'Stilbenes', 'description': 'This compound belongs to the class of organic compounds known as stilbenes. These are organic compounds containing a 1,2-diphenylethylene moiety. Stilbenes (C6-C2-C6 ) are derived from the common phenylpropene (C6-C3) skeleton building block. The introduction of one or more hydroxyl groups to a phenyl ring lead to stilbenoids.', 'direct-parent': 'Stilbenes', 'kingdom': 'Organic compounds', 'superclass': 'Phenylpropanoids and polyketides'}, 'approved_countries': ['Canada', 'US'], 'usan_stem_definition': None, 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"2733526"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CHEMBL1742981', 'id_source': 'CHEMBL', 'pubchem_id': None, 'chebi_id': None, 'chembl_id': 'CHEMBL1742981', 'drugbank_id': None, 'synonym': 'Abagovomab', 'inchi': None, 'inchi_key': None, 'taxonomy': None, 'approved_countries': [], 'usan_stem_definition': 'monoclonal antibodies', 'source_url': 'http://mychem.info/v1/query?q=chembl.pref_name:abagovomab&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CHEMBL1742981', 'id_source': 'CHEMBL', 'pubchem_id': None, 'chebi_id': None, 'chembl_id': 'CHEMBL1742981', 'drugbank_id': None, 'synonym': 'Abagovomab', 'inchi': None, 'inchi_key': None, 'taxonomy': None, 'approved_countries': [], 'usan_stem_definition': 'monoclonal antibodies: mouse, antiviral indications', 'source_url': 'http://mychem.info/v1/query?q=chembl.pref_name:abagovomab&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'},
{'id': 'CID68740', 'id_source': 'PUBCHEM', 'pubchem_id': 'CID68740', 'chebi_id': 'CHEBI:46557', 'chembl_id': 'CHEMBL924', 'drugbank_id': 'DB00399', 'synonym': 'ZOLEDRONIC ACID', 'inchi': 'InChI=1S/C5H10N2O7P2/c8-5(15(9,10)11,16(12,13)14)3-7-2-1-6-4-7/h1-2,4,8H,3H2,(H2,9,10,11)(H2,12,13,14)', 'inchi_key': 'XRASPMIURGNCCH-UHFFFAOYSA-N', 'taxonomy': {'class': 'Organic phosphonic acids and derivatives', 'description': 'This compound belongs to the class of organic compounds known as bisphosphonates. These are organic compounds containing two phosphonate groups linked together through a carbon atoms.', 'direct-parent': 'Bisphosphonates', 'kingdom': 'Organic compounds', 'subclass': 'Bisphosphonates', 'superclass': 'Organic acids and derivatives'}, 'approved_countries': ['Canada', 'EU', 'US'], 'usan_stem_definition': 'calcium metabolism regulators', 'source_url': 'http://mychem.info/v1/query?q=pubchem.cid:"68740"&fields=chebi.id,chebi.inchi,chebi.inchi_key,chebi.name,chembl.molecule_chembl_id,chembl.pref_name,chembl.inchi,chembl.inchi_key,chembl.molecule_synonyms,chembl.usan_stem_definition,pubchem.cid,pubchem.inchi,pubchem.inchi_key,drugbank.id,drugbank.inchi,drugbank.inchi_key,drugbank.products.approved,drugbank.products.country,drugbank.taxonomy.class,drugbank.taxonomy.direct-parent,drugbank.taxonomy.kingdom,drugbank.taxonomy.subclass,drugbank.taxonomy.superclass,drugbank.taxonomy.description&size=1'}
]

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