diff --git a/tests/data/fixtures/query_fixtures.json b/tests/data/fixtures/query_fixtures.json index 9d6e4db6..b5c29d19 100644 --- a/tests/data/fixtures/query_fixtures.json +++ b/tests/data/fixtures/query_fixtures.json @@ -3597,6 +3597,7 @@ "trade_names": [], "xrefs": [ "chembl:CHEMBL11359", + "iuphar.ligand:5343", "rxcui:2555", "drugbank:DB00515", "chemidplus:15663-27-1" diff --git a/tests/data/wikidata/wikidata_2023-05-12.json b/tests/data/wikidata/wikidata_2023-05-12.json deleted file mode 100644 index 3d492c3e..00000000 --- a/tests/data/wikidata/wikidata_2023-05-12.json +++ /dev/null @@ -1,2170 +0,0 @@ -[ - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "d-1-phenyl-2-methylaminopropane", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "d-deoxyephedrine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "d-desoxyephedrine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "d-meth", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "d-N-methylamphetamine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "d-phenylisopropylmethylamine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "desoxyephedrine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "Dextromethamphetamine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "metamfetamine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "Metamfetamine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "M\u00e9tamf\u00e9tamine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "Metamfetaminum", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "Metanfetamina", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "meth", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "Methamphetamine, methylamphetamine", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "Methamphetaminum", - "itemLabel": "D-methamphetamine", - "rxnorm": "6816", - "chembl": "CHEMBL1201201", - "pubchemCompound": "10836" - }, - { - "item": "http://www.wikidata.org/entity/Q191924", - "drugbank": "01577", - "casRegistry": "537-46-2", - "alias": "Methyl-beta-phenylisopropylamine", - "itemLabel": 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"pubchemCompound": "174174", - "casRegistry": "51-55-8", - "alias": "dl-tropyltropate", - "rxnorm": "1223", - "itemLabel": "atropine" - }, - { - "item": "http://www.wikidata.org/entity/Q26272", - "drugbank": "00572", - "pubchemCompound": "174174", - "casRegistry": "51-55-8", - "alias": "dl-tropyltropate", - "rxnorm": "1223", - "itemLabel": "atropine" - }, - { - "item": "http://www.wikidata.org/entity/Q26272", - "drugbank": "00572", - "pubchemCompound": "174174", - "casRegistry": "51-55-8", - "alias": "Mydriasine", - "rxnorm": "1223", - "itemLabel": "atropine" - }, - { - "item": "http://www.wikidata.org/entity/Q26272", - "drugbank": "00572", - "pubchemCompound": "174174", - "casRegistry": "51-55-8", - "alias": "Mydriasine", - "rxnorm": "1223", - "itemLabel": "atropine" - }, - { - "item": "http://www.wikidata.org/entity/Q26272", - "drugbank": "00572", - "pubchemCompound": "174174", - "casRegistry": "51-55-8", - "alias": "Tropine tropate", - "rxnorm": "1223", - "itemLabel": "atropine" - }, - { - "item": "http://www.wikidata.org/entity/Q26272", - "drugbank": "00572", - "pubchemCompound": "174174", - "casRegistry": "51-55-8", - "alias": "Tropine tropate", - "rxnorm": "1223", - "itemLabel": "atropine" - }, - { - "item": "http://www.wikidata.org/entity/Q27287118", - "drugbank": "14793", - "chembl": "CHEMBL2386346", - "pubchemCompound": "57406853", - "casRegistry": "939981-39-2", - "alias": "RG7112", - "itemLabel": "ro-5045337" - }, - { - "item": "http://www.wikidata.org/entity/Q27287118", - "drugbank": "14793", - "chembl": "CHEMBL2386346", - "pubchemCompound": "57406853", - "casRegistry": "939981-39-2", - "alias": "RO 5045337", - "itemLabel": "ro-5045337" - }, - { - "item": "http://www.wikidata.org/entity/Q422265", - "alias": "spiramycin I", - "itemLabel": "spiramycin", - "rxnorm": "9991", - "chembl": "CHEMBL1256397", - "pubchemCompound": "5356392", - "casRegistry": "8025-81-8" - } -] \ No newline at end of file diff --git a/tests/data/wikidata/wikidata_2023-07-26.json b/tests/data/wikidata/wikidata_2023-07-26.json new file mode 100644 index 00000000..043fcfe8 --- /dev/null +++ b/tests/data/wikidata/wikidata_2023-07-26.json @@ -0,0 +1,93 @@ +[ + { + "item": "http://www.wikidata.org/entity/Q407241", + "itemLabel": "phenobarbital", + "casRegistry": "50-06-6", + "pubchemCompound": "4763", + "chembl": "CHEMBL40", + "rxnorm": "8134", + "drugbank": "01174", + "guideToPharmacology": "2804", + "aliases": "PHENYLETHYLMALONYLUREA, Phenylethylmalonylurea, Phenylethylbarbitursaeure, Phenylethylbarbituric Acid, Phenylethylbarbiturate, phenylethylbarbiturate, Phenylaethylbarbitursaeure, Phenobarbituric Acid, Phenobarbitone, Phenobarbitol, phenobarbital sodium, Luminal\u00ae, fenobarbital, 5-Phenyl-5-ethylbarbituric acid, 5-ethyl-5-phenylpyrimidine-2,4,6(1H,3H,5H)-trione, 5-Ethyl-5-phenylbarbituric acid, 5-Ethyl-5-phenyl-pyrimidine-2,4,6-trione, 5-ethyl-5-phenyl-2,4,6(1H,3H,5H)-pyrimidinetrione, Phenobarbital" + }, + { + "item": "http://www.wikidata.org/entity/Q412415", + "itemLabel": "cisplatin", + "casRegistry": "15663-27-1", + "pubchemCompound": "5702198", + "chembl": "CHEMBL11359", + "rxnorm": "2555", + "drugbank": "00515", + "guideToPharmacology": "5343", + "aliases": "Platinol-AQ, Platinol, cis-diamminedichloroplatinum(II), CIS-DDP, Cis-DDP, CDDP" + }, + { + "item": "http://www.wikidata.org/entity/Q418702", + "itemLabel": "basiliximab", + "casRegistry": "179045-86-4", + "chembl": "CHEMBL1201439", + "rxnorm": "196102", + "drugbank": "00074", + "guideToPharmacology": "6879", + "aliases": "SDZ-CHI-621, chimeric mouse-human antiCD25, CHI621, CHI-621, Ig gamma-1 chain C region" + }, + { + "item": "http://www.wikidata.org/entity/Q27287118", + "itemLabel": "ro-5045337", + "casRegistry": "939981-39-2", + "pubchemCompound": "57406853", + "chembl": "CHEMBL2386346", + "drugbank": "14793", + "guideToPharmacology": "9599", + "aliases": "RO 5045337, RG7112" + }, + { + "item": "http://www.wikidata.org/entity/Q26272", + "itemLabel": "atropine", + "casRegistry": "51-55-8", + "pubchemCompound": "174174", + "chembl": "CHEMBL517712", + "rxnorm": "1223", + "drugbank": "00572", + "guideToPharmacology": "320", + "aliases": "Tropine tropate, Mydriasine, dl-tropyltropate, dl-Hyoscyamine, 8-Methyl-8-azabicyclo[3.2.1]oct-3-yl tropate, 8-Methyl-8-azabicyclo[3.2.1]oct-3-yl 3-hydroxy-2-phenylpropanoate, [(1S,5R)-8-Methyl-8-azabicyclo[3.2.1]oct-3-yl] 3-hydroxy-2-phenyl-propanoate, (3-Endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl tropate, (+,-)-Tropyl tropate, (+-)-Hyoscyamine, (+-)-Atropine, (\u00b1)-hyoscyamine, (\u00b1)-atropine" + }, + { + "item": "http://www.wikidata.org/entity/Q191924", + "itemLabel": "D-methamphetamine", + "casRegistry": "537-46-2", + "pubchemCompound": "10836", + "chembl": "CHEMBL1201201", + "rxnorm": "6816", + "drugbank": "01577", + "aliases": "fast, ice, crystal, pure, chalk, glass, speed, crank, base, wax, tweak, S-methamphetamine, N-methylamphetamine, methylamphetamine, methyl-\u03b2-phenylisopropylamine, methamphetamine, meth, metamfetamine, desoxyephedrine, d-phenylisopropylmethylamine, d-N-methylamphetamine, d-meth, d-desoxyephedrine, d-deoxyephedrine, d-1-phenyl-2-methylaminopropane, crystal meth, (\u03b1S)-N,\u03b1-dimethylbenzeneethanamine, (S)-N,\u03b1-dimethylbenzeneethanamine, (+)-(S)-P-\u03b1-dimethylphenethylamine, whiz, crypto, methyl-beta-phenylisopropylamine, dextromethamphetamine, (S)-N,alpha-dimethylbenzeneethanamine, (alphaS)-N,alpha-dimethylbenzeneethanamine, (+)-(S)-N-alpha-dimethylphenethylamine" + }, + { + "item": "http://www.wikidata.org/entity/Q251698", + "itemLabel": "amifostine", + "casRegistry": "20537-88-6", + "pubchemCompound": "2141", + "chembl": "CHEMBL1006", + "rxnorm": "1545987", + "drugbank": "01143", + "aliases": "WR-2721, SAPEP, Gammaphos, Ethyol, Ethiofos, Apaetp, Aminopropylaminoethyl Thiophosphate, Aminopropylaminoethyl thiophosphate, Amifostinum, Amifostine Ethiofos, Amifostine anhydrous, amifostine anhydrous, Amifostina, Amifostine, WR-1065" + }, + { + "item": "http://www.wikidata.org/entity/Q422265", + "itemLabel": "spiramycin", + "casRegistry": "8025-81-8", + "pubchemCompound": "5356392", + "chembl": "CHEMBL1256397", + "rxnorm": "9991", + "aliases": "spiramycin I" + }, + { + "item": "http://www.wikidata.org/entity/Q15353101", + "itemLabel": "interferon alfacon-1", + "casRegistry": "118390-30-0", + "chembl": "CHEMBL1201557", + "rxnorm": "59744", + "drugbank": "00069", + "aliases": "Recombinant methionyl human consensus interferon, Recombinant Consensus Interferon, rCon-IFN, methionyl-interferon-consensus, methionyl interferon consensus, Interferon Consensus, Methionyl, IFN Alfacon-1, consensus interferon, CIFN" + } +] \ No newline at end of file diff --git a/tests/unit/test_wikidata.py b/tests/unit/test_wikidata.py index 96ac49b9..98c9aebd 100644 --- a/tests/unit/test_wikidata.py +++ b/tests/unit/test_wikidata.py @@ -34,6 +34,7 @@ def cisplatin(): "drugbank:DB00515", "rxcui:2555", "chemidplus:15663-27-1", + "iuphar.ligand:5343", ], "associated_with": ["pubchem.compound:5702198"], "trade_names": [], @@ -51,7 +52,8 @@ def interferon_alfacon_1(): "CIFN", "consensus interferon", "IFN Alfacon-1", - "Interferon Consensus, Methionyl", + "Interferon Consensus", + "Methionyl", "methionyl interferon consensus", "methionyl-interferon-consensus", "rCon-IFN", @@ -118,7 +120,10 @@ def atropine(): "8-Methyl-8-azabicyclo[3.2.1]oct-3-yl tropate", ], "approval_ratings": [], - "xrefs": ["drugbank:DB00572", "chemidplus:51-55-8", "rxcui:1223"], + "xrefs": [ + "drugbank:DB00572", "chemidplus:51-55-8", "rxcui:1223", + "chembl:CHEMBL517712", "iuphar.ligand:320", + ], "associated_with": [ "pubchem.compound:174174", ], @@ -139,6 +144,7 @@ def basiliximab(): "rxcui:196102", "chembl:CHEMBL1201439", "chemidplus:179045-86-4", + "iuphar.ligand:6879", ], ) diff --git a/therapy/etl/wikidata.py b/therapy/etl/wikidata.py index bde19de4..846377c6 100644 --- a/therapy/etl/wikidata.py +++ b/therapy/etl/wikidata.py @@ -23,6 +23,7 @@ "rxnorm": NamespacePrefix.RXNORM.value, "drugbank": NamespacePrefix.DRUGBANK.value, "wikidata": NamespacePrefix.WIKIDATA.value, + "guideToPharmacology": NamespacePrefix.GUIDETOPHARMACOLOGY.value, } # Provide standard concept ID prefixes @@ -36,13 +37,16 @@ SPARQL_QUERY = """ SELECT ?item ?itemLabel ?casRegistry ?pubchemCompound ?pubchemSubstance ?chembl ?rxnorm - ?drugbank ?alias + ?drugbank ?guideToPharmacology + (GROUP_CONCAT(DISTINCT ?alias; separator=", ") AS ?aliases) WHERE { { ?item (wdt:P31/(wdt:P279*)) wd:Q12140. } UNION { ?item (wdt:P366/(wdt:P279*)) wd:Q12140. } UNION { ?item (wdt:P31/(wdt:P279*)) wd:Q35456. } + UNION + { ?item wdt:P2868 wd:Q12187. } OPTIONAL { ?item skos:altLabel ?alias. FILTER((LANG(?alias)) = "en") @@ -71,8 +75,14 @@ ?item p:P715 ?wds6. ?wds6 ps:P715 ?drugbank. } + OPTIONAL { + ?item p:P595 ?wds7. + ?wds7 ps:P595 ?guideToPharmacology + } SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } } +GROUP BY ?item ?itemLabel ?casRegistry ?pubchemCompound ?pubchemSubstance ?chembl + ?rxnorm ?drugbank ?guideToPharmacology """ @@ -153,19 +163,18 @@ def _transform_data(self) -> None: fmted_xref = f"{NAMESPACES[key]}:{ref}" xrefs.append(fmted_xref) else: - fmted_assoc = f"{NAMESPACES[key]}:" \ - f"{ref}" + fmted_assoc = f"{NAMESPACES[key]}:{ref}" associated_with.append(fmted_assoc) item["xrefs"] = xrefs item["associated_with"] = associated_with if "itemLabel" in record.keys(): item["label"] = record["itemLabel"] items[concept_id] = item - if "alias" in record.keys(): + if "aliases" in record.keys(): if "aliases" in items[concept_id].keys(): - items[concept_id]["aliases"].append(record["alias"]) + items[concept_id]["aliases"] += record["aliases"].split(", ") else: - items[concept_id]["aliases"] = [record["alias"]] + items[concept_id]["aliases"] = record["aliases"].split(", ") for item in items.values(): self._load_therapy(item)