TreatKB
TreatKB is a text-mined knowledge base of drug-treats-disease (treatment) relationships developed by the Rong Xu lab at Case Western Reserve University. Treatment pairs are extracted and combined from multiple lines of evidence, including MEDLINE/PubMed literature, the FDA Adverse Event Reporting System (FAERS), and ClinicalTrials.gov records, alongside a curated gold-standard set of drug-disease treatment pairs. The data are distributed as plain-text files from the Xu lab public data server. TreatKB has been used as a source to construct GP-KG.
[{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://case.edu/medicine/aicenter/about/faculty-and-staff/rong-xu"}], "label": "Xu Lab, Case Western Reserve University"}]
[{"category": "DocumentationProduct", "description": "Peer-reviewed publication from the Xu lab describing the large-scale text-mining method used to extract accurate drug-disease treatment pairs from biomedical literature, the approach underlying TreatKB.", "id": "treatkb.publication", "name": "TreatKB Method Publication", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "treatkb"}], "product_url": "https://doi.org/10.1186/1471-2105-14-181"}, {"category": "Product", "description": "Curated gold-standard set of drug-disease treatment pairs distributed as a plain-text file, the core reference data of TreatKB. Companion files at the same location hold treatment-pair evidence counts derived from MEDLINE, FAERS, and ClinicalTrials.gov.", "format": "txt", "id": "treatkb.goldstandard", "name": "TreatKB gold-standard treatment pairs", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "treatkb"}], "product_file_size": 336182, "product_url": "http://nlp.case.edu/public/data/treatKB/drug_disease_goldstandard.txt"}, {"category": "GraphProduct", "description": "GP_KG.txt", "edge_count": 1246726, "format": "txt", "id": "gp-kg.graph", "name": "GP-KG", "node_count": 61146, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "gp-kg"}, {"relation_type": "prov:wasDerivedFrom", "source": "drugbank"}, {"relation_type": "prov:wasDerivedFrom", "source": "mgi"}, {"relation_type": "prov:wasDerivedFrom", "source": "go"}, {"relation_type": "prov:wasDerivedFrom", "source": "goa"}, {"relation_type": "prov:wasDerivedFrom", "source": "gtex"}, {"relation_type": "prov:wasDerivedFrom", "source": "hp"}, {"relation_type": "prov:wasDerivedFrom", "source": "mp"}, {"relation_type": "prov:wasDerivedFrom", "source": "omim"}, {"relation_type": "prov:wasDerivedFrom", "source": "umls"}, {"relation_type": "prov:wasDerivedFrom", "source": "uberon"}, {"relation_type": "prov:wasDerivedFrom", "source": "pubchem"}, {"relation_type": "prov:wasDerivedFrom", "source": "uniprot"}, {"relation_type": "prov:wasDerivedFrom", "source": "faers"}, {"relation_type": "prov:wasDerivedFrom", "source": "phenomebrowser"}, {"relation_type": "prov:wasDerivedFrom", "source": "treatkb"}], "product_file_size": 48397035, "product_url": "http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt"}]
{"activity_status": "active", "category": "DataSource", "contacts": [{"category": "Organization", "contact_details": [{"contact_type": "url", "value": "https://case.edu/medicine/aicenter/about/faculty-and-staff/rong-xu"}], "label": "Xu Lab, Case Western Reserve University"}], "creation_date": "2026-06-18T00:00:00Z", "description": "TreatKB is a text-mined knowledge base of drug-treats-disease (treatment) relationships developed by the Rong Xu lab at Case Western Reserve University. Treatment pairs are extracted and combined from multiple lines of evidence, including MEDLINE/PubMed literature, the FDA Adverse Event Reporting System (FAERS), and ClinicalTrials.gov records, alongside a curated gold-standard set of drug-disease treatment pairs. The data are distributed as plain-text files from the Xu lab public data server. TreatKB has been used as a source to construct GP-KG.", "domains": ["drug discovery", "clinical", "literature", "pharmacology"], "homepage_url": "http://nlp.case.edu/public/data/treatKB/", "id": "treatkb", "last_modified_date": "2026-07-02T00:00:00Z", "layout": "resource_detail", "license": {"id": "", "label": "Not specified"}, "name": "TreatKB", "products": [{"category": "DocumentationProduct", "description": "Peer-reviewed publication from the Xu lab describing the large-scale text-mining method used to extract accurate drug-disease treatment pairs from biomedical literature, the approach underlying TreatKB.", "id": "treatkb.publication", "name": "TreatKB Method Publication", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "treatkb"}], "product_url": "https://doi.org/10.1186/1471-2105-14-181"}, {"category": "Product", "description": "Curated gold-standard set of drug-disease treatment pairs distributed as a plain-text file, the core reference data of TreatKB. Companion files at the same location hold treatment-pair evidence counts derived from MEDLINE, FAERS, and ClinicalTrials.gov.", "format": "txt", "id": "treatkb.goldstandard", "name": "TreatKB gold-standard treatment pairs", "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "treatkb"}], "product_file_size": 336182, "product_url": "http://nlp.case.edu/public/data/treatKB/drug_disease_goldstandard.txt"}, {"category": "GraphProduct", "description": "GP_KG.txt", "edge_count": 1246726, "format": "txt", "id": "gp-kg.graph", "name": "GP-KG", "node_count": 61146, "original_source": [{"relation_type": "prov:hadPrimarySource", "source": "gp-kg"}, {"relation_type": "prov:wasDerivedFrom", "source": "drugbank"}, {"relation_type": "prov:wasDerivedFrom", "source": "mgi"}, {"relation_type": "prov:wasDerivedFrom", "source": "go"}, {"relation_type": "prov:wasDerivedFrom", "source": "goa"}, {"relation_type": "prov:wasDerivedFrom", "source": "gtex"}, {"relation_type": "prov:wasDerivedFrom", "source": "hp"}, {"relation_type": "prov:wasDerivedFrom", "source": "mp"}, {"relation_type": "prov:wasDerivedFrom", "source": "omim"}, {"relation_type": "prov:wasDerivedFrom", "source": "umls"}, {"relation_type": "prov:wasDerivedFrom", "source": "uberon"}, {"relation_type": "prov:wasDerivedFrom", "source": "pubchem"}, {"relation_type": "prov:wasDerivedFrom", "source": "uniprot"}, {"relation_type": "prov:wasDerivedFrom", "source": "faers"}, {"relation_type": "prov:wasDerivedFrom", "source": "phenomebrowser"}, {"relation_type": "prov:wasDerivedFrom", "source": "treatkb"}], "product_file_size": 48397035, "product_url": "http://nlp.case.edu/public/data/GPKG-Predict/data/GP_KG.txt"}], "publications": [{"authors": ["Rong Xu", "QuanQiu Wang"], "doi": "10.1186/1471-2105-14-181", "id": "doi:10.1186/1471-2105-14-181", "journal": "BMC Bioinformatics", "preferred": true, "title": "Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing", "year": "2013"}]}