SPOKE
Scalable Precision Medicine Open Knowledge Engine (SPOKE) is a comprehensive biomedical knowledge graph that connects diverse data from multiple domains to enable discovery and precision medicine applications.
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{"activity_status": "active", "category": "KnowledgeGraph", "collection": ["okn"], "contacts": [{"category": "Individual", "contact_details": [{"contact_type": "email", "value": "sergio.baranzini@ucsf.edu"}], "label": "Sergio Baranzini"}, {"category": "Individual", "contact_details": [{"contact_type": "email", "value": "sui.huang@ucsf.edu"}], "label": "Sui Huang"}, {"category": "Organization", "label": "University of California, San Francisco"}], "description": "Scalable Precision Medicine Open Knowledge Engine (SPOKE) is a comprehensive biomedical knowledge graph that connects diverse data from multiple domains to enable discovery and precision medicine applications.", "domains": ["biomedical", "health", "genomics", "clinical", "drug discovery", "precision medicine", "pharmacology"], "evaluation_page": "resource/spoke/spoke_eval.html", "homepage_url": "https://spoke.ucsf.edu/", "id": "spoke", "infores_id": "spoke", "layout": "resource_detail", "license": {"id": "https://spoke.rbvi.ucsf.edu/docs/licenses.html", "label": "Multiple licenses (see individual data sources)"}, "name": "SPOKE", "products": [{"category": "GraphProduct", "description": "The SPOKE knowledge graph containing nodes and edges from multiple biomedical data sources.", "id": "spoke.graph", "name": "SPOKE Graph", "original_source": ["ncbigene", "pubmed", "mesh", "pid", "doid", "diseases", "drugcentral", "go", "gwascatalog", "reactome", "lincs-l1000", "uberon", "wikipathways", "bindingdb", "drugbank", "sider", "bgee", "uniprot", "string", "omim", "chembl", "foodb", "civic", "gdsc", "clinicaltrialsgov", "hpa", "cl", "kegg", "metacyc", "bv-brc", "ncbitaxon", "pathophenodb", "pfam", "interpro", "protcid"], "secondary_source": ["spoke"]}, {"category": "GraphicalInterface", "description": "Web interface that allows searching SPOKE for a node of interest and viewing its immediate connectivity neighborhood.", "format": "http", "id": "spoke.neighborhood_explorer", "name": "SPOKE Neighborhood Explorer", "product_url": "https://spoke.rbvi.ucsf.edu/neighborhood.html"}, {"category": "ProgrammingInterface", "description": "SPARQL endpoint for querying SPOKE knowledge graph via the OKN FRINK service", "id": "spoke.sparql", "name": "SPOKE SPARQL Endpoint", "original_source": ["spoke"], "product_url": "https://frink.apps.renci.org/spoke-okn/sparql"}], "publications": [{"authors": ["John H Morris", "Karthik Soman", "Riley E Akbas", "X Zhou", "B Smith", "Elaine C Meng", "CC Huang", "Gabriel Cerono", "G Schenk", "Angela Rizk-Jackson", "Sergio E Baranzini"], "id": "https://doi.org/10.1093/bioinformatics/btad080", "journal": "Bioinformatics", "preferred": true, "title": "The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information", "year": "2023"}, {"authors": ["Charlotte A Nelson", "Atul J Butte", "Sergio E Baranzini"], "id": "https://doi.org/10.1038/s41467-019-11069-0", "journal": "Nature Communications", "title": "Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings", "year": "2019"}, {"authors": ["Daniel Scott Himmelstein", "Antoine Lizee", "Christine Hessler", "Leo Brueggeman", "Sabrina L Chen", "Dexter Hadley", "Ari Green", "Pouya Khankhanian", "Sergio E Baranzini"], "id": "https://doi.org/10.7554/eLife.26726", "journal": "eLife", "title": "Systematic integration of biomedical knowledge prioritizes drugs for repurposing", "year": "2017"}], "repository": "https://github.com/baranzini-lab/SPOKE", "taxon": ["NCBITaxon:9606"], "version": "2.0"}