{"doi":"10.1093/bioinformatics/btad080","title":"The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information","abstract":"MOTIVATION: Knowledge graphs (KGs) are being adopted in industry, commerce and academia. Biomedical KG presents a challenge due to the complexity, size and heterogeneity of the underlying information. RESULTS: In this work, we present the Scalable Precision Medicine Open Knowledge Engine (SPOKE), a biomedical KG connecting millions of concepts via semantically meaningful relationships. SPOKE contains 27 million nodes of 21 different types and 53 million edges of 55 types downloaded from 41 databases. The graph is built on the framework of 11 ontologies that maintain its structure, enable mappings and facilitate navigation. SPOKE is built weekly by python scripts which download each resource, check for integrity and completeness, and then create a 'parent table' of nodes and edges. Graph queries are translated by a REST API and users can submit searches directly via an API or a graphical user interface. Conclusions/Significance: SPOKE enables the integration of seemingly disparate information to support precision medicine efforts. AVAILABILITY AND IMPLEMENTATION: The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.","journal":"Bioinformatics","year":2023,"id":316676,"datarank":2.103593206504282,"base_score":4.564348191467836,"endowment":4.564348191467836,"self_citation_contribution":0.6846522287201755,"citation_network_contribution":1.4189409777841067,"self_endowment_contribution":0.6846522287201755,"citer_contribution":1.4189409777841067,"corpus_percentile":89.88164307263867,"corpus_rank":1309,"citation_count":95,"citer_count":76,"citers_with_citation_signal":44,"citers_with_endowment":44,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6469,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":12.5,"fair_percentile":28.767960868236013,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":6473,"name":"Karthik Soman","orcid":"0000-0002-3490-9306","position":1,"is_corresponding":false},{"id":1020931,"name":"Rabia E Akbas","orcid":"0009-0009-0217-9554","position":2,"is_corresponding":false},{"id":840115,"name":"Xiaoyuan Zhou","orcid":"0000-0001-7410-3625","position":3,"is_corresponding":false},{"id":109707,"name":"Brett Smith","orcid":"0000-0002-2586-5014","position":4,"is_corresponding":false},{"id":30005,"name":"Elaine C. Meng","orcid":null,"position":5,"is_corresponding":false},{"id":30002,"name":"Conrad C. Huang","orcid":null,"position":6,"is_corresponding":false},{"id":989521,"name":"Gabriel Cerono","orcid":"0000-0002-9411-2526","position":7,"is_corresponding":false},{"id":56634,"name":"Gundolf Schenk","orcid":"0000-0003-1240-9949","position":8,"is_corresponding":false},{"id":955156,"name":"Angela Rizk‐Jackson","orcid":"0000-0002-1732-8550","position":9,"is_corresponding":false},{"id":267236,"name":"Adil Harroud","orcid":"0000-0003-2616-7274","position":10,"is_corresponding":false},{"id":37834,"name":"Lauren M. Sanders","orcid":"0000-0001-9393-0861","position":11,"is_corresponding":false},{"id":37877,"name":"Sylvain V. Costes","orcid":"0000-0002-8542-2389","position":12,"is_corresponding":false},{"id":1021808,"name":"Krish Bharat","orcid":null,"position":13,"is_corresponding":false},{"id":1021809,"name":"Arjun Chakraborty","orcid":null,"position":14,"is_corresponding":false},{"id":246283,"name":"Alexander R. Pico","orcid":"0000-0001-5706-2163","position":15,"is_corresponding":false},{"id":7132,"name":"Taline Mardirossian","orcid":null,"position":16,"is_corresponding":false},{"id":97,"name":"Michael J. Keiser","orcid":"0000-0002-1240-2192","position":17,"is_corresponding":false},{"id":70899,"name":"Alice Tang","orcid":"0000-0003-4745-0714","position":18,"is_corresponding":false},{"id":983194,"name":"Josef Hardi","orcid":"0000-0002-2533-6681","position":19,"is_corresponding":false},{"id":62617,"name":"Yongmei Shi","orcid":null,"position":20,"is_corresponding":false},{"id":113,"name":"Mark A. Musen","orcid":"0000-0003-3325-793X","position":21,"is_corresponding":false},{"id":37890,"name":"Sharat Israni","orcid":"0000-0003-0100-5826","position":22,"is_corresponding":false},{"id":37887,"name":"Sui Huang","orcid":"0000-0002-3545-4665","position":23,"is_corresponding":false},{"id":19244,"name":"Peter W. Rose","orcid":"0000-0001-9981-9750","position":24,"is_corresponding":false},{"id":1311,"name":"Charlotte A. Nelson","orcid":"0000-0002-3687-1102","position":25,"is_corresponding":false},{"id":1310,"name":"Sergio E. Baranzini","orcid":"0000-0003-0067-194X","position":26,"is_corresponding":false},{"id":54676,"name":"John H. Morris","orcid":"0000-0003-0290-7979","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-07-19T01:06:44.698773Z","pmid":"36759942","pmcid":"PMC9940622","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":22.2222,"fair_a":25.0,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":-0.8688,"fair_rationale":{"fair_score":12.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":22.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu.","grounded":false,"rationale":"The paper gives a web address (https://spoke.rbvi.ucsf.edu) as the location of the data, but this is not a persistent identifier scheme (DOI, Handle, ARK, or repository accession). 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[majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper only applies a CC-BY license to the article itself, not to the data; no license is named for the SPOKE dataset.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"SPOKE is implemented as a Neo4j Community instance","grounded":true,"rationale":"The paper names the specific software (Neo4j Community) used to implement the data, which qualifies as a named tool for provenance. 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A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide identifiers (accessions, DOIs, RRIDs) for any external resources used; it only cites them by name or reference. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state when the data become available or how long they persist; no timing or retention commitment is made.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the chemistry / materials repository accession (e.g. from Zenodo, PubChem or the Cambridge Structural Database (CSD)) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:05:26.603729Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}