The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information is a dataset published in Bioinformatics (2023). On theSindex it has a DataRank of 2.1, placing it in the top 10.1% of the data-sharing corpus. It has been cited 95 times, with 76 citing works in its 1-hop citation network. Its calibrated FAIR score is 13/100.
Ranks in the top 10% for downstream scientific impact
DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Full FAIR picture · advisory
The headline score is computed from the scored criteria — the fact-shaped checks (a repository, an accession, a licence) that two independent models agree on. The advisory criteria below are real FAIR guidance but rest on judgment calls that models read differently, so they inform without moving the number.
“The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu.”— not found in the paper; verdict downgraded
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). [downgraded to 'no' — no verifiable quote from the paper]
RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit · RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier' · FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'
“The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu.”— not found in the paper; verdict downgraded
The data are hosted on a UCSF website (https://spoke.rbvi.ucsf.edu), which is a non-repository host, not a curated data repository. [downgraded to 'no' — no verifiable quote from the paper]
RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed ( · NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived · NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten
No identifier for the SPOKE dataset appears anywhere in the paper; the article's own DOI is for the paper, not the data.
FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first- · RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes · FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'
Advisory · not in the published score
“To preserve integrity of the original databases and prevent redistribution of content under multiple licenses, SPOKE is not available as a bulk download.”
The data availability statement declares that the data cannot be shared as a bulk download and offers no route to obtain the data directly.
Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li · Springer Nature research data policy — Data Availability Statements: standard statement templat · RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes
“The current release contains more than 27 056 367 nodes of 21 different types ( Table 1) and 53 264 489 edges of 55 types (Supplementary Table S1).”
The paper provides an itemized inventory of the dataset's node types, counts, and sources in Table 1, which is a structural description of the data.
RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential) · FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability' · FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'
“The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu.”— not found in the paper; verdict downgraded
The paper provides a URL to the SPOKE neighborhood explorer with no stated precondition, implying the data are publicly accessible via that interface. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]
RDA-A1.1-01D — 'Data is accessible through a free access protocol' · FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data' · NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'
Advisory · not in the published score
No access-level label is applied to the data; the paper only notes that SPOKE is not available as a bulk download, implying restricted access but without using any standard access-rights vocabulary term.
FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data' · RDA-A1-01M — metadata contains information to enable the user to get access to the data · COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl
The data are not sensitive or human-subject; SPOKE is a knowledge graph built from public databases, and no gatekeeper is named.
NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee · RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and · NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse
The paper does not state when the data become available or how long they persist; no timing or retention commitment is made.
NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines · NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy' · RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'
No file format is named for the released SPOKE data; the data are accessed via an API, not as downloadable files.
FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co · RDA-R1.3-02D — data is expressed in a machine-understandable community standard · RDA-I1-01D — data uses a knowledge representation expressed in a standardised format
Advisory · not in the published score
“SPOKE also adheres to the Biolink model.”
The paper explicitly names the Biolink model as a data/metadata community standard that SPOKE adheres to.
RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential) · RDA-R1.3-01D — 'Data complies with a community standard' · RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'
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)]
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'
The paper only applies a CC-BY license to the article itself, not to the data; no license is named for the SPOKE dataset.
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'
The paper describes the data as 'the current release' but provides no version number, date, or other snapshot identifier.
DataCite Metadata Schema 4.6 — the 'Version' property · RDA-R1.2-01M — provenance information (which version was used is provenance) · NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'
No locator is given for the study's own code; the paper only mentions Python scripts but does not provide a repository URL or DOI.
NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code' · FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear · FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)
“The development of SPOKE and its applications are being funded by grants from the National Science Foundation [NSF_2033569], NIH/NCATS [NIH_NOA_1OT2TR003450] and the Marcus Program in Precision Medicine Innovation.”
The paper provides specific grant numbers from funding agencies, which are alphanumeric award identifiers.
DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award · Crossref Funder Registry — canonical funder identifiers for funding metadata · RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco
Advisory · not in the published score
“SPOKE is implemented as a Neo4j Community instance”
The paper names the specific software (Neo4j Community) used to implement the data, which qualifies as a named tool for provenance. [majority verdict 'yes' (3/5 passes agreed)]
RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa · FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati · W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance
“The current release contains more than 27 056 367 nodes of 21 different types ( Table 1) and 53 264 489 edges of 55 types (Supplementary Table S1).”
Variable-level definitions (node types, counts, sources) are provided inside the article in Table 1, but no separate documentation object is said to accompany the data.
RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu · FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data' · NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
Base Score Contribution
0.685
From this paper's citation signal
Citation Network Contribution
1.4
From 44 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 76 citers.