{"doi":"10.1093/nar/gkac979","title":"CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase","abstract":"CIViC (Clinical Interpretation of Variants in Cancer; civicdb.org) is a crowd-sourced, public domain knowledgebase composed of literature-derived evidence characterizing the clinical utility of cancer variants. As clinical sequencing becomes more prevalent in cancer management, the need for cancer variant interpretation has grown beyond the capability of any single institution. CIViC contains peer-reviewed, published literature curated and expertly-moderated into structured data units (Evidence Items) that can be accessed globally and in real time, reducing barriers to clinical variant knowledge sharing. We have extended CIViC's functionality to support emergent variant interpretation guidelines, increase interoperability with other variant resources, and promote widespread dissemination of structured curated data. To support the full breadth of variant interpretation from basic to translational, including integration of somatic and germline variant knowledge and inference of drug response, we have enabled curation of three new Evidence Types (Predisposing, Oncogenic and Functional). The growing CIViC knowledgebase has over 300 contributors and distributes clinically-relevant cancer variant data currently representing >3200 variants in >470 genes from >3100 publications.","journal":"Nucleic Acids Research","year":2022,"id":240327,"datarank":1.040132474840104,"base_score":3.8501476017100584,"endowment":3.8501476017100584,"self_citation_contribution":0.5775221402565088,"citation_network_contribution":0.4626103345835951,"self_endowment_contribution":0.5775221402565088,"citer_contribution":0.4626103345835951,"corpus_percentile":80.53686083391351,"corpus_rank":2517,"citation_count":46,"citer_count":34,"citers_with_citation_signal":21,"citers_with_endowment":21,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9456,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":52.0833,"fair_percentile":67.4411494955671,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":827671,"name":"Arpad Danos","orcid":"0000-0001-9815-2288","position":1,"is_corresponding":false},{"id":827674,"name":"Jason Saliba","orcid":"0000-0003-3035-2296","position":2,"is_corresponding":false},{"id":18428,"name":"Joshua F. McMichael","orcid":"0000-0002-0197-2245","position":3,"is_corresponding":false},{"id":827672,"name":"Adam Coffman","orcid":"0000-0003-0944-3126","position":4,"is_corresponding":false},{"id":235662,"name":"Susanna Kiwala","orcid":"0000-0003-4378-7328","position":5,"is_corresponding":false},{"id":231269,"name":"Erica K. Barnell","orcid":"0000-0003-1631-1201","position":6,"is_corresponding":false},{"id":827673,"name":"Lana Sheta","orcid":"0000-0002-6259-8074","position":7,"is_corresponding":false},{"id":734682,"name":"Cameron J. Grisdale","orcid":"0000-0003-1923-6972","position":8,"is_corresponding":false},{"id":827675,"name":"Lynzey Kujan","orcid":"0000-0001-9225-7361","position":9,"is_corresponding":false},{"id":827676,"name":"Shahil Pema","orcid":"0000-0002-0741-8501","position":10,"is_corresponding":false},{"id":691041,"name":"Jake Lever","orcid":"0000-0001-8198-2939","position":11,"is_corresponding":false},{"id":867637,"name":"Sarah Ridd","orcid":"0000-0001-9444-3803","position":12,"is_corresponding":false},{"id":231270,"name":"Nicholas C. Spies","orcid":"0000-0002-5873-351X","position":13,"is_corresponding":false},{"id":867638,"name":"Veronica Andric","orcid":"0000-0002-8262-2115","position":14,"is_corresponding":false},{"id":827677,"name":"Andreea Chiorean","orcid":"0000-0003-4088-4069","position":15,"is_corresponding":false},{"id":251188,"name":"Damian Rieke","orcid":"0000-0003-0027-7977","position":16,"is_corresponding":false},{"id":828095,"name":"Kaitlin A. Clark","orcid":null,"position":17,"is_corresponding":false},{"id":816379,"name":"Caralyn Reisle","orcid":"0000-0002-4318-4626","position":18,"is_corresponding":false},{"id":868280,"name":"Ajay C Venigalla","orcid":null,"position":19,"is_corresponding":false},{"id":698365,"name":"Mark G. Evans","orcid":"0000-0001-9358-9843","position":20,"is_corresponding":false},{"id":827678,"name":"Payal Jani","orcid":"0000-0002-8151-6177","position":21,"is_corresponding":false},{"id":827679,"name":"Hideaki Takahashi","orcid":"0000-0002-3184-2513","position":22,"is_corresponding":false},{"id":868281,"name":"Avila Suda","orcid":null,"position":23,"is_corresponding":false},{"id":827680,"name":"Peter Horak","orcid":"0000-0003-4536-9306","position":24,"is_corresponding":false},{"id":251189,"name":"Deborah Ritter","orcid":"0009-0005-2930-4010","position":25,"is_corresponding":false},{"id":252141,"name":"Xin Zhou","orcid":"0000-0003-3979-8200","position":26,"is_corresponding":false},{"id":827681,"name":"Benjamin J. Ainscough","orcid":"0000-0001-8340-514X","position":27,"is_corresponding":false},{"id":827682,"name":"Sean DeLong","orcid":"0000-0003-0342-7862","position":28,"is_corresponding":false},{"id":482868,"name":"Chimene Kesserwan","orcid":"0000-0001-6043-2065","position":29,"is_corresponding":false},{"id":828096,"name":"Mario Lamping","orcid":null,"position":30,"is_corresponding":false},{"id":841809,"name":"Haolin Shen","orcid":"0000-0003-1550-2831","position":31,"is_corresponding":false},{"id":827683,"name":"Alexander Marr","orcid":"0000-0002-1448-7353","position":32,"is_corresponding":false},{"id":867639,"name":"My Hoang","orcid":"0000-0003-1736-6319","position":33,"is_corresponding":false},{"id":867640,"name":"Kartik Singhal","orcid":"0000-0002-3855-7950","position":34,"is_corresponding":false},{"id":867641,"name":"Mariam Khanfar","orcid":"0000-0002-3650-2665","position":35,"is_corresponding":false},{"id":827684,"name":"Brian V Li","orcid":"0000-0001-8094-2054","position":36,"is_corresponding":false},{"id":827685,"name":"Wan‐Hsin Lin","orcid":"0000-0002-1807-5815","position":37,"is_corresponding":false},{"id":828097,"name":"Panieh Terraf","orcid":null,"position":38,"is_corresponding":false},{"id":867642,"name":"Laura Corson","orcid":"0000-0003-2772-3375","position":39,"is_corresponding":false},{"id":828098,"name":"Yasser Salama","orcid":null,"position":40,"is_corresponding":false},{"id":226341,"name":"Katie M. Campbell","orcid":"0000-0001-6491-4432","position":41,"is_corresponding":false},{"id":827686,"name":"Kirsten M. Farncombe","orcid":"0000-0001-9413-201X","position":42,"is_corresponding":false},{"id":827687,"name":"Jianling Ji","orcid":"0000-0003-4941-3538","position":43,"is_corresponding":false},{"id":446030,"name":"Xiaonan Zhao","orcid":"0000-0003-2003-6177","position":44,"is_corresponding":false},{"id":827689,"name":"Xinjie Xu","orcid":"0000-0001-8373-1834","position":45,"is_corresponding":false},{"id":250530,"name":"Rashmi Kanagal‐Shamanna","orcid":"0000-0001-7829-5249","position":46,"is_corresponding":false},{"id":418481,"name":"Ian King","orcid":"0000-0003-3405-9767","position":47,"is_corresponding":false},{"id":577341,"name":"Kelsy C. Cotto","orcid":"0000-0003-0890-6889","position":48,"is_corresponding":false},{"id":231259,"name":"Zachary L. Skidmore","orcid":"0000-0003-1928-7139","position":49,"is_corresponding":false},{"id":235669,"name":"Jason Walker","orcid":"0000-0001-7547-5789","position":50,"is_corresponding":false},{"id":1812,"name":"Jinghui Zhang","orcid":"0000-0003-3350-9682","position":51,"is_corresponding":false},{"id":62231,"name":"Aleksandar Milosavljevic","orcid":"0000-0001-5482-2825","position":52,"is_corresponding":false},{"id":63733,"name":"Ronak Y. Patel","orcid":"0000-0001-8111-7363","position":53,"is_corresponding":false},{"id":399413,"name":"Rachel H. Giles","orcid":"0000-0001-9133-2008","position":54,"is_corresponding":false},{"id":605919,"name":"Raymond H. Kim","orcid":"0000-0002-2147-8674","position":55,"is_corresponding":false},{"id":19861,"name":"Lynn M. Schriml","orcid":"0000-0001-8910-9851","position":56,"is_corresponding":false},{"id":1278,"name":"Elaine R. Mardis","orcid":"0000-0002-5892-1553","position":57,"is_corresponding":false},{"id":14377,"name":"Steven J.M. Jones","orcid":"0000-0003-3394-2208","position":58,"is_corresponding":false},{"id":251190,"name":"Gordana Raca","orcid":"0000-0002-5259-1784","position":59,"is_corresponding":false},{"id":570214,"name":"Shruti Rao","orcid":"0000-0002-7235-0777","position":60,"is_corresponding":false},{"id":225702,"name":"Subha Madhavan","orcid":"0000-0001-7617-3547","position":61,"is_corresponding":false},{"id":95767,"name":"Alex H. Wagner","orcid":"0000-0002-2502-8961","position":62,"is_corresponding":false},{"id":231287,"name":"Malachi Griffith","orcid":"0000-0002-6388-446X","position":63,"is_corresponding":false},{"id":231288,"name":"Obi L. Griffith","orcid":"0000-0002-0843-4271","position":64,"is_corresponding":false},{"id":251183,"name":"Kilannin Krysiak","orcid":"0000-0002-6299-9230","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":null,"created_at":"2026-07-19T00:22:46.554789Z","pmid":"36373660","pmcid":"PMC9825608","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":33.3333,"fair_a":50.0,"fair_i":60.0,"fair_r":70.8333,"fair_zscore":0.698,"fair_rationale":{"fair_score":52.08,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":33.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed onhttps: //civicdb.org.","grounded":true,"rationale":"The paper gives a web address (https://civicdb.org) rather than a persistent-identifier scheme string for its own dataset. [majority verdict 'partial' (3/4 passes agreed)]","anchors":["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'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org.","grounded":false,"rationale":"The host is a project website (civicdb.org), not a recognised curated repository from re3data/FAIRsharing. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/4 passes agreed)]","anchors":["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"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org. All underlying code is available on GitHub under an MIT license (https://github.com/griffithlab/civic-v2). Data is available via API (https://griffithlab.github.io/civic-v2/) and regular releases in TSV and VCF format (https://civicdb.org/releases/main).","grounded":false,"rationale":"The statement points to a website (CIViCdb) and a GitHub repository, not to a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 passes agreed)]","anchors":["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"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Table 1. CIViC curation statistics from original publication to current","grounded":true,"rationale":"The paper includes a table that itemises the dataset's content (variants, genes, sources, etc.), serving as an itemised inventory. [majority verdict 'yes' (3/4 passes agreed)]","anchors":["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'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org.","grounded":false,"rationale":"The dataset identifier (URL) appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/4 passes agreed)]","anchors":["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'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org.","grounded":false,"rationale":"The data availability statement provides a direct link to the data with no precondition stated. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","anchors":["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'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"CIViC is an open-access, open-source, fully transparent knowledgebase for the expert crowdsourcing of Clinical Interpretation of Variants in Cancer ( civicdb.org) first released in 2017 (1)( F i g u r e1).","grounded":true,"rationale":"The paper labels the data as 'open-access' and as being under a 'public domain dedication', which are explicit access-level labels. [majority verdict 'yes' (3/4 passes agreed)]","anchors":["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"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The CIViC data are literature-derived variant interpretations, not sensitive human-subject data, and no gatekeeper is named.","anchors":["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"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state how long the data will remain available or make any persistence commitment. [majority verdict 'no' (3/4 passes agreed)]","anchors":["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'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"TSV and VCF","grounded":false,"rationale":"The paper states that data are released in TSV and VCF formats, both of which are open, community-standard formats. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","anchors":["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"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Human Phenotype Ontology (HPO) (23) terms were added as anewfieldtoEIDs.","grounded":true,"rationale":"The paper names Human Phenotype Ontology (HPO), an OBO ontology and a community data standard. [majority verdict 'yes' (3/4 passes agreed)]","anchors":["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'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not give a specific identifier (accession, DOI, RRID) for any external resource it builds on; external resources appear only as bare names or reference-list entries.","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":70.83,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"CIViC data is available under a creative commons CC0 (public domain dedication)","grounded":true,"rationale":"CC0 is an open standard licence conformant with the Open Definition.","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":0.0,"verdict":"no","evidence":"CIViC Curators extract detailed evidence of the clinical significance of variants in cancer from the peer-reviewed, published literature and selected conference abstracts to contribute to the resource.","grounded":false,"rationale":"The production method is described in generic terms (curation from literature) without naming specific instruments, kits, or software versions. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/4 passes agreed)]","anchors":["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"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Additional documentation and help can be found in our help documentation: https://civicdb.org/pages/help.","grounded":true,"rationale":"The paper references external documentation but does not include a codebook within the article or state that it ships with the data. [majority verdict 'partial' (2/4 passes agreed)]","anchors":["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"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"(N = 328 as of 15 August 2022, Supplemental Figure S1)","grounded":true,"rationale":"The paper uses a date ('15 August 2022') to pin the snapshot of the data, but no version token is given.","anchors":["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'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"All underlying code is available on GitHub under an MIT license (https://github.com/griffithlab/civic-v2).","grounded":true,"rationale":"The paper gives a machine-resolvable code-repository URL (GitHub) for the study's own code.","anchors":["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)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"U01CA209936, U24CA237719","grounded":true,"rationale":"The paper lists specific grant numbers (e.g., U01CA209936, U24CA237719) attached to named funders.","anchors":["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"],"scored":true,"signal":null}]}},"actions":[{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org.","why":"The host is a project website (civicdb.org), not a recognised curated repository from re3data/FAIRsharing. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/4 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed onhttps: //civicdb.org.","why":"The paper gives a web address (https://civicdb.org) rather than a persistent-identifier scheme string for its own dataset. [majority verdict 'partial' (3/4 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org.","why":"The data availability statement provides a direct link to the data with no precondition stated. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org.","why":"The dataset identifier (URL) appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/4 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"TSV and VCF","why":"The paper states that data are released in TSV and VCF formats, both of which are open, community-standard formats. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"(N = 328 as of 15 August 2022, Supplemental Figure S1)","why":"The paper uses a date ('15 August 2022') to pin the snapshot of the data, but no version token is given.","gain":2.08,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"CIViC data is available under a creative commons CC0 (public domain dedication) and can be viewed on https://civicdb.org. All underlying code is available on GitHub under an MIT license (https://github.com/griffithlab/civic-v2). Data is available via API (https://griffithlab.github.io/civic-v2/) and regular releases in TSV and VCF format (https://civicdb.org/releases/main).","why":"The statement points to a website (CIViCdb) and a GitHub repository, not to a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"CIViC Curators extract detailed evidence of the clinical significance of variants in cancer from the peer-reviewed, published literature and selected conference abstracts to contribute to the resource.","why":"The production method is described in generic terms (curation from literature) without naming specific instruments, kits, or software versions. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/4 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Additional documentation and help can be found in our help documentation: https://civicdb.org/pages/help.","why":"The paper references external documentation but does not include a codebook within the article or state that it ships with the data. [majority verdict 'partial' (2/4 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The CIViC data are literature-derived variant interpretations, not sensitive human-subject data, and no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). 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 give a specific identifier (accession, DOI, RRID) for any external resource it builds on; external resources appear only as bare names or reference-list entries.","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 how long the data will remain available or make any persistence commitment. [majority verdict 'no' (3/4 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF."],"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":"2026-07-20T11:23:38.073649Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}