{"doi":"10.1038/s42003-025-08496-9","title":"The Consortium for Genomic Diversity, Ancestry, and Health in Colombia (CÓDIGO): building local capacity in genomics and bioinformatics","abstract":"The Consortium for Genomic Diversity, Ancestry, and Health in Colombia (CÓDIGO) aims to build a community of Colombian researchers in support of local capacity in genomics, bioinformatics, and precision health. Here, we present the first CÓDIGO data release and the consortium web platform, including annotations for more than 95 million genetic variants from 1441 samples representing 14 populations from across the country. CÓDIGO samples show a wide range of African (16.7%), Indigenous American (32.8%), and European (50.6%) genetic ancestry components, with five distinct ancestry clusters. Thousands of ancestry-enriched variants, with divergent allele frequencies across clusters, show pharmacogenomic and clinical genetic associations. Examples include African ancestry-enriched variants associated with fast metabolism of the immunosuppressive drug tacrolimus and malaria resistance, and European ancestry-enriched variants associated with nicotine dependence and hereditary hemochromatosis. CÓDIGO reveals the nexus between ancestry and health in Colombia and underscores the utility of collaborative genome sequence analysis efforts.","journal":"Communications Biology","year":2025,"id":517554,"datarank":0.4112325278811583,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.08164884128072535,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.08164884128072535,"corpus_percentile":55.17908254041928,"corpus_rank":5795,"citation_count":8,"citer_count":8,"citers_with_citation_signal":4,"citers_with_endowment":4,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9596,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":31.25,"fair_percentile":47.04983185570162,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":910411,"name":"Shivam Sharma","orcid":"0000-0003-3577-1596","position":1,"is_corresponding":false},{"id":1384544,"name":"James Matthew Hamilton","orcid":null,"position":2,"is_corresponding":false},{"id":117418,"name":"T. Nguyen","orcid":null,"position":3,"is_corresponding":false},{"id":284171,"name":"Sonali Gupta","orcid":"0000-0002-1663-0838","position":4,"is_corresponding":false},{"id":1384545,"name":"Aravinth Venkatesh Natarajan","orcid":null,"position":5,"is_corresponding":false},{"id":700569,"name":"Shashwat Deepali Nagar","orcid":"0000-0001-7393-7054","position":6,"is_corresponding":false},{"id":1384546,"name":"Jay Landon Menuey","orcid":null,"position":7,"is_corresponding":false},{"id":1383870,"name":"Wei‐An Chen","orcid":"0000-0001-9087-5414","position":8,"is_corresponding":false},{"id":1383871,"name":"Adalberto Sánchez","orcid":"0000-0003-2478-7576","position":9,"is_corresponding":false},{"id":1384547,"name":"José María Satizábal-Soto","orcid":null,"position":10,"is_corresponding":false},{"id":211318,"name":"B. Martinez","orcid":"0000-0002-5653-3338","position":11,"is_corresponding":false},{"id":608895,"name":"Javier Marrugo","orcid":"0000-0001-9157-4269","position":12,"is_corresponding":false},{"id":1384548,"name":"Miguel A Medina-Rivas","orcid":null,"position":13,"is_corresponding":false},{"id":701330,"name":"Juan Esteban Gallo","orcid":null,"position":14,"is_corresponding":false},{"id":517393,"name":"I. King Jordan","orcid":"0000-0003-4996-2203","position":15,"is_corresponding":false},{"id":700570,"name":"Augusto Valderrama-Aguirre","orcid":"0000-0002-5255-1440","position":16,"is_corresponding":false},{"id":306053,"name":"Leonardo Mariño‐Ramírez","orcid":"0000-0002-5716-8512","position":0,"is_corresponding":true}],"reference_count":56,"raw_metadata":null,"created_at":"2026-07-19T02:48:59.410472Z","pmid":"40676265","pmcid":"PMC12271396","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":44.4444,"fair_a":43.75,"fair_i":20.0,"fair_r":29.1667,"fair_zscore":-0.1266,"fair_rationale":{"fair_score":31.25,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":44.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"https://codigo.biosci.gatech.edu/","grounded":true,"rationale":"The paper gives a web URL for the data, not a persistent identifier from a recognised PID scheme. [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":0.5,"verdict":"partial","evidence":"CÓDIGO summary statistics are made available on the CÓDIGO web platform: https://codigo.biosci.gatech.edu/","grounded":true,"rationale":"The named holder is the CÓDIGO web platform, a project/consortium website, not a curated repository listed in re3data/FAIRsharing. [majority verdict 'partial' (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":"CÓDIGO summary statistics are made available on the CÓDIGO web platform: https://codigo.biosci.gatech.edu/ Access to the primary, de-identified genomic data are available on request from the individual data contributors. Requests should be addressed to CÓDIGO General Director Augusto Valderrama-Aguirre: a.valderramaa@uniandes.edu.co.","grounded":false,"rationale":"The statement points to a web platform URL for summary statistics and to a person for primary data, not to a repository record with an accession. [downgraded to 'no' — no verifiable quote from the paper]","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 | CÓDIGO genomic variant dataset","grounded":true,"rationale":"The paper contains an itemised table (Table 1) that inventories the eight independent datasets, including sample counts, variant counts, technology, and other details.","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":"Secondary summary statistics calculated from the primary data, together with variant annotations, are made freely available via the CÓDIGO database and web platform at https://codigo.biosci.gatech.edu/.","grounded":false,"rationale":"The dataset URL appears only in the body text (data availability statement and methods), not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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":43.75,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Secondary summary statistics calculated from the primary data, together with variant annotations, are made freely available via the CÓDIGO database and web platform at https://codigo.biosci.gatech.edu/.","grounded":false,"rationale":"The summary statistics are stated to be freely available without any precondition, satisfying the 'yes' class for at least part of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 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":0.5,"verdict":"partial","evidence":"Secondary summary statistics calculated from the primary data, together with variant annotations, are made freely available via the CÓDIGO database and web platform at https://codigo.biosci.gatech.edu/.","grounded":false,"rationale":"The paper explicitly labels the summary statistics as 'freely available', which is a natural-language equivalent of the open-access label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":0.5,"verdict":"partial","evidence":"Access to the primary, de-identified genomic data are available on request from the individual data contributors.","grounded":true,"rationale":"The gatekeeper for the primary data is the individual data contributors, who are natural persons, not an institutional committee or repository.","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 makes no statement about when the data become available or how long they persist. [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":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name any file format for the released summary statistics or the primary data.","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":0.5,"verdict":"partial","evidence":"Searches can be performed using GRCh38 (hg38) or GRCh37 (hg19) human genome build coordinates.","grounded":false,"rationale":"The paper explicitly names human genome reference builds GRCh38 and GRCh37, which are community standards for genome coordinates. [downgraded to 'partial' — no verifiable quote from the paper]","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":"The ancestry-enriched variant found at chromosome 7 position 99,767,460 (rs4646437) maps to an intron of the Cytochrome P450 Family 3 Subfamily A Member 4 (CYP3A4) encoding gene.","grounded":false,"rationale":"The paper includes rsIDs (dbSNP identifiers) for variants, which are identifiers for an external resource (dbSNP). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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":29.17,"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 does not name any licence or reuse terms for the data; the CC-BY 4.0 licence applies only to the article.","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":0.5,"verdict":"partial","evidence":"Custom variant file format conversion scripts and Plink version 1.9, with the fixed allele setting, were used to convert genomic variant datasets to Plink file formats bed/bim/fam.","grounded":false,"rationale":"The paper names specific software and versions (e.g., Plink version 1.9, GATK version 4.0.10) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"Table 1 | CÓDIGO genomic variant dataset","grounded":true,"rationale":"The variable-level definitions (source, sample count, variant count, technology, etc.) are provided inside the article in Table 1, not in a separate documentation object shipped with the data. [majority verdict 'partial' (3/4 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":"The CÓDIGO dataset release 1.0 is made up of 1441 Colombian genomic variant samples contributed by investigators from a variety of participating institutions across the country (Table 1 and Fig. 1).","grounded":false,"rationale":"The paper explicitly states the version as 'release 1.0', providing a version token for the snapshot. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","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":0.0,"verdict":"no","evidence":"Code used to produce the published results is available on request from CÓDIGO General Director Augusto Valderrama-Aguirre: a.valderramaa@uniandes.edu.co.","grounded":true,"rationale":"The only offered route for code is a discretionary request to a person, which is not a machine-resolvable locator.","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":"L.M.R. and S.G. were supported by the Division of Intramural Research (DIR) of the National Institute on Minority Health and Health Disparities (NIMHD) at NIH (Award Number: 1ZIAMD000018).","grounded":true,"rationale":"The paper provides specific grant numbers (e.g., 1ZIAMD000018, RF383, PVI0122029) 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":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any licence or reuse terms for the data; the CC-BY 4.0 licence applies only to the article.","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"https://codigo.biosci.gatech.edu/","why":"The paper gives a web URL for the data, not a persistent identifier from a recognised PID scheme. [majority verdict 'partial' (3/4 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"CÓDIGO summary statistics are made available on the CÓDIGO web platform: https://codigo.biosci.gatech.edu/","why":"The named holder is the CÓDIGO web platform, a project/consortium website, not a curated repository listed in re3data/FAIRsharing. [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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Secondary summary statistics calculated from the primary data, together with variant annotations, are made freely available via the CÓDIGO database and web platform at https://codigo.biosci.gatech.edu/.","why":"The summary statistics are stated to be freely available without any precondition, satisfying the 'yes' class for at least part of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Secondary summary statistics calculated from the primary data, together with variant annotations, are made freely available via the CÓDIGO database and web platform at https://codigo.biosci.gatech.edu/.","why":"The dataset URL appears only in the body text (data availability statement and methods), not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any file format for the released summary statistics or the primary data.","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Code used to produce the published results is available on request from CÓDIGO General Director Augusto Valderrama-Aguirre: a.valderramaa@uniandes.edu.co.","why":"The only offered route for code is a discretionary request to a person, which is not a machine-resolvable locator.","gain":8.33,"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":"The CÓDIGO dataset release 1.0 is made up of 1441 Colombian genomic variant samples contributed by investigators from a variety of participating institutions across the country (Table 1 and Fig. 1).","why":"The paper explicitly states the version as 'release 1.0', providing a version token for the snapshot. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","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":"CÓDIGO summary statistics are made available on the CÓDIGO web platform: https://codigo.biosci.gatech.edu/ Access to the primary, de-identified genomic data are available on request from the individual data contributors. Requests should be addressed to CÓDIGO General Director Augusto Valderrama-Aguirre: a.valderramaa@uniandes.edu.co.","why":"The statement points to a web platform URL for summary statistics and to a person for primary data, not to a repository record with an accession. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Secondary summary statistics calculated from the primary data, together with variant annotations, are made freely available via the CÓDIGO database and web platform at https://codigo.biosci.gatech.edu/.","why":"The paper explicitly labels the summary statistics as 'freely available', which is a natural-language equivalent of the open-access label. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In clinical / human-subjects, describe the data with OMOP CDM, CDISC SDTM or HL7 FHIR.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Searches can be performed using GRCh38 (hg38) or GRCh37 (hg19) human genome build coordinates.","why":"The paper explicitly names human genome reference builds GRCh38 and GRCh37, which are community standards for genome coordinates. [downgraded to 'partial' — no verifiable quote from the paper]","gain":0.0,"priority":"important","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":"partial","current":0.5,"evidence":"Custom variant file format conversion scripts and Plink version 1.9, with the fixed allele setting, were used to convert genomic variant datasets to Plink file formats bed/bim/fam.","why":"The paper names specific software and versions (e.g., Plink version 1.9, GATK version 4.0.10) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"Table 1 | CÓDIGO genomic variant dataset","why":"The variable-level definitions (source, sample count, variant count, technology, etc.) are provided inside the article in Table 1, not in a separate documentation object shipped with the data. [majority verdict 'partial' (3/4 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 clinical / human-subjects data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Access to the primary, de-identified genomic data are available on request from the individual data contributors.","why":"The gatekeeper for the primary data is the individual data contributors, who are natural persons, not an institutional committee or repository.","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":"The ancestry-enriched variant found at chromosome 7 position 99,767,460 (rs4646437) maps to an intron of the Cytochrome P450 Family 3 Subfamily A Member 4 (CYP3A4) encoding gene.","why":"The paper includes rsIDs (dbSNP identifiers) for variants, which are identifiers for an external resource (dbSNP). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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 makes no statement about when the data become available or how long they persist. [majority verdict 'no' (3/4 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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.","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects data, deposit in dbGaP or the European Genome-phenome Archive (EGA).","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 clinical / human-subjects repository accession (e.g. from dbGaP or the European Genome-phenome Archive (EGA)) 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":"2026-07-20T12:35:36.041442Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}