{"doi":"10.1093/nar/gkaf1341","title":"The IGVF catalog—from genetic variation to function","abstract":"Genomic variation between individuals is essential for understanding how differences in the genome sequence affect molecular and cellular processes. The Impact of Genomic Variation on Function (IGVF) Consortium aims to uncover the relationships among genomic variation, genome function, and phenotypes by combining experimental techniques, such as single-cell mapping and genomic perturbation assays, with computational approaches such as machine learning-based predictive modeling. The IGVF Data and Administrative Coordinating Centers collect, analyze, and disseminate data and results from across the consortium through an open-source platform called the IGVF Catalog. This resource includes, but is not limited to, data on the effects of coding variants on protein abundance and function, noncoding variants on enhancer activity (measured by MPRA or predicted computationally), and associations between variants and quantitative traits. All data are organized within a graph database comprising over 50 types of data collections with nearly 3 billion nodes and over 7.5 billion edges. The Catalog offers public API endpoints (https://api.catalogkg.igvf.org/) and a user-friendly interface for exploring, querying, and visualizing the data at https://catalog.igvf.org. We expect that this open-access platform will support the broader scientific community to advance our understanding of how genomic variation influences biology and disease.","journal":"Nucleic Acids Research","year":2025,"id":527757,"datarank":0.21865642877663732,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.0107122746086537,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.0107122746086537,"corpus_percentile":37.162528042082464,"corpus_rank":8122,"citation_count":3,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5071,"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":62.5,"fair_percentile":81.0149801284011,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":69083,"name":"Shane Liu","orcid":null,"position":1,"is_corresponding":false},{"id":1016446,"name":"Pedro Assis","orcid":"0000-0001-9289-0677","position":2,"is_corresponding":false},{"id":1016445,"name":"Mingjie Li","orcid":"0000-0001-5337-4901","position":3,"is_corresponding":false},{"id":714560,"name":"Shengcheng Dong","orcid":"0000-0001-5728-8090","position":4,"is_corresponding":false},{"id":1159180,"name":"Ian Whaling","orcid":"0000-0002-2683-9299","position":5,"is_corresponding":false},{"id":1016447,"name":"Otto Jolanki","orcid":"0000-0001-8601-4849","position":6,"is_corresponding":false},{"id":418371,"name":"Meenakshi S. Kagda","orcid":"0000-0003-0545-0185","position":7,"is_corresponding":false},{"id":24569,"name":"Wenjin Zhang","orcid":"0000-0002-5979-0102","position":8,"is_corresponding":false},{"id":376499,"name":"Juan F Macias-Velasco","orcid":"0000-0003-2827-4647","position":9,"is_corresponding":false},{"id":1405137,"name":"Tianjie Liu","orcid":"0000-0002-2321-1869","position":10,"is_corresponding":false},{"id":24451,"name":"Sarah Cody","orcid":null,"position":11,"is_corresponding":false},{"id":24433,"name":"Lucinda Antonacci-Fulton","orcid":null,"position":12,"is_corresponding":false},{"id":831915,"name":"Yuanhao Huang","orcid":"0000-0002-8878-1520","position":13,"is_corresponding":false},{"id":277585,"name":"Jie Liu","orcid":"0000-0002-9504-0587","position":14,"is_corresponding":false},{"id":240435,"name":"Michael T. Montgomery","orcid":"0000-0002-6748-2329","position":15,"is_corresponding":false},{"id":991205,"name":"Daniel Zeiberg","orcid":"0000-0002-6919-7572","position":16,"is_corresponding":false},{"id":443681,"name":"Shantanu Jain","orcid":"0000-0002-7169-9483","position":17,"is_corresponding":false},{"id":74962,"name":"Vikas Pejaver","orcid":"0000-0002-1943-0284","position":18,"is_corresponding":false},{"id":49887,"name":"Timothy Bergquist","orcid":"0000-0001-5614-8977","position":19,"is_corresponding":false},{"id":889517,"name":"Yile Chen","orcid":"0000-0002-8424-8059","position":20,"is_corresponding":false},{"id":17057,"name":"PREDRAG RADIVOJAC","orcid":"0000-0002-6769-0793","position":21,"is_corresponding":false},{"id":29946,"name":"Charles A. Gersbach","orcid":"0000-0003-1478-4013","position":22,"is_corresponding":false},{"id":1405645,"name":"Rintsen N. Sherpa","orcid":null,"position":23,"is_corresponding":false},{"id":651288,"name":"Christopher P. Castro","orcid":"0000-0001-9727-1357","position":24,"is_corresponding":false},{"id":242216,"name":"Alan P. Boyle","orcid":"0000-0002-2081-1105","position":25,"is_corresponding":false},{"id":95807,"name":"Lea M. Starita","orcid":"0000-0003-2870-5099","position":26,"is_corresponding":false},{"id":262399,"name":"Douglas M. Fowler","orcid":"0000-0001-7614-1713","position":27,"is_corresponding":false},{"id":6730,"name":"Nadav Ahituv","orcid":"0000-0002-7434-8144","position":28,"is_corresponding":false},{"id":6116,"name":"Kushal K. Dey","orcid":"0000-0002-3520-2345","position":29,"is_corresponding":false},{"id":4376,"name":"William H. Majoros","orcid":"0000-0001-7284-9335","position":30,"is_corresponding":false},{"id":27827,"name":"Timothy E. Reddy","orcid":"0000-0002-7629-061X","position":31,"is_corresponding":false},{"id":306781,"name":"Mark Craven","orcid":"0000-0002-8917-7464","position":32,"is_corresponding":false},{"id":1266543,"name":"Riya Sinha","orcid":null,"position":33,"is_corresponding":false},{"id":1405138,"name":"Yuriy Sverchkov","orcid":"0000-0002-9851-8582","position":34,"is_corresponding":false},{"id":1405646,"name":"Xiangmeng Cai","orcid":null,"position":35,"is_corresponding":false},{"id":1405647,"name":"Mpathi Nzima","orcid":null,"position":36,"is_corresponding":false},{"id":63406,"name":"Michael A. Calderwood","orcid":"0000-0001-6475-1418","position":37,"is_corresponding":false},{"id":11731,"name":"Joel Rozowsky","orcid":"0000-0002-3565-0762","position":38,"is_corresponding":false},{"id":108504,"name":"Mark Gerstein","orcid":"0000-0002-9746-3719","position":39,"is_corresponding":false},{"id":51348,"name":"Jian Ma","orcid":"0000-0002-4202-5834","position":40,"is_corresponding":false},{"id":43220,"name":"Feng Yue","orcid":"0000-0002-7954-5462","position":41,"is_corresponding":false},{"id":11685,"name":"J. Michael Cherry","orcid":"0000-0001-9163-5180","position":42,"is_corresponding":false},{"id":29945,"name":"Michael I. Love","orcid":"0000-0001-8401-0545","position":43,"is_corresponding":false},{"id":3038,"name":"Jesse M. Engreitz","orcid":"0000-0002-5754-1719","position":44,"is_corresponding":false},{"id":43021,"name":"Benjamin C. Hitz","orcid":"0000-0003-3361-3594","position":45,"is_corresponding":false},{"id":24564,"name":"Ting Wang","orcid":"0000-0002-6800-242X","position":46,"is_corresponding":false},{"id":417526,"name":"Daofeng Li","orcid":"0000-0001-7492-3703","position":0,"is_corresponding":true}],"reference_count":38,"raw_metadata":null,"created_at":"2026-07-19T02:50:44.062153Z","pmid":"41359121","pmcid":"PMC12807646","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":61.1111,"fair_a":81.25,"fair_i":100.0,"fair_r":58.3333,"fair_zscore":1.1103,"fair_rationale":{"fair_score":62.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The IGVF Catalog is freely available at https://catalog.igvf.org/","grounded":true,"rationale":"The paper gives a web URL for the data, not a persistent-identifier scheme string (no DOI, Handle, ARK, or repository accession).","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":"The IGVF Catalog is freely available at https://catalog.igvf.org/","grounded":true,"rationale":"The data are held by the IGVF Catalog platform, a named host that is not a curated repository listed in re3data.","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":0.5,"verdict":"partial","evidence":"The IGVF Catalog is freely available at https://catalog.igvf.org/ , with detailed documentation and user guidance provided at https://docs.catalog.igvf.org . 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All of the code for the IGVF catalog backend, including database and API, is available at Zenedo (10.5281/zenodo.17468372).","grounded":true,"rationale":"The DAS points to a website and API, not to a repository record with an accession for the dataset itself, so it falls under Colavizza category 2 (link to article/supplement) or category 3 but not to a repository record; the code has a DOI but the data does not.","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. 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[majority verdict 'partial' (3/5 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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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).","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.","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."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:12:00.322490Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}