{"doi":"10.1093/nar/gkaf394","title":"The UniProt website API: facilitating programmatic access to protein knowledge","abstract":"The UniProt REST API is a freely available, open-access resource that powers the UniProt.org website and gives users flexible programmatic interaction with protein knowledge data. It provides access to UniProtKB, UniRef, UniParc, Proteomes, GeneCentric, ARBA, UniRule, and the ID Mapping tool, along with supporting data and controlled vocabularies. Users can access the API with their favorite programming language and generate example code snippets to access the UniProt databases using the API documentation page (https://www.uniprot.org/api-documentation) in various languages. API results can be returned and downloaded in various formats. With an average of 303 million requests per month over the last year, the API enables structured search queries using logical operators and parentheses, allows users to specify fields of interest within results, and customize downloads for direct integration into workflows. The API is a powerful tool that empowers users to fully utilize UniProt data across multiple datasets, enabling download, analysis, and extraction of valuable research insights. This website is free and open to all users, and there is no login requirement.","journal":"Nucleic Acids Research","year":2025,"id":508735,"datarank":1.2280366748562788,"base_score":5.0369526024136295,"endowment":5.0369526024136295,"self_citation_contribution":0.7555428903620446,"citation_network_contribution":0.4724937844942342,"self_endowment_contribution":0.7555428903620446,"citer_contribution":0.4724937844942342,"corpus_percentile":83.2985224723447,"corpus_rank":2160,"citation_count":153,"citer_count":100,"citers_with_citation_signal":30,"citers_with_endowment":30,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8697,"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":20.8333,"fair_percentile":36.38031183124427,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":103490,"name":"Leonardo Jose da Costa Gonzales","orcid":"0000-0002-7674-9558","position":1,"is_corresponding":false},{"id":103478,"name":"Emily Bowler-Barnett","orcid":"0000-0003-4785-7231","position":2,"is_corresponding":false},{"id":103512,"name":"Daniel L Rice","orcid":"0000-0002-2972-0365","position":3,"is_corresponding":false},{"id":1145198,"name":"Minjoon Kim","orcid":"0000-0003-3167-8538","position":4,"is_corresponding":false},{"id":1145609,"name":"Supun Wijerathne","orcid":null,"position":5,"is_corresponding":false},{"id":103498,"name":"Aurélien Luciani","orcid":"0000-0003-3175-8394","position":6,"is_corresponding":false},{"id":104536,"name":"Swaathi Kandasaamy","orcid":"0000-0002-7160-3242","position":7,"is_corresponding":false},{"id":103499,"name":"Jie Luo","orcid":"0000-0001-9404-1302","position":8,"is_corresponding":false},{"id":103522,"name":"Xavier Watkins","orcid":"0000-0001-9327-5887","position":9,"is_corresponding":false},{"id":1362233,"name":"Edd Turner","orcid":null,"position":10,"is_corresponding":false},{"id":57226,"name":"María Martin","orcid":"0000-0001-5454-2815","position":11,"is_corresponding":false},{"id":228792,"name":"Alex Bateman","orcid":"0000-0002-6982-4660","position":12,"is_corresponding":false},{"id":5925,"name":"Sandra Orchard","orcid":"0000-0002-8878-3972","position":14,"is_corresponding":false},{"id":92022,"name":"Michele Magrane","orcid":"0000-0003-3544-996X","position":15,"is_corresponding":false},{"id":499508,"name":"Shiqi Ye","orcid":"0009-0007-9070-443X","position":16,"is_corresponding":false},{"id":1169904,"name":"Aduragbemi S. Adesina","orcid":"0000-0002-1029-4159","position":17,"is_corresponding":false},{"id":1198609,"name":"David C. J. Carpentier","orcid":"0000-0002-8172-9121","position":20,"is_corresponding":false},{"id":103485,"name":"Paul Denny","orcid":"0000-0003-4659-6893","position":21,"is_corresponding":false},{"id":103487,"name":"Jun Fan","orcid":"0000-0003-3899-2191","position":22,"is_corresponding":false},{"id":56291,"name":"Abdulrahman Hussein","orcid":"0000-0002-4954-9147","position":24,"is_corresponding":false},{"id":103492,"name":"Alexandr Ignatchenko","orcid":"0000-0002-6083-941X","position":25,"is_corresponding":false},{"id":103493,"name":"Giuseppe Insana","orcid":"0000-0002-8186-1026","position":26,"is_corresponding":false},{"id":103494,"name":"Rizwan Ishtiaq","orcid":"0000-0001-8041-7321","position":27,"is_corresponding":false},{"id":103496,"name":"Vishal Joshi","orcid":"0000-0002-2542-8885","position":28,"is_corresponding":false},{"id":103497,"name":"Dushyanth Jyothi","orcid":"0000-0002-0448-5303","position":29,"is_corresponding":false},{"id":95739,"name":"Antonia Lock","orcid":"0000-0003-1179-5999","position":31,"is_corresponding":false},{"id":103500,"name":"Yvonne Lussi","orcid":"0000-0002-5753-0235","position":34,"is_corresponding":false},{"id":1145611,"name":"Juan Marín","orcid":null,"position":35,"is_corresponding":false},{"id":838591,"name":"Pedro Raposo","orcid":"0000-0001-6149-9456","position":36,"is_corresponding":false},{"id":838593,"name":"James Stephenson","orcid":"0000-0002-6427-5703","position":38,"is_corresponding":false},{"id":838594,"name":"Prabhat Totoo","orcid":"0000-0001-5923-4467","position":39,"is_corresponding":false},{"id":378740,"name":"Nadya Urakova","orcid":"0000-0003-3499-8158","position":40,"is_corresponding":false},{"id":103519,"name":"Preethi Vasudev","orcid":null,"position":41,"is_corresponding":false},{"id":1145610,"name":"Khawaja Talal Ibrahim","orcid":null,"position":43,"is_corresponding":false},{"id":1198611,"name":"C. Yu","orcid":"0000-0002-6478-5762","position":45,"is_corresponding":false},{"id":103525,"name":"Alan Bridge","orcid":"0000-0003-2148-9135","position":46,"is_corresponding":false},{"id":103527,"name":"Lucila Aimo","orcid":"0000-0003-0943-6401","position":47,"is_corresponding":false},{"id":103528,"name":"Ghislaine Argoud‐Puy","orcid":"0000-0002-2979-8613","position":48,"is_corresponding":false},{"id":103529,"name":"Andrea H Auchincloss","orcid":"0000-0002-5297-5390","position":49,"is_corresponding":false},{"id":103530,"name":"Kristian B. Axelsen","orcid":"0000-0003-3889-2879","position":50,"is_corresponding":false},{"id":103531,"name":"Parit Bansal","orcid":"0000-0002-0875-1680","position":51,"is_corresponding":false},{"id":103532,"name":"Delphine Baratin","orcid":"0000-0002-4873-3030","position":52,"is_corresponding":false},{"id":840279,"name":"Teresa M Batista Neto","orcid":null,"position":53,"is_corresponding":false},{"id":103533,"name":"Marie-Claude Blatter","orcid":"0000-0002-7474-1499","position":54,"is_corresponding":false},{"id":19090,"name":"Jerven T. Bolleman","orcid":"0000-0002-7449-1266","position":55,"is_corresponding":false},{"id":103534,"name":"Emmanuel Boutet","orcid":"0000-0002-3743-4203","position":56,"is_corresponding":false},{"id":103535,"name":"Lionel Breuza","orcid":"0000-0002-8075-8625","position":57,"is_corresponding":false},{"id":103536,"name":"Cristina Casals‐Casas","orcid":"0000-0001-8769-177X","position":58,"is_corresponding":false},{"id":103537,"name":"Kamal Chikh Echioukh","orcid":null,"position":59,"is_corresponding":false},{"id":103538,"name":"Elisabeth Coudert","orcid":"0000-0001-8314-404X","position":60,"is_corresponding":false},{"id":103539,"name":"Beatrice Cuche","orcid":null,"position":61,"is_corresponding":false},{"id":796874,"name":"Edouard de Castro","orcid":"0000-0001-5436-7383","position":62,"is_corresponding":false},{"id":103542,"name":"Anne Estreicher","orcid":"0000-0001-6828-2508","position":63,"is_corresponding":false},{"id":103543,"name":"Maria Livia Famiglietti","orcid":"0000-0002-5283-6593","position":64,"is_corresponding":false},{"id":103544,"name":"Marc Feuermann","orcid":"0000-0002-4187-2863","position":65,"is_corresponding":false},{"id":103545,"name":"Elisabeth Gasteiger","orcid":"0000-0003-1829-162X","position":66,"is_corresponding":false},{"id":5919,"name":"Pascale Gaudet","orcid":"0000-0003-1813-6857","position":67,"is_corresponding":false},{"id":103546,"name":"Sébastien Géhant","orcid":"0000-0003-1608-9954","position":68,"is_corresponding":false},{"id":103547,"name":"Vivienne Baillie Gerritsen","orcid":null,"position":69,"is_corresponding":false},{"id":103548,"name":"Arnaud Gos","orcid":"0000-0002-5018-1378","position":70,"is_corresponding":false},{"id":158456,"name":"Nadine Gruaz","orcid":null,"position":71,"is_corresponding":false},{"id":103551,"name":"Chantal Hulo","orcid":"0000-0001-8176-7999","position":72,"is_corresponding":false},{"id":103552,"name":"Nevila Hyka‐Nouspikel","orcid":"0000-0001-7855-209X","position":73,"is_corresponding":false},{"id":103553,"name":"Florence Jungo","orcid":"0000-0002-7456-8390","position":74,"is_corresponding":false},{"id":30352,"name":"Arnaud Kerhornou","orcid":"0000-0002-2890-295X","position":75,"is_corresponding":false},{"id":103555,"name":"Philippe Le Mercier","orcid":"0000-0001-8528-090X","position":76,"is_corresponding":false},{"id":103556,"name":"Damien Lieberherr","orcid":"0000-0002-9724-1710","position":77,"is_corresponding":false},{"id":103559,"name":"Patrick Masson","orcid":"0000-0001-7646-0052","position":78,"is_corresponding":false},{"id":796873,"name":"Anne Morgat","orcid":"0000-0002-1216-2969","position":79,"is_corresponding":false},{"id":840281,"name":"Salvo Paesano","orcid":null,"position":80,"is_corresponding":false},{"id":796876,"name":"Ivo Pedruzzi","orcid":"0000-0001-8561-7170","position":81,"is_corresponding":false},{"id":840282,"name":"Sandrine Pilbout","orcid":null,"position":82,"is_corresponding":false},{"id":838596,"name":"Lucille Pourcel","orcid":"0000-0003-1522-9900","position":83,"is_corresponding":false},{"id":103526,"name":"Sylvain Poux","orcid":"0000-0001-7299-6685","position":84,"is_corresponding":false},{"id":796877,"name":"Monica Pozzato","orcid":"0000-0002-3080-5243","position":85,"is_corresponding":false},{"id":840283,"name":"Manuela Pruess","orcid":null,"position":86,"is_corresponding":false},{"id":58252,"name":"Nicole Redaschi","orcid":"0000-0001-8890-2268","position":87,"is_corresponding":false},{"id":104543,"name":"Catherine Rivoire","orcid":"0000-0002-5979-8382","position":88,"is_corresponding":false},{"id":104544,"name":"Christian J A Sigrist","orcid":"0000-0002-4348-0070","position":89,"is_corresponding":false},{"id":840284,"name":"Karin Sonesson","orcid":null,"position":90,"is_corresponding":false},{"id":838597,"name":"Shyamala Sundaram","orcid":"0000-0003-4209-460X","position":91,"is_corresponding":false},{"id":1145199,"name":"Anastasia Sveshnikova","orcid":"0000-0001-9291-0965","position":92,"is_corresponding":false},{"id":57230,"name":"Cathy Wu","orcid":"0000-0001-6379-8601","position":93,"is_corresponding":false},{"id":476473,"name":"Chuming Chen","orcid":"0000-0002-7287-9013","position":94,"is_corresponding":false},{"id":626464,"name":"Hongzhan Huang","orcid":"0000-0001-9594-9304","position":95,"is_corresponding":false},{"id":1145612,"name":"Kati Laiho","orcid":null,"position":96,"is_corresponding":false},{"id":1145613,"name":"Minna Lehväslaiho","orcid":null,"position":97,"is_corresponding":false},{"id":225703,"name":"Peter B. McGarvey","orcid":"0000-0002-8312-6017","position":98,"is_corresponding":false},{"id":57228,"name":"Darren A. Natale","orcid":"0000-0001-5809-9523","position":99,"is_corresponding":false},{"id":103476,"name":"Shadab Ahmad","orcid":"0000-0001-7208-5785","position":0,"is_corresponding":true}],"reference_count":7,"raw_metadata":null,"created_at":"2026-07-19T02:47:00.188082Z","pmid":"40331428","pmcid":"PMC12230682","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":11.1111,"fair_a":75.0,"fair_i":0.0,"fair_r":8.3333,"fair_zscore":-0.5389,"fair_rationale":{"fair_score":20.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":11.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not assign a persistent identifier (DOI, Handle, ARK, or repository accession) to its own dataset; the API URL is not a PID scheme. [majority verdict 'no' (4/5 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":null,"grounded":false,"rationale":"The paper does not name a repository holding the study's own data; the data is the API service itself, not deposited in a repository.","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":"API is freely available at https://rest.uniprot.org/ . API documentation is freely available at https://www.uniprot.org/api-documentation/","grounded":true,"rationale":"The data-availability statement points to a URL (the API endpoint), not a repository record with an accession or DOI, so it falls under Colavizza category 2 (data in the article or supplementary) or a link. However, the statement exists and provides a URL, which is not a repository record, so it is partial. [majority verdict 'partial' (4/5 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide an itemised inventory of the dataset's files, variables, or samples; it describes the API and the UniProt databases generically.","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":null,"grounded":false,"rationale":"No identifier for the study's own dataset appears in the reference list or body text; the paper describes an API, not a dataset. [majority verdict 'no' (4/5 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":75.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"This website is free and open to all users, and there is no login requirement.","grounded":true,"rationale":"The text states the API is freely available without any precondition such as login, registration, or embargo. [majority verdict 'yes' (3/5 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":"The UniProt REST API is a freely available, open-access resource","grounded":true,"rationale":"The paper explicitly labels the API as 'open-access' and 'freely available', which is a natural-language equivalent of the standard access-label vocabulary. [majority verdict 'yes' (3/5 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 paper does not involve sensitive or human-subject data; no gatekeeper is named or needed.","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 any retention period or persistence commitment for the study's own data (the API service).","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":0.0,"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 mentions that the API returns data in formats like JSON, XML, FASTA, but these are formats for the response, not for the study's own dataset. The study's own data (the API) has no file format named. [majority verdict 'no' (3/5 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community-standard vocabulary or checklist (e.g., MIAME, GO) is explicitly named and applied to the study's own data.","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 study does not produce a dataset that could depend on other resources; no identifiers for external resources are provided in the context of the study's own data. [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":8.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license is attached to the study's data (the API); the CC-BY license at the footer applies to the article, not the data.","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":null,"grounded":false,"rationale":"The paper does not name specific instruments, assays, or software used to produce the study's own data (the API is a service, not a dataset produced by a method). [majority verdict 'no' (3/5 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (README, codebook, data dictionary) is named as travelling with the study's data; the API documentation is separate. [majority verdict 'no' (4/5 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper mentions a data release version (2025_01) for the UniProt data, but not for the study's own data (the API). No version token is given for the API itself.","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":null,"grounded":false,"rationale":"The paper does not provide a locator (URL, DOI, or package identifier) for the study's own code; the API is a service, not shared 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":"U24HG007822","grounded":true,"rationale":"The paper includes an award number (U24HG007822) from the National Institutes of Health, which is an alphanumeric grant identifier.","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_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":"no","current":0.0,"evidence":null,"why":"The paper does not assign a persistent identifier (DOI, Handle, ARK, or repository accession) to its own dataset; the API URL is not a PID scheme. [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"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 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":null,"why":"The paper does not name a repository holding the study's own data; the data is the API service itself, not deposited in a repository.","gain":16.67,"priority":"essential","scored":true},{"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":"No license is attached to the study's data (the API); the CC-BY license at the footer applies to the article, not the data.","gain":16.67,"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":null,"why":"No identifier for the study's own dataset appears in the reference list or body text; the paper describes an API, not a dataset. [majority verdict 'no' (4/5 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":"no","current":0.0,"evidence":null,"why":"The paper mentions that the API returns data in formats like JSON, XML, FASTA, but these are formats for the response, not for the study's own dataset. The study's own data (the API) has no file format named. [majority verdict 'no' (3/5 passes agreed)]","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":null,"why":"The paper does not provide a locator (URL, DOI, or package identifier) for the study's own code; the API is a service, not shared code.","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":"no","current":0.0,"evidence":null,"why":"The paper mentions a data release version (2025_01) for the UniProt data, but not for the study's own data (the API). No version token is given for the API itself.","gain":4.17,"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":"partial","current":0.5,"evidence":"API is freely available at https://rest.uniprot.org/ . API documentation is freely available at https://www.uniprot.org/api-documentation/","why":"The data-availability statement points to a URL (the API endpoint), not a repository record with an accession or DOI, so it falls under Colavizza category 2 (data in the article or supplementary) or a link. However, the statement exists and provides a URL, which is not a repository record, so it is partial. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide an itemised inventory of the dataset's files, variables, or samples; it describes the API and the UniProt databases generically.","gain":0.0,"priority":"essential","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 genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No community-standard vocabulary or checklist (e.g., MIAME, GO) is explicitly named and applied to the study's own data.","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":"no","current":0.0,"evidence":null,"why":"The paper does not name specific instruments, assays, or software used to produce the study's own data (the API is a service, not a dataset produced by a method). [majority verdict 'no' (3/5 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":"no","current":0.0,"evidence":null,"why":"No documentation object (README, codebook, data dictionary) is named as travelling with the study's data; the API documentation is separate. [majority verdict 'no' (4/5 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 paper does not involve sensitive or human-subject data; no gatekeeper is named or needed.","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 study does not produce a dataset that could depend on other resources; no identifiers for external resources are provided in the context of the study's own data. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state any retention period or persistence commitment for the study's own data (the API service).","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For 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).","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.","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":"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":"2026-07-20T10:58:00.080513Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}