{"doi":"10.1093/nar/gkac1052","title":"UniProt: the Universal Protein Knowledgebase in 2023","abstract":"The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data processing pipeline and to our website to adapt to an ever-increasing information content. The number of sequences in UniProtKB has risen to over 227 million and we are working towards including a reference proteome for each taxonomic group. We continue to extract detailed annotations from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations provided by automated systems using a variety of machine-learning techniques. In addition, the scientific community continues their contributions of publications and annotations to UniProt entries of their interest. Finally, we describe our new website (https://www.uniprot.org/), designed to enhance our users' experience and make our data easily accessible to the research community. This interface includes access to AlphaFold structures for more than 85% of all entries as well as improved visualisations for subcellular localisation of proteins.","journal":"Nucleic Acids Research","year":2022,"id":231536,"datarank":7.822412882321765,"base_score":8.87458787627932,"endowment":8.87458787627932,"self_citation_contribution":1.331188181441898,"citation_network_contribution":6.491224700879867,"self_endowment_contribution":1.331188181441898,"citer_contribution":6.491224700879867,"corpus_percentile":97.84946236559139,"corpus_rank":279,"citation_count":7147,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9495,"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":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":57226,"name":"María Martin","orcid":"0000-0001-5454-2815","position":1,"is_corresponding":false},{"id":5925,"name":"Sandra Orchard","orcid":"0000-0002-8878-3972","position":2,"is_corresponding":false},{"id":92022,"name":"Michele Magrane","orcid":"0000-0003-3544-996X","position":3,"is_corresponding":false},{"id":103476,"name":"Shadab Ahmad","orcid":"0000-0001-7208-5785","position":4,"is_corresponding":false},{"id":103477,"name":"Emanuele Alpi","orcid":"0000-0003-4822-9472","position":5,"is_corresponding":false},{"id":103478,"name":"Emily Bowler-Barnett","orcid":"0000-0003-4785-7231","position":6,"is_corresponding":false},{"id":103479,"name":"Ramona Britto","orcid":"0000-0003-1011-5410","position":7,"is_corresponding":false},{"id":103481,"name":"Hema Bye‐A‐Jee","orcid":"0000-0003-2464-7688","position":8,"is_corresponding":false},{"id":103483,"name":"Austra Cukura","orcid":null,"position":9,"is_corresponding":false},{"id":103485,"name":"Paul Denny","orcid":"0000-0003-4659-6893","position":10,"is_corresponding":false},{"id":52615,"name":"Tunca Doğan","orcid":"0000-0002-1298-9763","position":11,"is_corresponding":false},{"id":103486,"name":"ThankGod E. 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For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"We provide customizable views and downloads in a range of formats via the website, and file sets at the FTP site ( www.uniprot.org/downloads )","why":"The only locator given for the data is a web address (www.uniprot.org/downloads), not a persistent identifier scheme. [majority verdict 'partial' (4/5 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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"UniProt releases are published every eight weeks. We provide customizable views and downloads in a range of formats via the website","why":"The host is the UniProt website, which is not a curated repository that issues PIDs. [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","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":"No locator for the study's own code is given; only third-party tools and the website are mentioned.","gain":8.33,"priority":"important","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. 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