{"doi":"10.1093/nar/gky1106","title":"The PRIDE database and related tools and resources in 2019: improving support for quantification data","abstract":"The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.","journal":"Nucleic Acids Research","year":2018,"id":9538,"datarank":15.035088467034736,"base_score":8.87905466204227,"endowment":8.87905466204227,"self_citation_contribution":1.3318581993063408,"citation_network_contribution":13.703230267728395,"self_endowment_contribution":1.3318581993063408,"citer_contribution":13.703230267728395,"corpus_percentile":87.46948738812043,"corpus_rank":155,"citation_count":7380,"citer_count":188,"citers_with_citation_signal":188,"citers_with_endowment":188,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9583,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2018-11-05","fair_score":37.2917,"fair_percentile":18.68953386103782,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":79923,"name":"Attila Csordas","orcid":null,"position":1,"is_corresponding":false},{"id":79924,"name":"Jingwen Bai","orcid":null,"position":2,"is_corresponding":false},{"id":79925,"name":"Manuel Bernal-Llinares","orcid":null,"position":3,"is_corresponding":false},{"id":79926,"name":"Suresh Hewapathirana","orcid":"0000-0002-7862-5022","position":4,"is_corresponding":false},{"id":79927,"name":"Deepti J Kundu","orcid":"0000-0003-2989-5971","position":5,"is_corresponding":false},{"id":79928,"name":"Avinash Inuganti","orcid":null,"position":6,"is_corresponding":false},{"id":79929,"name":"Johannes Griss","orcid":"0000-0003-2206-9511","position":7,"is_corresponding":false},{"id":79930,"name":"Gerhard Mayer","orcid":"0000-0002-1767-2343","position":8,"is_corresponding":false},{"id":79931,"name":"Martin Eisenacher","orcid":"0000-0003-2687-7444","position":9,"is_corresponding":false},{"id":79932,"name":"Enrique Pérez","orcid":"0000-0003-1091-8926","position":10,"is_corresponding":false},{"id":79933,"name":"Julian Uszkoreit","orcid":"0000-0001-7522-4007","position":11,"is_corresponding":false},{"id":79934,"name":"Julianus Pfeuffer","orcid":"0000-0001-8948-9209","position":12,"is_corresponding":false},{"id":79935,"name":"Timo Sachsenberg","orcid":"0000-0002-2833-6070","position":13,"is_corresponding":false},{"id":79936,"name":"Şule Yılmaz","orcid":"0000-0002-5329-3324","position":14,"is_corresponding":false},{"id":79937,"name":"Shivani Tiwary","orcid":"0000-0002-5860-1306","position":15,"is_corresponding":false},{"id":79938,"name":"Jürgen Cox","orcid":null,"position":16,"is_corresponding":false},{"id":79939,"name":"Enrique Audain","orcid":"0000-0002-9201-7840","position":17,"is_corresponding":false},{"id":79940,"name":"Mathias Walzer","orcid":"0000-0003-4538-2754","position":18,"is_corresponding":false},{"id":79941,"name":"Andrew F. Jarnuczak","orcid":"0000-0001-6368-3951","position":19,"is_corresponding":false},{"id":79942,"name":"Tobias Ternent","orcid":"0000-0003-0279-7335","position":20,"is_corresponding":false},{"id":32867,"name":"Ann-Christine Syvanen","orcid":null,"position":21,"is_corresponding":false},{"id":17887,"name":"Juan Antonio Vizcaino","orcid":"0000-0002-3905-4335","position":22,"is_corresponding":false},{"id":79943,"name":"Attila Csordás","orcid":"0000-0003-3576-1793","position":24,"is_corresponding":false},{"id":79944,"name":"Manuel Bernal Llinares","orcid":"0000-0002-7368-180X","position":25,"is_corresponding":false},{"id":33701,"name":"Joëlle Pineau","orcid":"0000-0003-0747-7250","position":26,"is_corresponding":false},{"id":19125,"name":"Yasset Perez-Riverol","orcid":"0000-0001-6579-6941","position":0,"is_corresponding":true}],"reference_count":41,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"30395289","pmcid":"PMC6323896","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":55.0,"fair_i":25.0,"fair_r":16.6667,"fair_zscore":-0.7164,"fair_rationale":{"fair_score":37.29,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper mentions some metadata (e.g., species, tissue, instrument) used in the repository interface, but does not provide a rich machine-readable metadata description for the paper itself."}]},"A":{"name":"Accessible","score":55.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper describes multiple access methods (web, REST API, FTP, Aspera) for PRIDE data, but does not clearly specify a direct access protocol for the data underlying this paper."}]},"I":{"name":"Interoperable","score":25.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper states use of standard formats like mzTab and mzIdentML and mentions controlled vocabularies, but does not detail how these standards are applied to the paper's own data."}]},"R":{"name":"Reusable","score":16.67,"criteria":[{"key":"r_license","label":"Clear, open reuse 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and software.","Provide a direct link or DOI to the dataset used in this study, with clear access instructions.","Explicitly state the license for the paper's supplementary data (e.g., CC0 or CC BY).","Use standard identifiers (e.g., DOIs) for all referenced datasets and tools.","Add a reproducibility section describing how to rerun analyses, including exact software versions and parameters."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:27:28.798895Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}