{"doi":"10.1093/nar/gky1078","title":"The European Nucleotide Archive in 2018","abstract":"The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided from EMBL-EBI, has for more than three decades been responsible for archiving the world's public sequencing data and presenting this important resource to the scientific community to support and accelerate the global research effort. Here, we outline ENA services and content in 2018 and provide an overview of a selection of focus areas of development work: extending data coordination services around ENA, sequence submissions through template expansion, early pre-submission validation tools and our move towards a new browser and retrieval infrastructure.","journal":"Nucleic Acids Research","year":2018,"id":5890,"datarank":5.278975415651154,"base_score":4.8283137373023015,"endowment":4.8283137373023015,"self_citation_contribution":0.7242470605953454,"citation_network_contribution":4.554728355055809,"self_endowment_contribution":0.7242470605953454,"citer_contribution":4.554728355055809,"corpus_percentile":71.68429617575265,"corpus_rank":349,"citation_count":127,"citer_count":117,"citers_with_citation_signal":95,"citers_with_endowment":95,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9429,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2018-11-05","fair_score":59.1667,"fair_percentile":92.10642040457344,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":34538,"name":"Blaise Alako","orcid":"0000-0001-6859-4421","position":1,"is_corresponding":false},{"id":18876,"name":"Clara Amid","orcid":"0000-0001-6534-7425","position":2,"is_corresponding":false},{"id":44742,"name":"Ana Cerdeño-Tárraga","orcid":"0000-0001-6635-3237","position":3,"is_corresponding":false},{"id":44744,"name":"Iain Cleland","orcid":"0000-0001-5515-2480","position":4,"is_corresponding":false},{"id":56290,"name":"Sam Holt","orcid":"0000-0002-3720-7836","position":5,"is_corresponding":false},{"id":56291,"name":"Abdulrahman Hussein","orcid":"0000-0002-4954-9147","position":6,"is_corresponding":false},{"id":56292,"name":"Suran Jayathilaka","orcid":"0000-0002-0154-8807","position":7,"is_corresponding":false},{"id":56293,"name":"Simon Kay","orcid":"0000-0001-7690-2711","position":8,"is_corresponding":false},{"id":15622,"name":"Thomas Keane","orcid":"0000-0001-7532-6898","position":9,"is_corresponding":false},{"id":29839,"name":"Rasko Leinonen","orcid":"0000-0002-2639-7187","position":10,"is_corresponding":false},{"id":56294,"name":"Xin Liu","orcid":"0000-0002-4570-850X","position":11,"is_corresponding":false},{"id":56295,"name":"Josué Martínez-Villacorta","orcid":null,"position":12,"is_corresponding":false},{"id":56296,"name":"Annalisa Milano","orcid":"0000-0002-9943-9018","position":13,"is_corresponding":false},{"id":44748,"name":"Nima Pakseresht","orcid":"0000-0001-8161-4204","position":14,"is_corresponding":false},{"id":37961,"name":"Jeena Rajan","orcid":"0000-0002-3613-0013","position":15,"is_corresponding":false},{"id":56297,"name":"Kethi Reddy","orcid":null,"position":16,"is_corresponding":false},{"id":56298,"name":"Edward Richards","orcid":null,"position":17,"is_corresponding":false},{"id":56299,"name":"Marc Rosello","orcid":null,"position":18,"is_corresponding":false},{"id":56300,"name":"Nicole Silvester","orcid":"0000-0002-6625-894X","position":19,"is_corresponding":false},{"id":56301,"name":"Dmitriy Smirnov","orcid":"0009-0006-4535-2132","position":20,"is_corresponding":false},{"id":56302,"name":"Ana-Luisa Toribio","orcid":null,"position":21,"is_corresponding":false},{"id":56303,"name":"Senthilnathan Vijayaraja","orcid":null,"position":22,"is_corresponding":false},{"id":11687,"name":"Guy Cochrane","orcid":"0000-0001-7954-7057","position":23,"is_corresponding":false},{"id":56304,"name":"E. G. Richards","orcid":"0000-0001-5975-6003","position":24,"is_corresponding":false},{"id":56289,"name":"Peter W. Harrison","orcid":"0000-0002-4007-2899","position":0,"is_corresponding":true}],"reference_count":10,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"30395270","pmcid":"PMC6323982","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"other-oa","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":77.5,"fair_a":67.5,"fair_i":50.0,"fair_r":41.6667,"fair_zscore":1.2623,"fair_rationale":{"fair_score":59.17,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":77.5,"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":0.75,"signal":null,"rationale":"The paper describes metadata-rich submissions via checklists and templates (e.g., 'template expansion', 'annotation checklists') but does not detail machine-readable metadata formats or standards for all data types."}]},"A":{"name":"Accessible","score":67.5,"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":0.75,"signal":null,"rationale":"Multiple access protocols are mentioned (RESTful API, Browser, programmatic retrieval, Swagger interface), but the access conditions for some services are implicit and not fully specified."}]},"I":{"name":"Interoperable","score":50.0,"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":1.0,"signal":null,"rationale":"The paper describes use of INSDC standards, GA4GH frameworks, GSC MIxS checklists, and FAANG metadata standards, showing strong adherence to community standards for interoperability."}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.667,"signal":null,"rationale":"Data availability statement and EMBL-EBI Terms of Use are provided, and the paper references open access (CC BY 4.0), but explicit license information for data and code is not detailed."}]}},"suggestions":["Specify the machine-readable metadata formats (e.g., XML, JSON schema) used for all submission types.","Provide explicit data access conditions for each service, including any authentication or rate-limiting requirements.","Include a data availability statement with persistent identifiers for the exact datasets discussed.","State the license for the code used (e.g., pre-submission validation tool) separately from the data license.","Include explicit reproducibility information, such as versioned data snapshots or analysis workflow availability."],"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":"2026-06-18T00:38:36.928529Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}