{"doi":"10.1093/genetics/iyad211","title":"FlyBase: updates to the <i>Drosophila</i> genes and genomes database","abstract":"FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction of single-cell RNA sequencing data, improved content and display of functional information, updated orthology pipelines, new chemical reports, and enhancements to our outreach resources.","journal":"Genetics","year":2024,"id":416079,"datarank":3.4552385165736594,"base_score":6.016157159698354,"endowment":6.016157159698354,"self_citation_contribution":0.9024235739547533,"citation_network_contribution":2.552814942618906,"self_endowment_contribution":0.9024235739547533,"citer_contribution":2.552814942618906,"corpus_percentile":93.54838709677419,"corpus_rank":835,"citation_count":409,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9576,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":103818,"name":"Steven J Marygold","orcid":"0000-0003-2759-266X","position":1,"is_corresponding":false},{"id":103814,"name":"Giulia Antonazzo","orcid":"0000-0003-0086-5621","position":2,"is_corresponding":false},{"id":103815,"name":"Helen Attrill","orcid":"0000-0003-3212-6364","position":3,"is_corresponding":false},{"id":839168,"name":"Damien Goutte-Gattat","orcid":"0000-0002-6095-8718","position":4,"is_corresponding":false},{"id":742276,"name":"Victoria K. Jenkins","orcid":"0000-0002-1567-7626","position":5,"is_corresponding":false},{"id":226981,"name":"Beverley Matthews","orcid":"0000-0002-0967-1076","position":6,"is_corresponding":false},{"id":226979,"name":"Gillian Millburn","orcid":"0000-0002-1139-1145","position":7,"is_corresponding":false},{"id":63125,"name":"Gilberto Dos Santos","orcid":null,"position":8,"is_corresponding":false},{"id":103822,"name":"Christopher J. Tabone","orcid":"0000-0001-8746-0680","position":9,"is_corresponding":false},{"id":14957,"name":"Norbert Perrimon","orcid":"0000-0001-7542-472X","position":10,"is_corresponding":false},{"id":229558,"name":"Susan Russo Gelbart","orcid":null,"position":11,"is_corresponding":false},{"id":229560,"name":"Kris Broll","orcid":null,"position":12,"is_corresponding":false},{"id":229561,"name":"Madeline A. Crosby","orcid":null,"position":13,"is_corresponding":false},{"id":103821,"name":"Kathleen Falls","orcid":null,"position":15,"is_corresponding":false},{"id":226978,"name":"L. Sian Gramates","orcid":"0000-0002-6700-3797","position":16,"is_corresponding":false},{"id":88118,"name":"Ian Longden","orcid":null,"position":18,"is_corresponding":false},{"id":840568,"name":"Jolene Seme","orcid":null,"position":20,"is_corresponding":false},{"id":103823,"name":"Pinglei Zhou","orcid":null,"position":22,"is_corresponding":false},{"id":229562,"name":"Mark Zytkovicz","orcid":null,"position":23,"is_corresponding":false},{"id":229563,"name":"Nick Brown","orcid":null,"position":24,"is_corresponding":false},{"id":226977,"name":"Aoife Larkin","orcid":"0000-0003-4970-5901","position":28,"is_corresponding":false},{"id":226983,"name":"Alex McLachlan","orcid":"0000-0002-5214-8125","position":30,"is_corresponding":false},{"id":226984,"name":"Clare Pilgrim","orcid":"0000-0002-1373-1705","position":32,"is_corresponding":false},{"id":45078,"name":"Thomas C. Kaufman","orcid":"0000-0003-1406-7671","position":34,"is_corresponding":false},{"id":226986,"name":"Brian R. Calvi","orcid":"0000-0001-5304-0047","position":35,"is_corresponding":false},{"id":1198900,"name":"Seth Campbell","orcid":"0000-0002-9620-8329","position":36,"is_corresponding":false},{"id":229564,"name":"Josh Goodman","orcid":null,"position":37,"is_corresponding":false},{"id":103825,"name":"Victor Strelets","orcid":null,"position":38,"is_corresponding":false},{"id":103826,"name":"Jim Thurmond","orcid":"0000-0002-5142-2583","position":39,"is_corresponding":false},{"id":226987,"name":"Richard M. Cripps","orcid":"0000-0001-6565-285X","position":40,"is_corresponding":false},{"id":229565,"name":"TyAnna L. Lovato","orcid":null,"position":41,"is_corresponding":false},{"id":226985,"name":"Arzu Öztürk‐Çolak","orcid":"0000-0002-8116-217X","position":0,"is_corresponding":true}],"reference_count":24,"raw_metadata":null,"created_at":"2026-07-19T01:56:20.964471Z","pmid":"38301657","pmcid":"PMC11075543","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":50.0,"fair_a":81.25,"fair_i":40.0,"fair_r":25.0,"fair_zscore":0.7804,"fair_rationale":{"fair_score":54.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All FlyBase data and tools are freely available at https://flybase.org/","grounded":true,"rationale":"The paper gives a web URL for the data, which is not a persistent identifier scheme (DOI, Handle, etc.). 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[majority verdict 'yes' (4/5 passes agreed)]","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":"No identifier for an external resource (e.g., another dataset, database build, or software) is provided; only paper DOIs are cited. [majority verdict 'no' (4/5 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":25.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper mentions a Creative Commons license for the article, but not for the data itself.","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":0.5,"verdict":"partial","evidence":"DIOPT v9.1","grounded":false,"rationale":"The paper names specific software tools (DIOPT v9.1, OrthoDB, VEP) used to produce the data. 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Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named for the released data.","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. 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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).","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. 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Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list."],"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":"2026-07-20T10:49:24.793731Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}