{"doi":"10.1093/molbev/msab259","title":"<i>Drosophila</i> Evolution over Space and Time (DEST): A New Population Genomics Resource","abstract":"Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.","journal":"Molecular Biology and Evolution","year":2021,"id":151098,"datarank":1.693265659495118,"base_score":4.465908118654584,"endowment":4.465908118654584,"self_citation_contribution":0.6698862177981877,"citation_network_contribution":1.0233794416969304,"self_endowment_contribution":0.6698862177981877,"citer_contribution":1.0233794416969304,"corpus_percentile":87.63827647559371,"corpus_rank":1599,"citation_count":86,"citer_count":46,"citers_with_citation_signal":38,"citers_with_endowment":38,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6824,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":406940,"name":"Joaquin C. B. Nunez","orcid":"0000-0002-3171-8918","position":1,"is_corresponding":false},{"id":642253,"name":"María Bogaerts-Márquez","orcid":"0000-0001-9107-984X","position":2,"is_corresponding":false},{"id":642254,"name":"Jesús Murga-Moreno","orcid":"0000-0002-1812-0399","position":3,"is_corresponding":false},{"id":642255,"name":"Margot Paris","orcid":"0000-0001-7328-3820","position":4,"is_corresponding":false},{"id":642256,"name":"Joseph Outten","orcid":"0000-0003-1588-4382","position":5,"is_corresponding":false},{"id":642257,"name":"Marta Coronado‐Zamora","orcid":"0000-0001-9779-9661","position":6,"is_corresponding":false},{"id":642258,"name":"Courtney Tern","orcid":"0000-0001-5029-595X","position":7,"is_corresponding":false},{"id":267476,"name":"Omar Rota‐Stabelli","orcid":"0000-0002-0030-7788","position":8,"is_corresponding":false},{"id":642259,"name":"Maria Pilar García Guerreiro","orcid":"0000-0001-9951-1879","position":9,"is_corresponding":false},{"id":642260,"name":"Sònia Casillas","orcid":"0000-0001-8191-0062","position":10,"is_corresponding":false},{"id":642261,"name":"Dorcas J. Orengo","orcid":"0000-0001-7911-3224","position":11,"is_corresponding":false},{"id":642262,"name":"Eva Puerma","orcid":"0000-0001-7261-187X","position":12,"is_corresponding":false},{"id":642263,"name":"Maaria Kankare","orcid":"0000-0003-1541-9050","position":13,"is_corresponding":false},{"id":642264,"name":"Lino Ometto","orcid":"0000-0002-2679-625X","position":14,"is_corresponding":false},{"id":642265,"name":"Volker Loeschcke","orcid":"0000-0003-1450-0754","position":15,"is_corresponding":false},{"id":642266,"name":"Banu Şebnem Önder","orcid":"0000-0002-3003-248X","position":16,"is_corresponding":false},{"id":642267,"name":"Jessica K. Abbott","orcid":"0000-0002-8743-2089","position":17,"is_corresponding":false},{"id":642268,"name":"Stephen W. Schaeffer","orcid":"0000-0003-2070-5342","position":18,"is_corresponding":false},{"id":484786,"name":"Subhash Rajpurohit","orcid":"0000-0001-9149-391X","position":19,"is_corresponding":false},{"id":642269,"name":"Emily L. Behrman","orcid":"0000-0002-2472-9635","position":20,"is_corresponding":false},{"id":642270,"name":"Mads F. Schou","orcid":"0000-0001-5521-5269","position":21,"is_corresponding":false},{"id":642271,"name":"Thomas Merritt","orcid":"0000-0002-4795-7534","position":22,"is_corresponding":false},{"id":642272,"name":"Brian P. Lazzaro","orcid":"0000-0002-3881-0995","position":23,"is_corresponding":false},{"id":642273,"name":"Amanda Glaser‐Schmitt","orcid":"0000-0002-1322-1000","position":24,"is_corresponding":false},{"id":642274,"name":"Eliza Argyridou","orcid":"0000-0002-6890-4642","position":25,"is_corresponding":false},{"id":642275,"name":"Fabian Staubach","orcid":"0000-0002-8097-2349","position":26,"is_corresponding":false},{"id":642276,"name":"Yun Wang","orcid":"0000-0002-2441-4182","position":27,"is_corresponding":false},{"id":642277,"name":"Eran Tauber","orcid":"0000-0003-4018-6535","position":28,"is_corresponding":false},{"id":642278,"name":"Svitlana Serga","orcid":"0000-0003-1875-3185","position":29,"is_corresponding":false},{"id":642279,"name":"Daniel K. Fabian","orcid":"0000-0002-9895-2848","position":30,"is_corresponding":false},{"id":642280,"name":"Kelly A. Dyer","orcid":"0000-0001-7480-2055","position":31,"is_corresponding":false},{"id":621339,"name":"Christopher W. Wheat","orcid":"0000-0003-1863-2340","position":32,"is_corresponding":false},{"id":642281,"name":"John Parsch","orcid":"0000-0001-9068-5549","position":33,"is_corresponding":false},{"id":642282,"name":"Sonja Grath","orcid":"0000-0003-3621-736X","position":34,"is_corresponding":false},{"id":554120,"name":"Marija Savić Veselinović","orcid":"0000-0001-8461-4373","position":35,"is_corresponding":false},{"id":554118,"name":"Marina Stamenković‐Radak","orcid":"0000-0002-6937-7282","position":36,"is_corresponding":false},{"id":554119,"name":"Mihailo Jelić","orcid":"0000-0002-1637-0933","position":37,"is_corresponding":false},{"id":643533,"name":"Antonio J. Buendía-Ruíz","orcid":null,"position":38,"is_corresponding":false},{"id":643534,"name":"Maria Josefa Gómez-Julián","orcid":null,"position":39,"is_corresponding":false},{"id":643535,"name":"Maria Luisa Espinosa-Jimenez","orcid":null,"position":40,"is_corresponding":false},{"id":643536,"name":"Francisco D. Gallardo-Jiménez","orcid":null,"position":41,"is_corresponding":false},{"id":642283,"name":"Aleksandra Patenković","orcid":"0000-0001-5763-6294","position":42,"is_corresponding":false},{"id":642284,"name":"Katarina Erić","orcid":"0000-0002-3456-2576","position":43,"is_corresponding":false},{"id":554121,"name":"Marija Tanasković","orcid":"0000-0003-1440-2257","position":44,"is_corresponding":false},{"id":642285,"name":"Anna Ullastres","orcid":"0009-0003-3681-0080","position":45,"is_corresponding":false},{"id":642286,"name":"Lain Guio","orcid":"0000-0002-5481-5200","position":46,"is_corresponding":false},{"id":642287,"name":"Miriam Merenciano","orcid":"0000-0001-8592-949X","position":47,"is_corresponding":false},{"id":95794,"name":"Sara Guirao‐Rico","orcid":"0000-0001-9896-4665","position":48,"is_corresponding":false},{"id":642288,"name":"Vivien Horváth","orcid":"0000-0001-6536-1710","position":49,"is_corresponding":false},{"id":642289,"name":"Darren J. Obbard","orcid":"0000-0001-5392-8142","position":50,"is_corresponding":false},{"id":513562,"name":"E. G. Pasyukova","orcid":"0000-0002-6491-8561","position":51,"is_corresponding":false},{"id":642290,"name":"В. Е. Алаторцев","orcid":"0000-0003-4713-6610","position":52,"is_corresponding":false},{"id":642291,"name":"Cristina P. Vieira","orcid":"0000-0002-7139-2107","position":53,"is_corresponding":false},{"id":642292,"name":"Jorge Vieira","orcid":"0000-0001-7032-5220","position":54,"is_corresponding":false},{"id":643537,"name":"Jorge Roberto Torres","orcid":null,"position":55,"is_corresponding":false},{"id":642293,"name":"Iryna Kozeretska","orcid":"0000-0002-6485-1408","position":56,"is_corresponding":false},{"id":642294,"name":"Oleksandr M. Maistrenko","orcid":"0000-0003-1961-7548","position":57,"is_corresponding":false},{"id":289352,"name":"Catherine Montchamp‐Moreau","orcid":"0000-0002-5044-9709","position":58,"is_corresponding":false},{"id":642295,"name":"Д. В. Муха","orcid":"0000-0002-7380-0776","position":59,"is_corresponding":false},{"id":483503,"name":"Heather E. Machado","orcid":"0000-0002-1523-3937","position":60,"is_corresponding":false},{"id":642296,"name":"Keric Lamb","orcid":"0009-0008-8898-7378","position":61,"is_corresponding":false},{"id":642297,"name":"Tânia F. Paulo","orcid":"0000-0002-8815-2636","position":62,"is_corresponding":false},{"id":642298,"name":"Leeban H. Yusuf","orcid":"0000-0001-6383-1176","position":63,"is_corresponding":false},{"id":642299,"name":"Antonio Barbadilla","orcid":"0000-0002-0374-1475","position":64,"is_corresponding":false},{"id":264408,"name":"Dmitri A. Petrov","orcid":"0000-0002-3664-9130","position":65,"is_corresponding":false},{"id":303839,"name":"Paul Schmidt","orcid":"0000-0002-8076-6705","position":66,"is_corresponding":false},{"id":499620,"name":"Josefa González","orcid":"0000-0001-9824-027X","position":67,"is_corresponding":false},{"id":642300,"name":"Thomas Flatt","orcid":"0000-0002-5990-1503","position":68,"is_corresponding":false},{"id":303840,"name":"Alan O. Bergland","orcid":"0000-0001-7145-7575","position":69,"is_corresponding":false},{"id":642252,"name":"Martin Kapun","orcid":"0000-0002-3810-0504","position":0,"is_corresponding":true}],"reference_count":128,"raw_metadata":null,"created_at":"2026-07-18T23:43:11.293086Z","pmid":"34469576","pmcid":"PMC8662648","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":38.8889,"fair_a":62.5,"fair_i":20.0,"fair_r":41.6667,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":38.89,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","grounded":true,"rationale":"The dataset is identified by a URL, not a persistent identifier scheme. [majority verdict 'partial' (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":0.5,"verdict":"partial","evidence":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","grounded":true,"rationale":"The data are hosted on a project website, not a curated repository. [majority verdict 'partial' (4/5 passes agreed)]","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":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","grounded":true,"rationale":"The statement points to a website, not a repository record with an accession.","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":"We provide data in two file formats (VCF and GDS)","grounded":false,"rationale":"The dataset's content is described in running prose, not an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","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":0.5,"verdict":"partial","evidence":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","grounded":true,"rationale":"The dataset identifier appears only in body text, not as a reference entry.","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":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio (last accessed September 6, 2021).","grounded":true,"rationale":"The text gives a route to the data with no stated precondition; the website is publicly accessible. [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":0.5,"verdict":"partial","evidence":"All data, tools, and supporting resources for the DEST data set, as well as reference tracks downloaded from FlyBase (v.6.12), are freely available at https://dest.bio","grounded":false,"rationale":"The paper explicitly labels the data as 'freely available'. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 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 data are Drosophila, not human subjects, so no gatekeeper is 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 how long the data will be retained.","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":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"We provide data in two file formats (VCF and GDS)","grounded":false,"rationale":"VCF is an open community-standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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 named data or metadata community standard is applied. [majority verdict 'no' (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 occurs in the text. [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":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence is named for the data; the article's CC BY-NC applies to the article only.","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":1.0,"verdict":"yes","evidence":"DrosEU samples from the 2014 collection were sequenced on an Illumina NextSeq 500 sequencer","grounded":true,"rationale":"The paper names specific instruments and kits used to produce the data. [majority verdict 'yes' (4/5 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":0.5,"verdict":"partial","evidence":"We assembled uniform metadata for all samples ( supplementary table S1 , Supplementary Material online). This information includes collection coordinates, collection date, and the number of flies per sample.","grounded":true,"rationale":"Variable definitions live inside the article (supplementary table), not in a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 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":"No version token or date is given for the DEST dataset; the data are referred to as a single release without a version identifier. [majority verdict 'no' (2/5 passes agreed)]","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":0.5,"verdict":"partial","evidence":"All scripts to make figures and perform analyses associated with this manuscript are available at: https://github.com/DEST-bio/data-paper (last accessed September 6, 2021) . All scripts to build the data set, including the mapping pipeline, SNP calling scripts, and metadata are available at: https://github.com/DEST-bio/DEST_freeze1 (last accessed September 6, 2021).","grounded":false,"rationale":"Machine-resolvable GitHub URLs are given for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","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":"M.K. was supported by the Austrian Science Foundation (grant no. FWF P32275)","grounded":true,"rationale":"Award numbers are attached to named funders. [majority verdict 'yes' (4/5 passes agreed)]","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":"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 licence is named for the data; the article's CC BY-NC applies to the article only.","gain":16.67,"priority":"essential","scored":true},{"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":"partial","current":0.5,"evidence":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","why":"The dataset is identified by a URL, 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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","why":"The data are hosted on a project website, not a curated repository. [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"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":"partial","current":0.5,"evidence":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","why":"The dataset identifier appears only in body text, not as a reference entry.","gain":4.17,"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":"partial","current":0.5,"evidence":"We provide data in two file formats (VCF and GDS)","why":"VCF is an open community-standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"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":"partial","current":0.5,"evidence":"All scripts to make figures and perform analyses associated with this manuscript are available at: https://github.com/DEST-bio/data-paper (last accessed September 6, 2021) . All scripts to build the data set, including the mapping pipeline, SNP calling scripts, and metadata are available at: https://github.com/DEST-bio/DEST_freeze1 (last accessed September 6, 2021).","why":"Machine-resolvable GitHub URLs are given for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"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":"No version token or date is given for the DEST dataset; the data are referred to as a single release without a version identifier. [majority verdict 'no' (2/5 passes agreed)]","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":"All output from the DEST pipeline, including intermediate output files, metadata, etc. can be found at: https://dest.bio","why":"The statement points to a website, not a repository record with an accession.","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":"We provide data in two file formats (VCF and GDS)","why":"The dataset's content is described in running prose, not an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All data, tools, and supporting resources for the DEST data set, as well as reference tracks downloaded from FlyBase (v.6.12), are freely available at https://dest.bio","why":"The paper explicitly labels the data as 'freely available'. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]","gain":0.0,"priority":"important","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 named data or metadata community standard is applied. [majority verdict 'no' (4/5 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":"partial","current":0.5,"evidence":"We assembled uniform metadata for all samples ( supplementary table S1 , Supplementary Material online). This information includes collection coordinates, collection date, and the number of flies per sample.","why":"Variable definitions live inside the article (supplementary table), not in a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 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 data are Drosophila, not human subjects, so no gatekeeper is 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":"No identifier for an external resource occurs in the text. [majority verdict 'no' (4/5 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 how long the data will be retained.","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).","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).","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":"2026-07-20T11:07:07.944251Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}