{"doi":"10.1093/nar/gkaa793","title":"The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals","abstract":"Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as 'healthy' or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.","journal":"Nucleic Acids Research","year":2020,"id":50219,"datarank":4.155195716261402,"base_score":5.3230099791384085,"endowment":5.3230099791384085,"self_citation_contribution":0.7984514968707613,"citation_network_contribution":3.3567442193906407,"self_endowment_contribution":0.7984514968707613,"citer_contribution":3.3567442193906407,"corpus_percentile":94.66233464841031,"corpus_rank":691,"citation_count":204,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9476,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":246087,"name":"Julien Roux","orcid":"0000-0002-4192-5099","position":1,"is_corresponding":false},{"id":246088,"name":"Anne Niknejad","orcid":"0000-0003-3308-6245","position":2,"is_corresponding":false},{"id":246089,"name":"Aurélie Comte","orcid":"0000-0003-4073-2524","position":3,"is_corresponding":false},{"id":246090,"name":"Sara Simões Costa","orcid":"0000-0001-7794-7997","position":4,"is_corresponding":false},{"id":246091,"name":"Tarcisio Mendes de Farias","orcid":"0000-0002-3175-5372","position":5,"is_corresponding":false},{"id":246092,"name":"Sébastien Moretti","orcid":"0000-0003-3947-488X","position":6,"is_corresponding":false},{"id":248467,"name":"Gilles Parmentier","orcid":null,"position":7,"is_corresponding":false},{"id":246093,"name":"Valentine Rech de Laval","orcid":"0000-0002-3020-1490","position":8,"is_corresponding":false},{"id":246094,"name":"Marta Rosikiewicz","orcid":"0000-0001-9123-1880","position":9,"is_corresponding":false},{"id":246095,"name":"Julien Wollbrett","orcid":"0000-0002-3099-3117","position":10,"is_corresponding":false},{"id":246096,"name":"Amina Echchiki","orcid":"0000-0003-3571-5420","position":11,"is_corresponding":false},{"id":248468,"name":"Angélique Escoriza","orcid":null,"position":12,"is_corresponding":false},{"id":246097,"name":"Walid H. Gharib","orcid":"0000-0003-4831-8408","position":13,"is_corresponding":false},{"id":248469,"name":"Mar Gonzales-Porta","orcid":null,"position":14,"is_corresponding":false},{"id":246098,"name":"Yohan Jarosz","orcid":"0000-0003-2047-0897","position":15,"is_corresponding":false},{"id":246099,"name":"Balazs Laurenczy","orcid":"0000-0003-1601-8945","position":16,"is_corresponding":false},{"id":246100,"name":"Philippe Moret","orcid":"0000-0002-3810-2091","position":17,"is_corresponding":false},{"id":248470,"name":"Emilie Person","orcid":null,"position":18,"is_corresponding":false},{"id":246101,"name":"Patrick Roelli","orcid":"0000-0002-5259-1434","position":19,"is_corresponding":false},{"id":248471,"name":"Komal Sanjeev","orcid":null,"position":20,"is_corresponding":false},{"id":246102,"name":"Mathieu Seppey","orcid":"0000-0003-3248-011X","position":21,"is_corresponding":false},{"id":25137,"name":"Marc Robinson‐Rechavi","orcid":"0000-0002-3437-3329","position":22,"is_corresponding":false},{"id":31298,"name":"Frederic Bastian","orcid":"0000-0002-9415-5104","position":0,"is_corresponding":true}],"reference_count":76,"raw_metadata":null,"created_at":"2026-07-18T20:38:25.860949Z","pmid":"33037820","pmcid":"PMC7778977","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":22.2222,"fair_a":62.5,"fair_i":60.0,"fair_r":75.0,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":22.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/.","grounded":false,"rationale":"The paper gives a web address (URL) for the data, not a persistent identifier scheme. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":0.0,"verdict":"no","evidence":"Bgee, documentation, and links to resources used, are available at https://bgee.org/.","grounded":false,"rationale":"The data are held on the Bgee website, which is a non-repository host (not a curated archive like GEO or Zenodo). [downgraded to 'no' — no verifiable quote from the paper]","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data-availability statement provides a link to the Bgee website but no accession or persistent identifier for a specific dataset record. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","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":1.0,"verdict":"yes","evidence":"Table 2. Data statistics for release Bgee 14.1 per species for the 29 species included in this version","grounded":true,"rationale":"The paper provides an itemised inventory of the data in a table (Table 2) listing per-species statistics. [majority verdict 'yes' (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":0.0,"verdict":"no","evidence":"Bgee, documentation, and links to resources used, are available at https://bgee.org/.","grounded":false,"rationale":"The dataset identifier (URL) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper]","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 data are published under the Creative Commons Zero license (CC0).","grounded":true,"rationale":"The data are stated to be published under CC0, implying unconditional open access with no precondition. [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 are published under the Creative Commons Zero license (CC0).","grounded":true,"rationale":"The paper licenses the data under CC0, which is a waiver of all rights and implies open access, but it does not explicitly label the access level with a standard vocabulary term like 'open access'. [majority verdict 'partial' (3/5 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":"All data are published under the Creative Commons Zero license (CC0).","grounded":true,"rationale":"The Bgee data are not sensitive and are released openly under CC0; no gatekeeper is named.","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":"Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/.","grounded":false,"rationale":"The paper states the data are available now but does not mention how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","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":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"We provide TSV files to retrieve, for each species: (i) annotated and processed expression values for RNA-Seq and Affymetrix data and (ii) calls of presence/absence of expression with confidence and rank scores generated from all data types.","grounded":false,"rationale":"The paper names TSV, an open, non-proprietary file format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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":0.5,"verdict":"partial","evidence":"To describe the anatomy of diverse animals, we use the Uberon ontology (17).","grounded":false,"rationale":"The paper names the Uberon ontology, a community standard for anatomy, and also uses Gene Ontology and NCBI Taxonomy. [downgraded to 'partial' — no verifiable quote from the paper]","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":1.0,"verdict":"yes","evidence":"We have curated the GTEx human dataset phs000424.v6.p1 (7).","grounded":true,"rationale":"The paper gives a dbGaP accession (phs000424.v6.p1) for an external resource (GTEx) that the data depend on. [majority verdict 'yes' (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":75.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All data are published under the Creative Commons Zero license (CC0).","grounded":true,"rationale":"The paper attaches an open standard license (CC0) to the data. [majority verdict 'yes' (4/5 passes agreed)]","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":"We use Kallisto (41) to generate pseudo-counts per transcript","grounded":true,"rationale":"The paper names specific tools (Kallisto, IQRray, gcRMA) used to produce the data. [majority verdict 'yes' (3/5 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":0.0,"verdict":"no","evidence":"We provide TSV files to retrieve, for each species: (i) annotated and processed expression values for RNA-Seq and Affymetrix data and (ii) calls of presence/absence of expression with confidence and rank scores generated from all data types.","grounded":false,"rationale":"Variable definitions are described in the article text and tables, but no separate documentation object is named as travelling with the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":1.0,"verdict":"yes","evidence":"Bgee release 14.1 includes 29 animal species","grounded":true,"rationale":"The paper gives a version token 'release 14.1' for the data. [majority verdict 'yes' (4/5 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":"Source code and annotations are available in the GitHub repository (https://github.com/BgeeDB).","grounded":false,"rationale":"The paper provides a machine-resolvable URL to a code repository (GitHub) for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper]","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":"Swiss National Science Foundation [31003A 173048, 31003A 153341, 31003A133011, CRSII3160723]; SystemsX project AgingX, PNR [407540167149 (BioSODA)]; NIH Award [U01CA215010 (OncoMX)]; European Union’s Horizon 2020 research and innovation program [863410].","grounded":true,"rationale":"The paper gives specific award numbers for multiple 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":"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":"no","current":0.0,"evidence":"Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/.","why":"The paper gives a web address (URL) for the data, not a persistent identifier scheme. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":16.67,"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":"no","current":0.0,"evidence":"Bgee, documentation, and links to resources used, are available at https://bgee.org/.","why":"The data are held on the Bgee website, which is a non-repository host (not a curated archive like GEO or Zenodo). [downgraded to 'no' — no verifiable quote from the paper]","gain":16.67,"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":"no","current":0.0,"evidence":"Bgee, documentation, and links to resources used, are available at https://bgee.org/.","why":"The dataset identifier (URL) appears only in the body text, not in the reference list. [downgraded to 'no' — no verifiable quote from the paper]","gain":8.33,"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 TSV files to retrieve, for each species: (i) annotated and processed expression values for RNA-Seq and Affymetrix data and (ii) calls of presence/absence of expression with confidence and rank scores generated from all data types.","why":"The paper names TSV, an open, non-proprietary file format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 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":"Source code and annotations are available in the GitHub repository (https://github.com/BgeeDB).","why":"The paper provides a machine-resolvable URL to a code repository (GitHub) for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper]","gain":4.17,"priority":"important","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":"no","current":0.0,"evidence":null,"why":"The data-availability statement provides a link to the Bgee website but no accession or persistent identifier for a specific dataset record. [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 are published under the Creative Commons Zero license (CC0).","why":"The paper licenses the data under CC0, which is a waiver of all rights and implies open access, but it does not explicitly label the access level with a standard vocabulary term like 'open access'. [majority verdict 'partial' (3/5 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":"partial","current":0.5,"evidence":"To describe the anatomy of diverse animals, we use the Uberon ontology (17).","why":"The paper names the Uberon ontology, a community standard for anatomy, and also uses Gene Ontology and NCBI Taxonomy. [downgraded to 'partial' — no verifiable quote from the paper]","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":"no","current":0.0,"evidence":"We provide TSV files to retrieve, for each species: (i) annotated and processed expression values for RNA-Seq and Affymetrix data and (ii) calls of presence/absence of expression with confidence and rank scores generated from all data types.","why":"Variable definitions are described in the article text and tables, but no separate documentation object is named as travelling with the data. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":"All data are published under the Creative Commons Zero license (CC0).","why":"The Bgee data are not sensitive and are released openly under CC0; no gatekeeper is named.","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":"Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/.","why":"The paper states the data are available now but does not mention how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["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.","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)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:54:32.231485Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}