{"doi":"10.1093/g3journal/jkae232","title":"A new high-quality genome assembly and annotation for the threatened Florida Scrub-Jay ( <i>Aphelocoma coerulescens</i> )","abstract":"The Florida Scrub-Jay (Aphelocoma coerulescens), a Federally Threatened, cooperatively-breeding bird, is an emerging model system in evolutionary biology and ecology. Extensive individual-based monitoring and genetic sampling for decades has yielded a wealth of data, allowing for the detailed study of social behavior, demography, and population genetics of this natural population. Here, we report a linkage map and a chromosome-level genome assembly and annotation for a female Florida Scrub-Jay made with long-read sequencing technology, chromatin conformation data, and the linkage map. We constructed a linkage map comprising 4,468 SNPs that had 34 linkage groups and a total sex-averaged autosomal genetic map length of 2446.78 cM. The new genome assembly is 1.33 Gb in length, consisting of 33 complete or near-complete autosomes and the sex chromosomes (ZW). This highly contiguous assembly has an NG50 of 68 Mb and a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score of 97.1% with respect to the Aves database. The annotated gene set has a BUSCO transcriptome completeness score of 95.5% and 17,964 identified protein-coding genes, 92.5% of which have associated functional annotations. This new, high-quality genome assembly and linkage map of the Florida Scrub-Jay provides valuable tools for future research into the evolutionary dynamics of small, natural populations of conservation concern.","journal":"G3 Genes Genomes Genetics","year":2024,"id":476081,"datarank":0.23895337014040222,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.031009215972418604,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.031009215972418604,"corpus_percentile":38.67873443180939,"corpus_rank":7926,"citation_count":3,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9287,"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":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":822545,"name":"Felix E.G. Beaudry","orcid":"0000-0002-1384-382X","position":1,"is_corresponding":false},{"id":1313725,"name":"Eyvind Hovmand Warner","orcid":null,"position":2,"is_corresponding":false},{"id":1292460,"name":"Tram N. Nguyen","orcid":"0000-0003-4809-6227","position":3,"is_corresponding":false},{"id":19197,"name":"John W. Fitzpatrick","orcid":"0000-0002-6330-8403","position":4,"is_corresponding":false},{"id":19196,"name":"Nancy Chen","orcid":"0000-0001-8966-3449","position":5,"is_corresponding":false},{"id":1313355,"name":"Faye G. Romero","orcid":"0000-0002-5415-1539","position":0,"is_corresponding":true}],"reference_count":85,"raw_metadata":null,"created_at":"2026-07-19T02:06:25.428435Z","pmid":"39328063","pmcid":"PMC11631490","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":94.4444,"fair_a":62.5,"fair_i":60.0,"fair_r":33.3333,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":94.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The genome assembly is available on NCBI under the accession GCA_041296385.1.","grounded":true,"rationale":"The paper provides a persistent identifier in the NCBI GenBank accession scheme (GCA_041296385.1) for its own genome assembly. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"The genome assembly is available on NCBI under the accession GCA_041296385.1. Raw sequence reads are available on NCBI under BioProjects PRJNA1076903 and PRJNA1097984. The genome annotation, repeat library and repeat annotation, and linkage maps are available in Figshare at: figshare.com/projects/Florida_Scrub-Jay_genome_assembly/220939 under the following DOIs: https://doi.org/10.6084/m9.figshare.27037915.v1 , https://doi.org/10.6084/m9.figshare.27037921.v1 , https://doi.org/10.6084/m9.figshare.27037966.v1 , https://doi.org/10.6084/m9.figshare.27037945.v1 , https://doi.org/10.6084/m9.figshare.27037942.v1 .","grounded":true,"rationale":"The paper names NCBI (a data repository) and Figshare (a data repository) as holders of the data. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"Data availability\nThe genome assembly is available on NCBI under the accession GCA_041296385.1. Raw sequence reads are available on NCBI under BioProjects PRJNA1076903 and PRJNA1097984. The genome annotation, repeat library and repeat annotation, and linkage maps are available in Figshare at: figshare.com/projects/Florida_Scrub-Jay_genome_assembly/220939 under the following DOIs: https://doi.org/10.6084/m9.figshare.27037915.v1 , https://doi.org/10.6084/m9.figshare.27037921.v1 , https://doi.org/10.6084/m9.figshare.27037966.v1 , https://doi.org/10.6084/m9.figshare.27037945.v1 , https://doi.org/10.6084/m9.figshare.27037942.v1 . All additional data and associated code are available at: github.com/faye-romero/FSJ-genome . Supplemental material available at G3 online.","grounded":true,"rationale":"The data availability statement points to public repositories (NCBI, Figshare) with accessions, which is Colavizza category 3. [majority verdict 'yes' (4/5 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 1. Basic assembly statistics for each step of the long-read Florida Scrub-Jay genome assembly.","grounded":true,"rationale":"The paper includes a table (Table 1) that itemizes assembly statistics, which is an itemised inventory of the dataset. [majority verdict 'yes' (4/5 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":"The genome assembly is available on NCBI under the accession GCA_041296385.1.","grounded":true,"rationale":"The dataset identifier appears only in the body text (Data availability section), not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","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":"The genome assembly is available on NCBI under the accession GCA_041296385.1. Raw sequence reads are available on NCBI under BioProjects PRJNA1076903 and PRJNA1097984. The genome annotation, repeat library and repeat annotation, and linkage maps are available in Figshare at: figshare.com/projects/Florida_Scrub-Jay_genome_assembly/220939 under the following DOIs: https://doi.org/10.6084/m9.figshare.27037915.v1 , https://doi.org/10.6084/m9.figshare.27037921.v1 , https://doi.org/10.6084/m9.figshare.27037966.v1 , https://doi.org/10.6084/m9.figshare.27037945.v1 , https://doi.org/10.6084/m9.figshare.27037942.v1 .","grounded":true,"rationale":"The data are deposited in public repositories with no stated precondition, making them freely accessible. [majority verdict 'yes' (4/5 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":"The genome assembly is available on NCBI under the accession GCA_041296385.1. Raw sequence reads are available on NCBI under BioProjects PRJNA1076903 and PRJNA1097984. The genome annotation, repeat library and repeat annotation, and linkage maps are available in Figshare at: figshare.com/projects/Florida_Scrub-Jay_genome_assembly/220939 under the following DOIs: https://doi.org/10.6084/m9.figshare.27037915.v1 , https://doi.org/10.6084/m9.figshare.27037921.v1 , https://doi.org/10.6084/m9.figshare.27037966.v1 , https://doi.org/10.6084/m9.figshare.27037945.v1 , https://doi.org/10.6084/m9.figshare.27037942.v1 .","grounded":true,"rationale":"The paper describes the action of accessing the data via repositories without explicitly labeling the access level. [majority verdict 'partial' (4/5 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":"The Florida Scrub-Jay (Aphelocoma coerulescens), a federally Threatened, cooperatively breeding bird, is an emerging model system in evolutionary biology and ecology.","grounded":false,"rationale":"The data are not human or sensitive, and no gatekeeper is named for any access restriction.","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 mention any timing for data availability or a retention period. [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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not specify the file format of the deposited data.","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":1.0,"verdict":"yes","evidence":"84.8% had an associated Gene Ontology (GO) term.","grounded":true,"rationale":"The paper uses Gene Ontology (GO), a community standard controlled vocabulary, for functional annotation. [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":1.0,"verdict":"yes","evidence":"We labelled linkage groups based on alignments with the Zebra Finch genome (NCBI accession GCA_000151805.2).","grounded":true,"rationale":"The paper provides an NCBI accession for the Zebra Finch genome, a resource external to this study. [majority verdict 'yes' (3/5 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":33.33,"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 does not state a license for the data; only the article's license is mentioned.","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":"The University of Delaware DNA Sequencing & Genotyping Center extracted DNA from the blood sample using a high molecular weight extraction protocol, then prepared a Pacific Biosciences (PacBio) library and sequenced it on 3 SMRT Cells (Sequel IIe system).","grounded":false,"rationale":"The paper names specific instruments and kits (PacBio Sequel IIe, Illumina NovaSeq6000, Qiagen DNeasy kits) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (e.g., README, data dictionary) is named as accompanying the data. [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":"The genome assembly is available on NCBI under the accession GCA_041296385.1.","grounded":true,"rationale":"The GenBank assembly accession includes a version number (the .1 suffix), which identifies a specific snapshot. [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":"All additional data and associated code are available at: github.com/faye-romero/FSJ-genome.","grounded":false,"rationale":"The paper provides a GitHub repository URL for the code, which is a machine-resolvable locator. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"National Science Foundation (grants DEB0855879 and DEB1257628)","grounded":true,"rationale":"The paper lists specific grant numbers (DEB0855879, DEB1257628, etc.) from 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":"The paper does not state a license for the data; only the article's license is mentioned.","gain":16.67,"priority":"essential","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":"no","current":0.0,"evidence":null,"why":"The paper does not specify the file format of the deposited data.","gain":8.33,"priority":"important","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":"The genome assembly is available on NCBI under the accession GCA_041296385.1.","why":"The dataset identifier appears only in the body text (Data availability section), not as a reference-list entry. [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":"All additional data and associated code are available at: github.com/faye-romero/FSJ-genome.","why":"The paper provides a GitHub repository URL for the code, which is a machine-resolvable locator. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"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":"The genome assembly is available on NCBI under the accession GCA_041296385.1. Raw sequence reads are available on NCBI under BioProjects PRJNA1076903 and PRJNA1097984. The genome annotation, repeat library and repeat annotation, and linkage maps are available in Figshare at: figshare.com/projects/Florida_Scrub-Jay_genome_assembly/220939 under the following DOIs: https://doi.org/10.6084/m9.figshare.27037915.v1 , https://doi.org/10.6084/m9.figshare.27037921.v1 , https://doi.org/10.6084/m9.figshare.27037966.v1 , https://doi.org/10.6084/m9.figshare.27037945.v1 , https://doi.org/10.6084/m9.figshare.27037942.v1 .","why":"The paper describes the action of accessing the data via repositories without explicitly labeling the access level. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The University of Delaware DNA Sequencing & Genotyping Center extracted DNA from the blood sample using a high molecular weight extraction protocol, then prepared a Pacific Biosciences (PacBio) library and sequenced it on 3 SMRT Cells (Sequel IIe system).","why":"The paper names specific instruments and kits (PacBio Sequel IIe, Illumina NovaSeq6000, Qiagen DNeasy kits) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"no","current":0.0,"evidence":null,"why":"No documentation object (e.g., README, data dictionary) is named as accompanying the data. [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":"The Florida Scrub-Jay (Aphelocoma coerulescens), a federally Threatened, cooperatively breeding bird, is an emerging model system in evolutionary biology and ecology.","why":"The data are not human or sensitive, and no gatekeeper is named for any access restriction.","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 mention any timing for data availability or a retention period. [majority verdict 'no' (4/5 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.","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.","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.","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).","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."],"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":"2026-07-20T13:14:14.330282Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}