{"doi":"10.1093/genetics/iyab089","title":"WormPaths: <i>Caenorhabditis elegans</i> metabolic pathway annotation and visualization","abstract":"In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology, and the response to therapeutic drugs. Visualization of the metabolic pathways that comprise the metabolic network is extremely useful for interpreting a wide variety of experiments. Detailed annotated metabolic pathway maps for C. elegans are mostly limited to pan-organismal maps, many with incomplete or inaccurate pathway and enzyme annotations. Here, we present WormPaths, which is composed of two parts: (1) the careful manual annotation of metabolic genes into pathways, categories, and levels, and (2) 62 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on the WormFlux website. We show that WormPaths provides easy-to-navigate maps and that the different levels in WormPaths can be used for metabolic pathway enrichment analysis of transcriptomic data. In the future, we envision further developing these maps to be more interactive, analogous to road maps that are available on mobile devices.","journal":"Genetics","year":2021,"id":165786,"datarank":0.8230498256690562,"base_score":3.58351893845611,"endowment":3.58351893845611,"self_citation_contribution":0.5375278407684165,"citation_network_contribution":0.28552198490063957,"self_endowment_contribution":0.5375278407684165,"citer_contribution":0.28552198490063957,"corpus_percentile":75.50088961089193,"corpus_rank":3168,"citation_count":35,"citer_count":23,"citers_with_citation_signal":14,"citers_with_endowment":14,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5442,"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":305725,"name":"Gabrielle E. Giese","orcid":"0000-0002-9338-2049","position":1,"is_corresponding":false},{"id":552373,"name":"Amy D. Holdorf","orcid":"0000-0001-5699-4081","position":2,"is_corresponding":false},{"id":553238,"name":"Sushila Bhattacharya","orcid":null,"position":3,"is_corresponding":false},{"id":552374,"name":"Cédric Diot","orcid":"0000-0003-2982-9392","position":4,"is_corresponding":false},{"id":70379,"name":"Aurian P. García-González","orcid":"0000-0003-4120-4408","position":5,"is_corresponding":false},{"id":552375,"name":"Brent B. Horowitz","orcid":"0000-0002-5744-7562","position":6,"is_corresponding":false},{"id":552376,"name":"Yong‐Uk Lee","orcid":"0000-0001-6639-7352","position":7,"is_corresponding":false},{"id":553239,"name":"Thomas B. Leland","orcid":null,"position":8,"is_corresponding":false},{"id":305728,"name":"Xuhang Li","orcid":"0000-0001-6071-9605","position":9,"is_corresponding":false},{"id":553240,"name":"Zeynep Mirza","orcid":null,"position":10,"is_corresponding":false},{"id":552377,"name":"Huimin Na","orcid":"0000-0002-7062-6813","position":11,"is_corresponding":false},{"id":352620,"name":"Shivani Nanda","orcid":"0000-0001-6358-2392","position":12,"is_corresponding":false},{"id":305726,"name":"Olga Ponomarova","orcid":"0000-0001-6331-9949","position":13,"is_corresponding":false},{"id":305727,"name":"Hefei Zhang","orcid":"0000-0002-5187-7166","position":14,"is_corresponding":false},{"id":552378,"name":"Jingyan Zhang","orcid":"0000-0002-3495-6225","position":15,"is_corresponding":false},{"id":352619,"name":"L. Şafak Yılmaz","orcid":"0000-0001-8258-4465","position":16,"is_corresponding":false},{"id":305730,"name":"Albertha J.M. Walhout","orcid":"0000-0001-5587-3608","position":17,"is_corresponding":false},{"id":281158,"name":"Melissa Walker","orcid":"0000-0001-6266-1638","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-18T23:45:40.838485Z","pmid":"34117752","pmcid":"PMC8864737","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":100.0,"fair_r":33.3333,"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 pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ).","grounded":true,"rationale":"The only identifier given is a URL, not a persistent identifier scheme (DOI, Handle, ARK, or repository accession).","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":"WormFlux website ( http://wormflux.umassmed.edu )","grounded":true,"rationale":"The data are hosted on a project website (WormFlux), not a named data repository listed in re3data or FAIRsharing. [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 pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ). All pathway maps are available in WormFlux ( http://wormflux.umassmed.edu/WormPaths/wormpaths.php ) and can be used interactively to visualize information related to metabolites, genes, reactions, and pathways in this website.","grounded":true,"rationale":"The statement points to a website and supplementary material, not to a repository record with an accession, so it is Colavizza category 2+3 but not a repository record. [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":"In total, WormPaths contains 62 maps covering major metabolic pathways (glycolysis/gluconeogenesis, TCA cycle, etc.), amino acid metabolism, and pathways fundamental to C. elegans physiology (collagen biosynthesis, ascaroside biosynthesis, propionate degradation, etc.).","grounded":false,"rationale":"The dataset's content is described in running prose, not an itemized 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 pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ).","grounded":true,"rationale":"The dataset identifier (a URL) appears only in the body text, not in the reference list. [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":"All pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ).","grounded":true,"rationale":"The paper gives a direct download link with no stated precondition, so the route is unconditional. [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":"All pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ).","grounded":true,"rationale":"The paper describes the action of downloading the data but does not label the access level with a standard term like 'open access' or 'publicly available'. [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":null,"grounded":false,"rationale":"The data are not sensitive or human-subject, and the paper does not mention any gatekeeper.","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 when the data become available or how long they persist; the 'last accessed' date is not a commitment.","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":100.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Each pathway map can be downloaded in PNG, PDF, and SVG formats from the corresponding pathway page.","grounded":true,"rationale":"SVG, PNG, and PDF are open, non-proprietary formats. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"Biochemical Genetic and Genomic (BiGG) database abbreviations","grounded":true,"rationale":"The paper names BiGG, a community-standard abbreviation system for metabolite names, as used in the data. [majority verdict 'yes' (3/5 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":"The recently updated version of this model includes 1314 genes, 907 metabolites, and 2230 reactions and is referred to as iCEL1314 ( Yilmaz et al. 2020 ).","grounded":true,"rationale":"The paper cites the iCEL1314 model with a DOI, which is an identifier for a resource other than the study's own dataset. [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 only licenses the article (CC BY 4.0) and does not explicitly attach a license to the data. [majority verdict 'no' (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":"Draft maps were drawn as SVG files in the open-source vector graphics editor Inkscape ( http://inkscape.org )","grounded":true,"rationale":"The paper names specific tools (Inkscape, Open Babel) 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":0.5,"verdict":"partial","evidence":"Supplementary Table S1","grounded":true,"rationale":"The definition of the data (gene-to-pathway annotations) is provided in a supplementary table that accompanies the article, not shipped with the data on the website. [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 released data; the model iCEL1314 has a version but that is not the data.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide a resolvable locator for the study's own code; only a website URL for the tool is given.","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":"This work was supported by grants from the National Institutes of Health GM122502, DK115690, and DK068429 to A.J.M.W.","grounded":true,"rationale":"Grant numbers are provided for the funding.","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 only licenses the article (CC BY 4.0) and does not explicitly attach a license to the data. [majority verdict 'no' (4/5 passes agreed)]","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 metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ).","why":"The only identifier given is a URL, not a persistent identifier scheme (DOI, Handle, ARK, or repository accession).","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 metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"WormFlux website ( http://wormflux.umassmed.edu )","why":"The data are hosted on a project website (WormFlux), not a named data repository listed in re3data or FAIRsharing. [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","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":"no","current":0.0,"evidence":null,"why":"The paper does not provide a resolvable locator for the study's own code; only a website URL for the tool is given.","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 metabolomics repository accession (e.g. from MetaboLights (MTBLS accession) or Metabolomics Workbench) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"All pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ).","why":"The dataset identifier (a URL) appears only in the body text, not in the reference list. [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 released data; the model iCEL1314 has a version but that is not the data.","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 pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ). All pathway maps are available in WormFlux ( http://wormflux.umassmed.edu/WormPaths/wormpaths.php ) and can be used interactively to visualize information related to metabolites, genes, reactions, and pathways in this website.","why":"The statement points to a website and supplementary material, not to a repository record with an accession, so it is Colavizza category 2+3 but not a repository record. [majority verdict 'partial' (4/5 passes agreed)]","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":"In total, WormPaths contains 62 maps covering major metabolic pathways (glycolysis/gluconeogenesis, TCA cycle, etc.), amino acid metabolism, and pathways fundamental to C. elegans physiology (collagen biosynthesis, ascaroside biosynthesis, propionate degradation, etc.).","why":"The dataset's content is described in running prose, not an itemized 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 pathway annotations from this study are available in the Supplementary Tables S1, S3–S5 and are downloadable from the WormFlux website ( http://wormflux.umassmed.edu/download.php, last accessed June 18, 2021 ).","why":"The paper describes the action of downloading the data but does not label the access level with a standard term like 'open access' or 'publicly available'. [majority verdict 'partial' (3/5 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":"Supplementary Table S1","why":"The definition of the data (gene-to-pathway annotations) is provided in a supplementary table that accompanies the article, not shipped with the data on the website. [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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive or human-subject, and the paper does not mention any gatekeeper.","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 when the data become available or how long they persist; the 'last accessed' date is not a commitment.","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 metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","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 metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","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).","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 metabolomics repository accession (e.g. from MetaboLights (MTBLS accession) or Metabolomics Workbench) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:30:42.404900Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}