{"doi":"10.1093/nar/gkab1062","title":"HMDB 5.0: the Human Metabolome Database for 2022","abstract":"The Human Metabolome Database or HMDB (https://hmdb.ca) has been providing comprehensive reference information about human metabolites and their associated biological, physiological and chemical properties since 2007. Over the past 15 years, the HMDB has grown and evolved significantly to meet the needs of the metabolomics community and respond to continuing changes in internet and computing technology. This year's update, HMDB 5.0, brings a number of important improvements and upgrades to the database. These should make the HMDB more useful and more appealing to a larger cross-section of users. In particular, these improvements include: (i) a significant increase in the number of metabolite entries (from 114 100 to 217 920 compounds); (ii) enhancements to the quality and depth of metabolite descriptions; (iii) the addition of new structure, spectral and pathway visualization tools; (iv) the inclusion of many new and much more accurately predicted spectral data sets, including predicted NMR spectra, more accurately predicted MS spectra, predicted retention indices and predicted collision cross section data and (v) enhancements to the HMDB's search functions to facilitate better compound identification. Many other minor improvements and updates to the content, the interface, and general performance of the HMDB website have also been made. Overall, we believe these upgrades and updates should greatly enhance the HMDB's ease of use and its potential applications not only in human metabolomics but also in exposomics, lipidomics, nutritional science, biochemistry and clinical chemistry.","journal":"Nucleic Acids Research","year":2021,"id":5104,"datarank":5.337150305280965,"base_score":7.829630389150193,"endowment":7.829630389150193,"self_citation_contribution":1.1744445583725291,"citation_network_contribution":4.162705746908436,"self_endowment_contribution":1.1744445583725291,"citer_contribution":4.162705746908436,"corpus_percentile":96.11665506304634,"corpus_rank":503,"citation_count":2513,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9553,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-11-19","fair_score":62.5,"fair_percentile":81.0149801284011,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":51860,"name":"AnChi Guo","orcid":null,"position":1,"is_corresponding":false},{"id":51861,"name":"Eponine Oler","orcid":null,"position":2,"is_corresponding":false},{"id":51129,"name":"Fei Wang","orcid":"0000-0001-6712-3468","position":3,"is_corresponding":false},{"id":51862,"name":"Afia Anjum","orcid":"0000-0002-8349-7811","position":4,"is_corresponding":false},{"id":51863,"name":"Harrison Peters","orcid":null,"position":5,"is_corresponding":false},{"id":51864,"name":"Raynard Dizon","orcid":null,"position":6,"is_corresponding":false},{"id":51865,"name":"Zinat Sayeeda","orcid":null,"position":7,"is_corresponding":false},{"id":51866,"name":"Siyang Tian","orcid":"0000-0002-7298-2520","position":8,"is_corresponding":false},{"id":51867,"name":"Brian L. Lee","orcid":null,"position":9,"is_corresponding":false},{"id":51868,"name":"Mark Berjanskii","orcid":null,"position":10,"is_corresponding":false},{"id":51869,"name":"Robert Mah","orcid":null,"position":11,"is_corresponding":false},{"id":51870,"name":"Mai Yamamoto","orcid":"0000-0003-0344-2747","position":12,"is_corresponding":false},{"id":51871,"name":"Juan Jovel","orcid":null,"position":13,"is_corresponding":false},{"id":51872,"name":"Claudia Torres-Calzada","orcid":"0000-0001-9372-7230","position":14,"is_corresponding":false},{"id":51873,"name":"Mickel Hiebert-Giesbrecht","orcid":"0000-0003-2947-187X","position":15,"is_corresponding":false},{"id":51874,"name":"Vicki W Lui","orcid":null,"position":16,"is_corresponding":false},{"id":51875,"name":"Dorna Varshavi","orcid":null,"position":17,"is_corresponding":false},{"id":51876,"name":"Dorsa Varshavi","orcid":"0000-0002-1425-8171","position":18,"is_corresponding":false},{"id":51877,"name":"Dana Allen","orcid":null,"position":19,"is_corresponding":false},{"id":51878,"name":"David Arndt","orcid":"0000-0003-0703-8469","position":20,"is_corresponding":false},{"id":51879,"name":"Nitya Khetarpal","orcid":"0000-0002-0881-4020","position":21,"is_corresponding":false},{"id":51880,"name":"Aadhavya Sivakumaran","orcid":"0000-0002-3975-1077","position":22,"is_corresponding":false},{"id":51881,"name":"Karxena Harford","orcid":null,"position":23,"is_corresponding":false},{"id":51882,"name":"Selena Sanford","orcid":null,"position":24,"is_corresponding":false},{"id":51883,"name":"Kristen Yee","orcid":null,"position":25,"is_corresponding":false},{"id":51884,"name":"Xuan Cao","orcid":"0000-0001-9713-4192","position":26,"is_corresponding":false},{"id":51885,"name":"Zachary Budinski","orcid":null,"position":27,"is_corresponding":false},{"id":51886,"name":"Jaanus Liigand","orcid":"0000-0002-8814-9111","position":28,"is_corresponding":false},{"id":51887,"name":"Lun Zhang","orcid":"0000-0002-0928-7568","position":29,"is_corresponding":false},{"id":51888,"name":"Jiamin Zheng","orcid":"0000-0002-6120-7035","position":30,"is_corresponding":false},{"id":51889,"name":"Rupasri Mandal","orcid":null,"position":31,"is_corresponding":false},{"id":51890,"name":"Naama Karu","orcid":"0000-0001-8005-0726","position":32,"is_corresponding":false},{"id":51891,"name":"Maija Dambrova","orcid":"0000-0002-1739-0928","position":33,"is_corresponding":false},{"id":51892,"name":"Helgi B. Schiöth","orcid":"0000-0001-7112-0921","position":34,"is_corresponding":false},{"id":51893,"name":"Russell Greiner","orcid":"0000-0001-8327-934X","position":35,"is_corresponding":false},{"id":51894,"name":"Vasuk Gautam","orcid":"0000-0002-9204-1963","position":36,"is_corresponding":false},{"id":51895,"name":"Dana G. Allen","orcid":null,"position":37,"is_corresponding":false},{"id":51896,"name":"Kristen S. Yee","orcid":null,"position":38,"is_corresponding":false},{"id":51859,"name":"David S. Wishart","orcid":"0000-0002-3207-2434","position":0,"is_corresponding":true}],"reference_count":45,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"34986597","pmcid":"PMC8728138","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":61.1111,"fair_a":75.0,"fair_i":60.0,"fair_r":41.6667,"fair_zscore":1.1103,"fair_rationale":{"fair_score":62.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The Human Metabolome Database or HMDB ( https://hmdb.ca )","grounded":true,"rationale":"The identifier is 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":1.0,"verdict":"yes","evidence":"All data is freely available from the HMDB website or from the HMDB download page.","grounded":true,"rationale":"The HMDB is named as the holder; it is a recognised curated database/repository. [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":0.5,"verdict":"partial","evidence":"All data is freely available from the HMDB website or from the HMDB download page.","grounded":true,"rationale":"The statement points to a website, not a repository record, so it is partial. [majority verdict 'partial' (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":0.5,"verdict":"partial","evidence":"HMDB 5.0 now has 217 920 annotated metabolite entries, as well as another 1 581 537 unannotated derivatized metabolite entries for GC–MS.","grounded":true,"rationale":"The dataset's content is described in running prose, not in an itemised inventory (section, table, or list). [majority verdict 'partial' (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":"The Human Metabolome Database or HMDB ( https://hmdb.ca )","grounded":true,"rationale":"The dataset URL appears in the body text but not in the reference list. [majority verdict 'partial' (3/5 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":75.0,"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 is freely available from the HMDB website or from the HMDB download page.","grounded":true,"rationale":"The text states the data are freely available without any precondition.","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":1.0,"verdict":"yes","evidence":"All data is freely available from the HMDB website or from the HMDB download page.","grounded":true,"rationale":"The text explicitly labels the data as 'freely available', which is an access-level label.","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 described as sensitive, and 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":null,"grounded":false,"rationale":"No sentence in the paper states how long the data will remain available; no retention commitment is made. [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":"The HMDB’s downloadable spectral data files are available in the universally readable nmrML and mzML formats.","grounded":false,"rationale":"Multiple open formats (nmrML, mzML, CSV, JSON, XML, etc.) are named for the data. [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":1.0,"verdict":"yes","evidence":"ChemFOnt was first introduced in HMDB 4.0 as a hierarchically structured ontology that was both OWL (Web Ontology Language) and OBO (Open Biological Ontology) compliant.","grounded":true,"rationale":"The paper names ChemFOnt (an ontology) as a community standard, and also states that nomenclature follows standard ontologies. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier (accession, DOI, RRID) for an external resource (e.g., KEGG, Reactome) is provided; only bibliographic references are given. [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":0.5,"verdict":"partial","evidence":"The data in the HMDB are released under a Creative Commons Attribution-NonCommercial 4.0 International License.","grounded":true,"rationale":"A license is named, but it is non-open (CC BY-NC 4.0), so it falls under class 2.","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":"The MS/MS predictions for HMDB 5.0 were performed by the latest version of the competitive fragment modeling tool for QTOF MS/MS spectral prediction, called CFM-ID version 4.0 ( 30 ).","grounded":true,"rationale":"A specific tool and version are named. [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":null,"grounded":false,"rationale":"No documentation object (README, codebook) is named as accompanying the data. [majority verdict 'no' (4/5 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":0.5,"verdict":"partial","evidence":"HMDB 5.0","grounded":false,"rationale":"The paper explicitly identifies the version as 'HMDB 5.0'. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No code repository URL, DOI, or package identifier is given for the software that created or manages the database.","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":0.5,"verdict":"partial","evidence":"Genome Alberta (a division of Genome Canada); Canada Foundation for Innovation (CFI); Natural Sciences and Engineering Research Council of Canada (NSERC); Canadian Institutes of Health Research (CIHR); Alberta Machine Intelligence Institute (AMII).","grounded":true,"rationale":"Funder names are listed, but no award/grant numbers are provided.","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 metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The Human Metabolome Database or HMDB ( https://hmdb.ca )","why":"The identifier is a URL, not a persistent identifier scheme. [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"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":"partial","current":0.5,"evidence":"The data in the HMDB are released under a Creative Commons Attribution-NonCommercial 4.0 International License.","why":"A license is named, but it is non-open (CC BY-NC 4.0), so it falls under class 2.","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":"No code repository URL, DOI, or package identifier is given for the software that created or manages the database.","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":"The Human Metabolome Database or HMDB ( https://hmdb.ca )","why":"The dataset URL appears in the body text but not in the reference list. [majority verdict 'partial' (3/5 passes agreed)]","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 metabolomics formats such as mzML or nmrML.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The HMDB’s downloadable spectral data files are available in the universally readable nmrML and mzML formats.","why":"Multiple open formats (nmrML, mzML, CSV, JSON, XML, etc.) are named for the data. [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":"partial","current":0.5,"evidence":"HMDB 5.0","why":"The paper explicitly identifies the version as 'HMDB 5.0'. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":2.08,"priority":"useful","scored":true},{"key":"x_funding_attribution","dimension":"R","label":"Funder and award number","action":"State the funder AND the award number in the paper, and put them in the dataset's FundingReference metadata. A funder name alone cannot be linked back to the award, so the funding provenance of the data is lost the moment the paper is indexed.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Genome Alberta (a division of Genome Canada); Canada Foundation for Innovation (CFI); Natural Sciences and Engineering Research Council of Canada (NSERC); Canadian Institutes of Health Research (CIHR); Alberta Machine Intelligence Institute (AMII).","why":"Funder names are listed, but no award/grant numbers are provided.","gain":2.08,"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 data is freely available from the HMDB website or from the HMDB download page.","why":"The statement points to a website, not a repository record, so it is partial. [majority verdict 'partial' (3/5 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":"partial","current":0.5,"evidence":"HMDB 5.0 now has 217 920 annotated metabolite entries, as well as another 1 581 537 unannotated derivatized metabolite entries for GC–MS.","why":"The dataset's content is described in running prose, not in an itemised inventory (section, table, or list). [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","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 (README, codebook) is named as accompanying the data. [majority verdict 'no' (4/5 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 described as sensitive, and no gatekeeper is named.","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 (accession, DOI, RRID) for an external resource (e.g., KEGG, Reactome) is provided; only bibliographic references are given. [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":"No sentence in the paper states how long the data will remain available; no retention commitment is made. [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 metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","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.","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.","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 metabolomics formats such as mzML or nmrML."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:45:27.466239Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}