{"doi":"10.1093/nar/gkab941","title":"The Natural Products Atlas 2.0: a database of microbially-derived natural products","abstract":"Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.","journal":"Nucleic Acids Research","year":2021,"id":145728,"datarank":4.313414326792794,"base_score":5.796057750765372,"endowment":5.796057750765372,"self_citation_contribution":0.8694086626148059,"citation_network_contribution":3.4440056641779875,"self_endowment_contribution":0.8694086626148059,"citer_contribution":3.4440056641779875,"corpus_percentile":94.87893556122843,"corpus_rank":663,"citation_count":328,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9358,"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":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":619733,"name":"Ella F Poynton","orcid":null,"position":1,"is_corresponding":false},{"id":619734,"name":"Dasha Iskakova","orcid":null,"position":2,"is_corresponding":false},{"id":619735,"name":"Emily McMann","orcid":null,"position":3,"is_corresponding":false},{"id":618630,"name":"Tyler A. Alsup","orcid":"0000-0001-5868-0254","position":4,"is_corresponding":false},{"id":618631,"name":"Trevor N. Clark","orcid":"0000-0002-8758-404X","position":5,"is_corresponding":false},{"id":619736,"name":"Claire H. Fergusson","orcid":null,"position":6,"is_corresponding":false},{"id":618632,"name":"David P. Fewer","orcid":"0000-0003-3978-4845","position":7,"is_corresponding":false},{"id":618633,"name":"Alison H. Hughes","orcid":"0000-0002-9670-0663","position":8,"is_corresponding":false},{"id":618634,"name":"Caitlin A. McCadden","orcid":"0009-0003-5165-4039","position":9,"is_corresponding":false},{"id":618635,"name":"Jonathan Parra","orcid":"0000-0001-7273-0406","position":10,"is_corresponding":false},{"id":618636,"name":"Sylvia Soldatou","orcid":"0000-0002-3868-102X","position":11,"is_corresponding":false},{"id":568959,"name":"Jeffrey D. Rudolf","orcid":"0000-0003-2718-9651","position":12,"is_corresponding":false},{"id":618637,"name":"Elisabeth M.‐L. Janssen","orcid":"0000-0002-5475-6730","position":13,"is_corresponding":false},{"id":242697,"name":"Katherine Duncan","orcid":"0000-0002-3670-4849","position":14,"is_corresponding":false},{"id":261980,"name":"Roger G. Linington","orcid":"0000-0003-1818-4971","position":15,"is_corresponding":false},{"id":295894,"name":"Jeffrey A. van Santen","orcid":"0000-0002-5424-804X","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":null,"created_at":"2026-07-18T23:42:12.871665Z","pmid":"34718710","pmcid":"PMC8728154","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":37.5,"fair_i":40.0,"fair_r":66.6667,"fair_zscore":0.7804,"fair_rationale":{"fair_score":54.17,"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":0.5,"verdict":"partial","evidence":"The database can be accessed via the new interactive website at https://www.npatlas.org.","grounded":true,"rationale":"The paper provides a web URL for the data, not a persistent identifier scheme identifier. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Zenodo repository","grounded":false,"rationale":"The paper names the Zenodo repository as the holder of previous versions of the database. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":0.0,"verdict":"no","evidence":"The Natural Products Atlas is available at https://www.npatlas.org.","grounded":false,"rationale":"The data availability statement points to a website URL, not a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper]","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":"The new release increases the size of the database by 8128 compounds: 3176 of fungal origin and 4952 of bacterial origin.","grounded":false,"rationale":"The dataset content is described in running prose, not in an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":0.0,"verdict":"no","evidence":"The Natural Products Atlas is available at https://www.npatlas.org.","grounded":false,"rationale":"The dataset identifier (URL) appears in the body text (Data Availability section), not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":37.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The Natural Products Atlas is available at https://www.npatlas.org.","grounded":false,"rationale":"The data availability statement gives a direct URL with no stated precondition to access the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":"The database is provided under a Creative Commons Attribution 4.0 International License (CC BY 4.0).","grounded":true,"rationale":"The paper states the license for the data, but does not explicitly label the access level using standard vocabulary such as 'open access' or 'freely available'; the license implies openness but the label must be inferred.","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, so 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":"The paper does not state how long the current version of the database will be retained or when it becomes available; only previous versions are mentioned as available via Zenodo. [majority verdict 'no' (3/5 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":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"In addition to the original TSV download of the full database we now offer an Excel version of the same TSV format, an SDF download of all compounds, a structured JSON format for the full database, and graphML exports of both the Cluster and Nodegraphs displayed in the Explore section of the website.","grounded":false,"rationale":"The paper names TSV, SDF, JSON, and graphML, all of which are open, non-proprietary formats. [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":"We have added classifications from both systems to every entry.","grounded":false,"rationale":"The paper names NPClassifier and ClassyFire, which are community standard chemical classification systems, and also references NCBI taxonomy. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No identifier for an external resource (e.g., DOI, accession, RRID) for any resource other than the paper's own dataset appears in the body text; the Zenodo DOI is for the previous version of the same dataset. [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":66.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The database is provided under a Creative Commons Attribution 4.0 International License (CC BY 4.0).","grounded":true,"rationale":"The paper explicitly states a standard open license (CC BY 4.0) for the data.","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 FastAPI framework for Python was used to build the API.","grounded":true,"rationale":"The paper names specific tools and frameworks used to build the database, such as FastAPI, PostgreSQL, and RDKit, as well as external databases like Mycobank and LPSN.","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":"In the new version of the database we have incorporated additional data from Mycobank and The List of Prokaryotic names with Standing in Nomenclature (LPSN) to include assignments at all taxonomic ranks.","grounded":false,"rationale":"The paper describes the database structure and fields in running prose, but no separate documentation object (e.g., README, codebook) is named as accompanying the data. [downgraded to 'no' — no verifiable quote from the paper]","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 Natural Products Atlas 2.0","grounded":true,"rationale":"The paper provides a version token (2.0) for the database. [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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not mention any code availability, no repository URL, DOI, or package identifier for the code used to build 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":1.0,"verdict":"yes","evidence":"National Institutes of Health [AT008718 to R.G.L., GM124461 to J.D.R.]","grounded":true,"rationale":"The paper provides specific grant numbers for the funding agencies.","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 database can be accessed via the new interactive website at https://www.npatlas.org.","why":"The paper provides a web URL for the data, not a persistent identifier scheme identifier. [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Zenodo repository","why":"The paper names the Zenodo repository as the holder of previous versions of the database. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The Natural Products Atlas is available at https://www.npatlas.org.","why":"The data availability statement gives a direct URL with no stated precondition to access the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the metabolomics repository accession (e.g. from MetaboLights (MTBLS accession) or Metabolomics Workbench) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The Natural Products Atlas is available at https://www.npatlas.org.","why":"The dataset identifier (URL) appears in the body text (Data Availability section), not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"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":"no","current":0.0,"evidence":null,"why":"The paper does not mention any code availability, no repository URL, DOI, or package identifier for the code used to build the database.","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 metabolomics formats such as mzML or nmrML.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"In addition to the original TSV download of the full database we now offer an Excel version of the same TSV format, an SDF download of all compounds, a structured JSON format for the full database, and graphML exports of both the Cluster and Nodegraphs displayed in the Explore section of the website.","why":"The paper names TSV, SDF, JSON, and graphML, all of which are open, non-proprietary formats. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","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":"The Natural Products Atlas is available at https://www.npatlas.org.","why":"The data availability statement points to a website URL, not a repository record with an accession or DOI. [downgraded to 'no' — no verifiable quote from the paper]","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":"The new release increases the size of the database by 8128 compounds: 3176 of fungal origin and 4952 of bacterial origin.","why":"The dataset content is described in running prose, not in an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 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":"The database is provided under a Creative Commons Attribution 4.0 International License (CC BY 4.0).","why":"The paper states the license for the data, but does not explicitly label the access level using standard vocabulary such as 'open access' or 'freely available'; the license implies openness but the label must be inferred.","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 metabolomics, describe the data with ISA-Tab or Metabolomics Standards Initiative (MSI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"We have added classifications from both systems to every entry.","why":"The paper names NPClassifier and ClassyFire, which are community standard chemical classification systems, and also references NCBI taxonomy. [downgraded to 'partial' — no verifiable quote from the paper] [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":"no","current":0.0,"evidence":"In the new version of the database we have incorporated additional data from Mycobank and The List of Prokaryotic names with Standing in Nomenclature (LPSN) to include assignments at all taxonomic ranks.","why":"The paper describes the database structure and fields in running prose, but no separate documentation object (e.g., README, codebook) is named as accompanying the data. [downgraded to 'no' — no verifiable quote from the paper]","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, so 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 for an external resource (e.g., DOI, accession, RRID) for any resource other than the paper's own dataset appears in the body text; the Zenodo DOI is for the previous version of the same dataset. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state how long the current version of the database will be retained or when it becomes available; only previous versions are mentioned as available via Zenodo. [majority verdict 'no' (3/5 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.","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.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For metabolomics data, deposit in MetaboLights (MTBLS accession) or Metabolomics Workbench.","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.","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":"2026-07-20T10:51:29.399010Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}