{"doi":"10.1016/j.celrep.2023.112046","title":"Network analysis of large-scale ImmGen and Tabula Muris datasets highlights metabolic diversity of tissue mononuclear phagocytes","abstract":"The diversity of mononuclear phagocyte (MNP) subpopulations across tissues is one of the key physiological characteristics of the immune system. Here, we focus on understanding the metabolic variability of MNPs through metabolic network analysis applied to three large-scale transcriptional datasets: we introduce (1) an ImmGen MNP open-source dataset of 337 samples across 26 tissues; (2) a myeloid subset of ImmGen Phase I dataset (202 MNP samples); and (3) a myeloid mouse single-cell RNA sequencing (scRNA-seq) dataset (51,364 cells) assembled based on Tabula Muris Senis. To analyze such large-scale datasets, we develop a network-based computational approach, genes and metabolites (GAM) clustering, for unbiased identification of the key metabolic subnetworks based on transcriptional profiles. We define 9 metabolic subnetworks that encapsulate the metabolic differences within MNP from 38 different tissues. Obtained modules reveal that cholesterol synthesis appears particularly active within the migratory dendritic cells, while glutathione synthesis is essential for cysteinyl leukotriene production by peritoneal and lung macrophages.","journal":"Cell Reports","year":2023,"id":325297,"datarank":1.0149559552540612,"base_score":3.4657359027997265,"endowment":3.4657359027997265,"self_citation_contribution":0.519860385419959,"citation_network_contribution":0.49509556983410224,"self_endowment_contribution":0.519860385419959,"citer_contribution":0.49509556983410224,"corpus_percentile":79.94120832366364,"corpus_rank":2594,"citation_count":31,"citer_count":26,"citers_with_citation_signal":18,"citers_with_endowment":18,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.925,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":566973,"name":"Denis A. Mogilenko","orcid":"0000-0001-5427-5243","position":1,"is_corresponding":false},{"id":431115,"name":"Li‐Hao Huang","orcid":null,"position":2,"is_corresponding":false},{"id":1042856,"name":"Helena Todorov","orcid":"0000-0002-1594-8609","position":3,"is_corresponding":false},{"id":623623,"name":"Vipin Narang","orcid":"0000-0001-8669-9964","position":4,"is_corresponding":false},{"id":247522,"name":"Ki-Wook Kim","orcid":"0000-0002-7207-4389","position":5,"is_corresponding":false},{"id":1043527,"name":"Lim Sheau Yng","orcid":null,"position":6,"is_corresponding":false},{"id":636944,"name":"Andrew Kent","orcid":"0000-0002-3680-5893","position":7,"is_corresponding":false},{"id":299895,"name":"Baosen Jia","orcid":null,"position":8,"is_corresponding":false},{"id":618279,"name":"Kumba Seddu","orcid":"0000-0002-0875-5833","position":9,"is_corresponding":false},{"id":366984,"name":"Karen Krchma","orcid":"0000-0003-0800-8456","position":10,"is_corresponding":false},{"id":1042857,"name":"Jun Wu","orcid":"0009-0003-9472-3794","position":11,"is_corresponding":false},{"id":297333,"name":"Karine Crozat","orcid":"0000-0003-4761-3675","position":12,"is_corresponding":false},{"id":1042858,"name":"Elena Tomasello","orcid":"0000-0002-6839-5219","position":13,"is_corresponding":false},{"id":297340,"name":"Regine J. Dress","orcid":"0000-0001-8785-5471","position":14,"is_corresponding":false},{"id":1042859,"name":"Peter See","orcid":"0000-0003-4428-7763","position":15,"is_corresponding":false},{"id":80080,"name":"Charlotte L. Scott","orcid":"0000-0003-4914-6580","position":16,"is_corresponding":false},{"id":297347,"name":"Sophie L. Gibbings","orcid":"0000-0001-9623-0705","position":17,"is_corresponding":false},{"id":297326,"name":"Geetika Bajpai","orcid":"0000-0003-2178-8055","position":18,"is_corresponding":false},{"id":231233,"name":"Jigar V. Desai","orcid":"0000-0002-8823-0796","position":19,"is_corresponding":false},{"id":173429,"name":"Barbara B. Maier","orcid":"0000-0002-7359-6576","position":20,"is_corresponding":false},{"id":459105,"name":"Sébastien This","orcid":"0000-0003-2931-9050","position":21,"is_corresponding":false},{"id":928659,"name":"Peter Wang","orcid":"0000-0001-7790-2596","position":22,"is_corresponding":false},{"id":297321,"name":"Stephanie Vargas Aguilar","orcid":"0000-0002-6584-0209","position":23,"is_corresponding":false},{"id":1042860,"name":"Lucie Poupel","orcid":"0000-0001-7015-8450","position":24,"is_corresponding":false},{"id":1042861,"name":"Sébastien Dussaud","orcid":"0000-0002-5365-8338","position":25,"is_corresponding":false},{"id":891353,"name":"Tyng-An Zhou","orcid":"0000-0003-4031-4947","position":26,"is_corresponding":false},{"id":297324,"name":"Véronique Angeli","orcid":"0000-0002-2759-3497","position":27,"is_corresponding":false},{"id":252509,"name":"J. Magarian Blander","orcid":"0000-0001-9207-1700","position":28,"is_corresponding":false},{"id":297330,"name":"Kyunghee Choi","orcid":"0000-0002-9634-9375","position":29,"is_corresponding":false},{"id":297334,"name":"Marc Dalod","orcid":"0000-0002-6436-7966","position":30,"is_corresponding":false},{"id":297341,"name":"Ivan Dzhagalov","orcid":"0000-0001-9209-4582","position":31,"is_corresponding":false},{"id":61571,"name":"Emmanuel L. Gautier","orcid":"0000-0003-2976-7566","position":32,"is_corresponding":false},{"id":61572,"name":"Claudia Jakubzick","orcid":"0000-0002-3731-0198","position":33,"is_corresponding":false},{"id":247530,"name":"Kory J. Lavine","orcid":"0000-0003-1948-9945","position":34,"is_corresponding":false},{"id":104225,"name":"Michail S. Lionakis","orcid":"0000-0003-4994-9500","position":35,"is_corresponding":false},{"id":459112,"name":"Helena Païdassi","orcid":"0000-0001-9915-4365","position":36,"is_corresponding":false},{"id":225203,"name":"Michael H. Sieweke","orcid":"0000-0002-3228-9537","position":37,"is_corresponding":false},{"id":71133,"name":"Florent Ginhoux","orcid":"0000-0002-2857-7755","position":38,"is_corresponding":false},{"id":124116,"name":"Martin Guilliams","orcid":"0000-0003-3525-7570","position":39,"is_corresponding":false},{"id":18715,"name":"Christophe Benoıst","orcid":"0000-0003-1172-6555","position":40,"is_corresponding":false},{"id":44523,"name":"Miriam Mérad","orcid":"0000-0002-4481-7827","position":41,"is_corresponding":false},{"id":61573,"name":"Gwendalyn J. Randolph","orcid":"0000-0001-9045-1195","position":42,"is_corresponding":false},{"id":756208,"name":"Alexey Sergushichev","orcid":"0000-0003-1159-7220","position":43,"is_corresponding":false},{"id":52958,"name":"Maxim N. Artyomov","orcid":"0000-0002-1133-4212","position":44,"is_corresponding":false},{"id":297344,"name":"Anastasiia Gainullina","orcid":"0000-0003-3796-2337","position":0,"is_corresponding":true}],"reference_count":65,"raw_metadata":null,"created_at":"2026-07-19T01:08:22.919783Z","pmid":"36708514","pmcid":"PMC10372199","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":83.3333,"fair_a":81.25,"fair_i":20.0,"fair_r":41.6667,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The ImmGen MNP Open Source RNA sequencing dataset generated during this study has been deposited at GEO repository (GSE122108) and is publicly available as of the date of publication.","grounded":true,"rationale":"The paper gives a GEO accession (GSE122108), which is a persistent identifier in the repository scheme. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The ImmGen MNP Open Source RNA sequencing dataset generated during this study has been deposited at GEO repository (GSE122108) and is publicly available as of the date of publication.","grounded":true,"rationale":"The paper names GEO as the repository holding the data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The ImmGen MNP Open Source RNA sequencing dataset generated during this study has been deposited at GEO repository (GSE122108) and is publicly available as of the date of publication. This paper also analyzes existing, publicly available data: The ImmGen Phase 1 dataset (GSE15907) and The Tabula Muris Senis dataset (GSE149590).","grounded":true,"rationale":"The statement points at a repository record (GEO) with an accession, i.e., Colavizza category 3. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The ImmGen MNP OS dataset totals 337 samples and provides a source of information about individual cell subpopulations","grounded":true,"rationale":"The dataset's content is described in running prose, not in an itemised inventory [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 ImmGen MNP Open Source RNA sequencing dataset generated during this study has been deposited at GEO repository (GSE122108) and is publicly available as of the date of publication.","grounded":true,"rationale":"The dataset's identifier (GSE122108) appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":81.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"The ImmGen MNP Open Source RNA sequencing dataset generated during this study has been deposited at GEO repository (GSE122108) and is publicly available as of the date of publication.","grounded":true,"rationale":"The text gives a route to the data with no stated precondition; the data are stated to be publicly available. [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":1.0,"verdict":"yes","evidence":"The ImmGen MNP Open Source RNA sequencing dataset generated during this study has been deposited at GEO repository (GSE122108) and is publicly available as of the date of publication.","grounded":true,"rationale":"The paper states the data are publicly available, which is an explicit access-level label for open access. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are from mice, not human subjects, 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":0.5,"verdict":"partial","evidence":"publicly available as of the date of publication","grounded":true,"rationale":"The paper states when the data are available (as of publication) but does not commit to how long they persist. [majority verdict 'partial' (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":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format is named for the released data.","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No community standard is named for the data. [majority verdict 'no' (4/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"This paper also analyzes existing, publicly available data: The ImmGen Phase 1 dataset (GSE15907) and The Tabula Muris Senis dataset (GSE149590).","grounded":true,"rationale":"The paper provides identifiers (GSE15907, GSE149590) for other datasets it uses, and also a DOI for the code. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No license is explicitly stated for the data; the CC BY-NC-ND license applies to the article only.","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":"All samples were sequenced in two separate NextSeq500 runs","grounded":true,"rationale":"The paper names the specific instrument (NextSeq500) and software (STAR, GENCODE) used to produce the data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"Variable definitions are in the supplementary material (Data S1), not a separate documentation object with 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No version token or date is given for the data snapshot. [majority verdict 'no' (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":1.0,"verdict":"yes","evidence":"All original code has been deposited at Zenodo and is publicly available as of the date of publication. DOI is listed in the key resources table.","grounded":true,"rationale":"The paper provides a machine-resolvable locator (Zenodo DOI and GitHub URL) for the code. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"This work was supported by ImmGen Consortium grant AI072073 (NIAID, NIH) and in part by the Division of Intramural Research of the NIAID, NIH. The work was also partly supported by R01-AI125618 (NIAID) to M.N.A..","grounded":true,"rationale":"The paper provides specific grant numbers (AI072073, R01-AI125618) attached to named funders. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No license is explicitly stated for the data; the CC BY-NC-ND license applies to the article only.","gain":16.67,"priority":"essential","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open metabolomics formats such as mzML or nmrML.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format is named for the released data.","gain":8.33,"priority":"important","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the 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 ImmGen MNP Open Source RNA sequencing dataset generated during this study has been deposited at GEO repository (GSE122108) and is publicly available as of the date of publication.","why":"The dataset's identifier (GSE122108) appears only in the body text, not as a reference-list entry. [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 data snapshot. [majority verdict 'no' (3/5 passes agreed)]","gain":4.17,"priority":"useful","scored":true},{"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":"The ImmGen MNP OS dataset totals 337 samples and provides a source of information about individual cell subpopulations","why":"The dataset's content is described in running prose, not in an itemised inventory [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","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":"no","current":0.0,"evidence":null,"why":"No community standard is named for the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"Variable definitions are in the supplementary material (Data S1), not a separate documentation object with 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 from mice, not human subjects, and no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"publicly available as of the date of publication","why":"The paper states when the data are available (as of publication) but does not commit to how long they persist. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open metabolomics formats such as mzML or nmrML.","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.","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.","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."],"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":"2026-07-20T11:34:44.517288Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}