{"doi":"10.1093/nar/gkac1033","title":"Pharos 2023: an integrated resource for the understudied human proteome","abstract":"The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other therapeutic modalities. Two main products from the IDG effort are the Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/), which curates and aggregates information, and Pharos (https://pharos.nih.gov/), a web interface for fusers to extract and visualize data from TCRD. Since the 2021 release, TCRD/Pharos has focused on developing visualization and analysis tools that help reveal higher-level patterns in the underlying data. The current iterations of TCRD and Pharos enable users to perform enrichment calculations based on subsets of targets, diseases, or ligands and to create interactive heat maps and UpSet charts of many types of annotations. Using several examples, we show how to address disease biology and drug discovery questions through enrichment calculations and UpSet charts.","journal":"Nucleic Acids Research","year":2022,"id":233339,"datarank":2.3282536275665833,"base_score":4.897839799950911,"endowment":4.897839799950911,"self_citation_contribution":0.7346759699926367,"citation_network_contribution":1.5935776575739464,"self_endowment_contribution":0.7346759699926367,"citer_contribution":1.5935776575739464,"corpus_percentile":90.81766844588844,"corpus_rank":1188,"citation_count":133,"citer_count":100,"citers_with_citation_signal":75,"citers_with_endowment":75,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9516,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":54.1667,"fair_percentile":68.66401712014674,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":251416,"name":"Timothy Sheils","orcid":"0000-0002-9987-3738","position":1,"is_corresponding":false},{"id":68165,"name":"Stephen L. Mathias","orcid":"0000-0002-7255-370X","position":2,"is_corresponding":false},{"id":68164,"name":"Jeremy J. Yang","orcid":"0000-0002-1476-6192","position":3,"is_corresponding":false},{"id":846317,"name":"Vincent T. Metzger","orcid":"0000-0002-8041-0370","position":4,"is_corresponding":false},{"id":251418,"name":"Vishal B. Siramshetty","orcid":"0000-0002-5980-8288","position":5,"is_corresponding":false},{"id":245756,"name":"Ðắc-Trung Nguyễn","orcid":"0000-0003-2591-9948","position":6,"is_corresponding":false},{"id":54677,"name":"Lars Juhl Jensen","orcid":"0000-0001-7885-715X","position":7,"is_corresponding":false},{"id":251419,"name":"D. Vidović","orcid":"0000-0001-9798-2108","position":8,"is_corresponding":false},{"id":64669,"name":"Stephan C. Schürer","orcid":"0000-0001-7180-0978","position":9,"is_corresponding":false},{"id":68163,"name":"Jayme Holmes","orcid":"0000-0003-3109-5228","position":10,"is_corresponding":false},{"id":233026,"name":"Karlie R. Sharma","orcid":"0000-0003-3435-7721","position":11,"is_corresponding":false},{"id":64668,"name":"Ajay Pillai","orcid":"0000-0002-9789-7189","position":12,"is_corresponding":false},{"id":68168,"name":"Cristian Bologa","orcid":"0000-0003-2232-4244","position":13,"is_corresponding":false},{"id":350432,"name":"Jeremy S. Edwards","orcid":"0000-0003-3694-3716","position":14,"is_corresponding":false},{"id":37894,"name":"Ewy A. Mathé","orcid":"0000-0003-4491-8107","position":15,"is_corresponding":false},{"id":68160,"name":"Tudor I. Oprea","orcid":"0000-0002-6195-6976","position":16,"is_corresponding":false},{"id":251417,"name":"Keith J. Kelleher","orcid":"0000-0002-8878-1539","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-19T00:21:25.223756Z","pmid":"36624666","pmcid":"PMC9825581","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":50.0,"fair_a":62.5,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":0.7804,"fair_rationale":{"fair_score":54.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","grounded":true,"rationale":"The only identifier given for the dataset is a URL, which is not a persistent identifier scheme like DOI or Handle. [majority verdict 'partial' (3/4 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":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","grounded":true,"rationale":"The data is hosted on an institutional website, not a named data repository from the re3data/FAIRsharing list. [majority verdict 'partial' (3/4 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":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ . Pharos is an open source web platform that can be accessed at: https://pharos.nih.gov/ .","grounded":true,"rationale":"The statement points to URLs rather than a repository record with an accession or DOI. [majority verdict 'partial' (3/4 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":"TCRD aggregates data from 79 sources and harmonizes the many different (often disjoint) identifiers that the data sources utilize for targets (proteins), diseases, and ligands.","grounded":true,"rationale":"The dataset's content is described in running prose rather than an itemised inventory. [majority verdict 'partial' (3/4 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":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","grounded":true,"rationale":"The dataset's URL appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (3/4 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":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","grounded":true,"rationale":"The text gives a URL with no stated precondition; the data are stated to be open source and accessible. [majority verdict 'yes' (3/4 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":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","grounded":true,"rationale":"The paper uses 'open source' to describe the database, but does not explicitly label the access level with standard vocabulary such as 'open access' or 'freely available'. [majority verdict 'partial' (2/4 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 human-subject data; no gatekeeper is named because none is needed.","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 any timing or persistence commitment for the data.","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":"One key enhancement since our last update (4) is the ability for users to readily download CSV-formatted tables of data from the website for further analysis or investigation.","grounded":false,"rationale":"CSV is an open, community-standard format named for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"Gene Ontology (GO)","grounded":false,"rationale":"The paper applies the Gene Ontology, a community standard vocabulary registered in FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 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":"a_access_conditions_stated","grounded":false,"rationale":"The paper does not provide a persistent identifier for any external resource; it only references publications. [majority verdict 'no' (2/4 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":"No licence is explicitly attached to the data; the article's CC-BY-NC licence does not cover the data itself.","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The data handling code was migrated into a workflow management tool, Apache Airflow.","grounded":false,"rationale":"The paper names specific software (Apache Airflow) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"The paper does not mention a documentation object shipped with the data, nor a variable-definition table inside the article.","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":"Pharos has reached version 3.14.1, which utilizes the latest TCRD version 6.13.4.","grounded":false,"rationale":"Version tokens are provided for both the database and the web platform. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"The front end code can be found on Github: https://github.com/ncats/pharos_frontend .","grounded":true,"rationale":"A machine-resolvable code repository URL is given for the study's own code. [majority verdict 'yes' (3/4 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":0.5,"verdict":"partial","evidence":"National Institutes of Health (NIH) Common Fund [U24 CA224370 ...]","grounded":false,"rationale":"Award/grant numbers are explicitly listed for the funding sources. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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 licence is explicitly attached to the data; the article's CC-BY-NC licence does not cover the data itself.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","why":"The only identifier given for the dataset is a URL, which is not a persistent identifier scheme like DOI or Handle. [majority verdict 'partial' (3/4 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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","why":"The data is hosted on an institutional website, not a named data repository from the re3data/FAIRsharing list. [majority verdict 'partial' (3/4 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 proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","why":"The dataset's URL appears only in the body text, not as a reference-list entry. [majority verdict 'partial' (3/4 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 proteomics formats such as mzML or mzIdentML.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"One key enhancement since our last update (4) is the ability for users to readily download CSV-formatted tables of data from the website for further analysis or investigation.","why":"CSV is an open, community-standard format named for the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"Pharos has reached version 3.14.1, which utilizes the latest TCRD version 6.13.4.","why":"Version tokens are provided for both the database and the web platform. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"National Institutes of Health (NIH) Common Fund [U24 CA224370 ...]","why":"Award/grant numbers are explicitly listed for the funding sources. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","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":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ . Pharos is an open source web platform that can be accessed at: https://pharos.nih.gov/ .","why":"The statement points to URLs rather than a repository record with an accession or DOI. [majority verdict 'partial' (3/4 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":"TCRD aggregates data from 79 sources and harmonizes the many different (often disjoint) identifiers that the data sources utilize for targets (proteins), diseases, and ligands.","why":"The dataset's content is described in running prose rather than an itemised inventory. [majority verdict 'partial' (3/4 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":"TCRD is an open source database that can be accessed at: http://juniper.health.unm.edu/tcrd/ .","why":"The paper uses 'open source' to describe the database, but does not explicitly label the access level with standard vocabulary such as 'open access' or 'freely available'. [majority verdict 'partial' (2/4 passes agreed)]","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 proteomics, describe the data with mzML or MIAPE.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Gene Ontology (GO)","why":"The paper applies the Gene Ontology, a community standard vocabulary registered in FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The data handling code was migrated into a workflow management tool, Apache Airflow.","why":"The paper names specific software (Apache Airflow) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"The paper does not mention a documentation object shipped with the data, nor a variable-definition table inside the article.","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 human-subject data; no gatekeeper is named because none is needed.","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":"a_access_conditions_stated","why":"The paper does not provide a persistent identifier for any external resource; it only references publications. [majority verdict 'no' (2/4 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 any timing or persistence commitment for the data.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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 proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) 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 proteomics formats such as mzML or mzIdentML."],"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":"2026-07-20T11:01:23.251483Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}