{"doi":"10.1093/genetics/iyaf027","title":"The Unified Phenotype Ontology : a framework for cross-species integrative phenomics","abstract":"Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.","journal":"Genetics","year":2025,"id":516133,"datarank":0.4063806603355596,"base_score":2.3978952727983707,"endowment":2.3978952727983707,"self_citation_contribution":0.3596842909197557,"citation_network_contribution":0.04669636941580391,"self_endowment_contribution":0.3596842909197557,"citer_contribution":0.04669636941580391,"corpus_percentile":54.73814496789665,"corpus_rank":5852,"citation_count":10,"citer_count":5,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5032,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":227448,"name":"Susan M. Bello","orcid":"0000-0003-4606-0597","position":1,"is_corresponding":false},{"id":95757,"name":"Ray Stefancsik","orcid":"0000-0001-8314-2140","position":2,"is_corresponding":false},{"id":1381000,"name":"Sarah M. Alghamdi","orcid":"0000-0001-5544-7166","position":3,"is_corresponding":false},{"id":227447,"name":"Anna V. Anagnostopoulos","orcid":"0000-0002-6490-7723","position":4,"is_corresponding":false},{"id":95726,"name":"James P. Balhoff","orcid":"0000-0002-8688-6599","position":5,"is_corresponding":false},{"id":983328,"name":"Meghan A. Balk","orcid":"0000-0003-2699-3066","position":6,"is_corresponding":false},{"id":492507,"name":"Yvonne M. Bradford","orcid":"0000-0002-9900-7880","position":7,"is_corresponding":false},{"id":1243409,"name":"Yasemin Bridges","orcid":"0009-0002-1371-3782","position":8,"is_corresponding":false},{"id":49890,"name":"Tiffany J. Callahan","orcid":"0000-0002-8169-9049","position":9,"is_corresponding":false},{"id":1178082,"name":"Harry Caufield","orcid":null,"position":10,"is_corresponding":false},{"id":616185,"name":"Alayne Cuzick","orcid":"0000-0001-8941-3984","position":11,"is_corresponding":false},{"id":49883,"name":"Leigh C Carmody","orcid":"0000-0001-7941-2961","position":12,"is_corresponding":false},{"id":857381,"name":"Anita R. Caron","orcid":"0000-0002-6523-4866","position":13,"is_corresponding":false},{"id":1014193,"name":"Vinícius de Souza","orcid":"0000-0003-3961-0247","position":14,"is_corresponding":false},{"id":103866,"name":"Stacia R. Engel","orcid":"0000-0001-5472-917X","position":15,"is_corresponding":false},{"id":103805,"name":"Petra Fey","orcid":"0000-0002-4532-2703","position":16,"is_corresponding":false},{"id":77633,"name":"Malcolm E Fisher","orcid":"0000-0003-1074-8103","position":17,"is_corresponding":false},{"id":241695,"name":"Sarah Gehrke","orcid":"0000-0003-3245-2880","position":18,"is_corresponding":false},{"id":1381001,"name":"Christian A Grove","orcid":"0000-0001-9076-6015","position":19,"is_corresponding":false},{"id":789844,"name":"Peter Hansen","orcid":"0000-0001-5535-2845","position":20,"is_corresponding":false},{"id":6466,"name":"Nomi L. Harris","orcid":"0000-0001-6315-3707","position":21,"is_corresponding":false},{"id":103849,"name":"Midori A. Harris","orcid":"0000-0003-4148-4606","position":22,"is_corresponding":false},{"id":88397,"name":"Laura W. Harris","orcid":"0000-0003-4312-7223","position":23,"is_corresponding":false},{"id":838682,"name":"Arwa Ibrahim","orcid":"0000-0001-6757-4744","position":24,"is_corresponding":false},{"id":78897,"name":"Julius O.B. Jacobsen","orcid":"0000-0002-3265-1591","position":25,"is_corresponding":false},{"id":106353,"name":"Sebastian Köhler","orcid":"0000-0002-5316-1399","position":26,"is_corresponding":false},{"id":49908,"name":"Julie A. McMurry","orcid":"0000-0002-9353-5498","position":27,"is_corresponding":false},{"id":266970,"name":"Violeta Muñoz‐Fuentes","orcid":"0000-0003-3574-546X","position":28,"is_corresponding":false},{"id":95743,"name":"Monica C Munoz-Torres","orcid":"0000-0001-8430-6039","position":29,"is_corresponding":false},{"id":2833,"name":"Helen Parkinson","orcid":"0000-0003-3035-4195","position":30,"is_corresponding":false},{"id":95748,"name":"Zoë May Pendlington","orcid":"0000-0002-4071-8397","position":31,"is_corresponding":false},{"id":226984,"name":"Clare Pilgrim","orcid":"0000-0002-1373-1705","position":32,"is_corresponding":false},{"id":336710,"name":"Sofia Robb","orcid":"0000-0002-3528-5267","position":33,"is_corresponding":false},{"id":49925,"name":"Peter N. Robinson","orcid":"0000-0002-0736-9199","position":34,"is_corresponding":false},{"id":616196,"name":"James Seager","orcid":"0000-0001-7487-610X","position":35,"is_corresponding":false},{"id":611899,"name":"Erik Segerdell","orcid":"0000-0002-9611-1279","position":36,"is_corresponding":false},{"id":11700,"name":"Damian Smedley","orcid":"0000-0002-5836-9850","position":37,"is_corresponding":false},{"id":88403,"name":"Elliot Sollis","orcid":"0000-0003-1322-388X","position":38,"is_corresponding":false},{"id":95720,"name":"Sabrina Toro","orcid":"0000-0002-4142-7153","position":39,"is_corresponding":false},{"id":49882,"name":"Nicole A. Vasilevsky","orcid":"0000-0001-5208-3432","position":40,"is_corresponding":false},{"id":95769,"name":"Valerie Wood","orcid":"0000-0001-6330-7526","position":41,"is_corresponding":false},{"id":4026,"name":"Melissa A Haendel","orcid":"0000-0001-9114-8737","position":42,"is_corresponding":false},{"id":6476,"name":"Christopher J. Mungall","orcid":"0000-0002-6601-2165","position":43,"is_corresponding":false},{"id":1019900,"name":"James Alastair McLaughlin","orcid":"0000-0002-8361-2795","position":44,"is_corresponding":false},{"id":95747,"name":"David Osumi-Sutherland","orcid":"0000-0002-7073-9172","position":45,"is_corresponding":false},{"id":49906,"name":"Nicolas A Matentzoglu","orcid":"0000-0002-7356-1779","position":0,"is_corresponding":true}],"reference_count":61,"raw_metadata":null,"created_at":"2026-07-19T02:48:44.647022Z","pmid":"40048704","pmcid":"PMC11912833","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":80.0,"fair_r":41.6667,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"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":"https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","grounded":true,"rationale":"The paper gives a URL for the data, not a persistent identifier scheme such as a DOI, Handle, or repository accession. [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":0.5,"verdict":"partial","evidence":"https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","grounded":true,"rationale":"The data are hosted on GitHub, a code repository that is not a dedicated data repository listed in re3data/FAIRsharing. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","grounded":true,"rationale":"The statement points to a GitHub URL, which is a link to an archived location but not a repository record with a persistent identifier. [majority verdict 'partial' (4/5 passes agreed)]","anchors":["Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li","Springer Nature research data policy — Data Availability Statements: standard statement templat","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"uPheno has 3 main components: the uPheno ontology, a library of design patterns (templates) for computationally tractable phenotype definitions, and a number of standardized mappings to connect disparate phenotype ontologies.","grounded":true,"rationale":"The dataset's content is described in running prose, not in an itemised inventory such as a table or bulleted list of files. [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 uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","grounded":true,"rationale":"The dataset identifier (GitHub URL) 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":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":"The uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","grounded":true,"rationale":"The paper gives a URL to GitHub where the data can be accessed without any stated precondition such as registration, embargo, or request. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"The uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","grounded":true,"rationale":"The paper provides a URL to access the data but does not use any explicit access-level label such as 'open access' or 'publicly available'. [majority verdict 'partial' (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 dataset is an ontology, not sensitive human-subject data, 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 when the data become available or how long they will persist.","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":80.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The uPheno ontology is a computational logic-based ontology built using the W3C Web Ontology Language (OWL).","grounded":true,"rationale":"The data are released in OWL, an open, community-standard format. 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[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":"The paper cites external ontologies by name and reference, but does not provide identifiers (e.g., DOIs, accessions) for those resources themselves. [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":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 for the data is mentioned in the paper; the CC-BY license applies only to the article.","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 release system of the uPheno ontology is implemented as an ODK workflow, which makes it easily executable in a platform-agnostic manner through Docker.","grounded":true,"rationale":"The paper names specific tools (ODK, Docker) and versions used to build the data. 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[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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide a version token or date for the uPheno dataset itself.","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 uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","grounded":true,"rationale":"The paper provides a machine-resolvable GitHub URL for the code/ontology, which is an authoritative locator. [majority verdict 'yes' (3/5 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 NIH National Human Genome Research Institute Phenomics First Resource, NIH-NHGRI # 5RM1 HG010860","grounded":true,"rationale":"The paper includes a specific award/grant number alongside the funder name. [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 for the data is mentioned in the paper; the CC-BY license applies only to the article.","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 neuroimaging data, deposit in OpenNeuro or NeuroVault.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","why":"The paper gives a URL for the data, not a persistent identifier scheme such as a DOI, Handle, or repository accession. [majority verdict 'partial' (4/5 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 neuroimaging data, deposit in OpenNeuro or NeuroVault.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","why":"The data are hosted on GitHub, a code repository that is not a dedicated data repository listed in re3data/FAIRsharing. [majority verdict 'partial' (4/5 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 neuroimaging repository accession (e.g. from OpenNeuro or NeuroVault) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","why":"The dataset identifier (GitHub URL) 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":"The paper does not provide a version token or date for the uPheno dataset itself.","gain":4.17,"priority":"useful","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","why":"The statement points to a GitHub URL, which is a link to an archived location but not a repository record with a persistent identifier. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"uPheno has 3 main components: the uPheno ontology, a library of design patterns (templates) for computationally tractable phenotype definitions, and a number of standardized mappings to connect disparate phenotype ontologies.","why":"The dataset's content is described in running prose, not in an itemised inventory such as a table or bulleted list of files. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The uPheno ontology, pattern library and associated files can be found here: https://github.com/obophenotype/upheno/blob/master/docs/reference/data-availability.md","why":"The paper provides a URL to access the data but does not use any explicit access-level label such as 'open access' or 'publicly available'. [majority verdict 'partial' (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":"The paper does not mention a README, data dictionary, or codebook shipped with 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 dataset is an ontology, not sensitive human-subject data, 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":"The paper cites external ontologies by name and reference, but does not provide identifiers (e.g., DOIs, accessions) for those resources themselves. [majority verdict 'no' (3/5 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 when the data become available or how long they will persist.","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 neuroimaging data, deposit in OpenNeuro or NeuroVault.","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 neuroimaging data, deposit in OpenNeuro or NeuroVault.","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 neuroimaging repository accession (e.g. from OpenNeuro or NeuroVault) 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."],"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":"2026-07-20T12:24:38.346660Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}