{"doi":"10.1016/j.gimo.2025.103429","title":"The ClinGen Syndromic Disorders Gene Curation Expert Panel: Assessing the clinical validity of 111 gene-disease relationships","abstract":"Purpose: The Clinical Genome Resource (ClinGen) Gene Curation Expert Panels have historically focused on specific organ systems or phenotypes; thus, the ClinGen Syndromic Disorders Gene Curation Expert Panel (SD-GCEP) was formed to address an unmet need. Methods: The SD-GCEP applied ClinGen's framework to evaluate the clinical validity of genes associated with rare syndromic disorders. A total of 111 gene-disease relationships (GDRs) associated with 100 genes spanning the clinical spectrum of syndromic disorders were curated. Results: From April 2020 through March 2024, 38 precurations were performed on genes with multiple disease relationships and were reviewed to determine if the disorders were part of a spectrum or distinct entities. A total of 14 genes were lumped into a single disease entity, and 24 were split into separate entities, of which 11 were curated by the SD-GCEP. A full review of 111 GDRs for 100 genes followed, with 78 classified as Definitive, 9 as Strong, 15 as Moderate, and 9 as Limited, highlighting cases in which further data are needed. All diseases involved 2 or more organ systems, whereas the majority (88/111 GDRs, 79.2%) had 5 or more organ systems affected. Conclusion: The SD-GCEP addresses a critical gap in gene curation efforts, enabling inclusion of genes for syndromic disorders in clinical testing and contributing to keeping pace with the rapid discovery of new genetic syndromes.","journal":"Genetics in Medicine Open","year":2025,"id":564019,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":0.0,"corpus_rank":10062,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7195,"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":41.6667,"fair_percentile":54.173035768878016,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1339135,"name":"Vanessa Gitau","orcid":null,"position":1,"is_corresponding":false},{"id":496089,"name":"Alicia B. Byrne","orcid":"0000-0002-8141-1818","position":2,"is_corresponding":false},{"id":1132664,"name":"Pamela Ajuyah","orcid":"0000-0002-5529-1461","position":3,"is_corresponding":false},{"id":984834,"name":"Marie Balzotti","orcid":null,"position":4,"is_corresponding":false},{"id":477827,"name":"Jonathan S. Berg","orcid":"0000-0003-2360-2664","position":5,"is_corresponding":false},{"id":639894,"name":"Krista Bluske","orcid":null,"position":6,"is_corresponding":false},{"id":1301592,"name":"B.M. Bowen","orcid":"0000-0002-3148-5667","position":7,"is_corresponding":false},{"id":88793,"name":"Matthew P. Brown","orcid":null,"position":8,"is_corresponding":false},{"id":1288489,"name":"Amanda Buchanan","orcid":null,"position":9,"is_corresponding":false},{"id":1288490,"name":"Brendan Burns","orcid":null,"position":10,"is_corresponding":false},{"id":1467193,"name":"Nicole J. Burns","orcid":null,"position":11,"is_corresponding":false},{"id":1287843,"name":"Anjana Chandrasekhar","orcid":"0009-0001-5113-5576","position":12,"is_corresponding":false},{"id":261289,"name":"Aditi Chawla","orcid":null,"position":13,"is_corresponding":false},{"id":991,"name":"Jessica X. Chong","orcid":"0000-0002-1616-2448","position":14,"is_corresponding":false},{"id":670855,"name":"Maya Chopra","orcid":"0000-0002-2574-3375","position":15,"is_corresponding":false},{"id":894008,"name":"Amanda Clause","orcid":"0000-0002-2078-7280","position":16,"is_corresponding":false},{"id":607765,"name":"Marina T. DiStefano","orcid":"0000-0002-8218-5111","position":17,"is_corresponding":false},{"id":364149,"name":"Stephanie DiTroia","orcid":"0000-0002-6847-6780","position":18,"is_corresponding":false},{"id":1071087,"name":"Marwa Elnagheeb","orcid":null,"position":19,"is_corresponding":false},{"id":1467194,"name":"Amanda N. Girod","orcid":null,"position":20,"is_corresponding":false},{"id":819046,"name":"Himanshu Goel","orcid":"0000-0001-6448-6618","position":21,"is_corresponding":false},{"id":276539,"name":"Katie Golden‐Grant","orcid":null,"position":22,"is_corresponding":false},{"id":660470,"name":"Thuong Ha","orcid":"0000-0002-4408-2613","position":23,"is_corresponding":false},{"id":36509,"name":"Ada Hamosh","orcid":"0000-0002-1780-5230","position":24,"is_corresponding":false},{"id":1467195,"name":"Jennifer M. Huang","orcid":null,"position":25,"is_corresponding":false},{"id":808749,"name":"Madeline Y. Hughes","orcid":null,"position":26,"is_corresponding":false},{"id":699290,"name":"Saumya Shekhar Jamuar","orcid":"0000-0003-2341-8349","position":27,"is_corresponding":false},{"id":1338684,"name":"Sylvia Kam","orcid":"0000-0001-7704-1917","position":28,"is_corresponding":false},{"id":593667,"name":"Akanchha Kesari","orcid":"0000-0003-4201-901X","position":29,"is_corresponding":false},{"id":1338685,"name":"Ai Ling Koh","orcid":"0000-0002-4514-6869","position":30,"is_corresponding":false},{"id":1339138,"name":"Rhonda N.T. Lassiter","orcid":null,"position":31,"is_corresponding":false},{"id":218155,"name":"S. E. A. Leigh","orcid":"0000-0003-3368-7059","position":32,"is_corresponding":false},{"id":557096,"name":"Gabrielle Lemire","orcid":"0000-0002-2834-6973","position":33,"is_corresponding":false},{"id":699293,"name":"Jiin Ying Lim","orcid":"0000-0003-3253-2768","position":34,"is_corresponding":false},{"id":335221,"name":"Alka Malhotra","orcid":"0000-0003-1174-688X","position":35,"is_corresponding":false},{"id":679099,"name":"Hannah McCurry","orcid":null,"position":36,"is_corresponding":false},{"id":1288494,"name":"Becky Milewski","orcid":null,"position":37,"is_corresponding":false},{"id":893184,"name":"Shahida Moosa","orcid":"0000-0002-4463-3067","position":38,"is_corresponding":false},{"id":266971,"name":"Stephen A. Murray","orcid":"0000-0002-0594-1702","position":39,"is_corresponding":false},{"id":1071089,"name":"Emma Owens","orcid":null,"position":40,"is_corresponding":false},{"id":243291,"name":"Elizabeth E. Palmer","orcid":"0000-0003-1844-215X","position":41,"is_corresponding":false},{"id":613946,"name":"Brooke C. Palus","orcid":null,"position":42,"is_corresponding":false},{"id":808748,"name":"Mayher Patel","orcid":null,"position":43,"is_corresponding":false},{"id":1288497,"name":"Revathi Rajkumar","orcid":null,"position":44,"is_corresponding":false},{"id":1339139,"name":"Julie Ratliff","orcid":null,"position":45,"is_corresponding":false},{"id":259398,"name":"F. Lucy Raymond","orcid":"0000-0003-2652-3355","position":46,"is_corresponding":false},{"id":1338686,"name":"Bruno Della Ripa Rodrigues Assis","orcid":"0000-0002-2133-1912","position":47,"is_corresponding":false},{"id":1287845,"name":"Samin A. Sajan","orcid":"0000-0002-9689-2597","position":48,"is_corresponding":false},{"id":760519,"name":"Zinayida Schlachetzki","orcid":null,"position":49,"is_corresponding":false},{"id":504888,"name":"Sarah Schmidt","orcid":"0000-0002-4200-9703","position":50,"is_corresponding":false},{"id":433620,"name":"Zornitza Stark","orcid":"0000-0001-8640-1371","position":51,"is_corresponding":false},{"id":941256,"name":"Samuel P. Strom","orcid":"0000-0003-3254-7564","position":52,"is_corresponding":false},{"id":1026781,"name":"Julie P. Taylor","orcid":"0000-0003-1819-3640","position":53,"is_corresponding":false},{"id":95764,"name":"Courtney L Thaxton","orcid":"0000-0002-6733-369X","position":54,"is_corresponding":false},{"id":1339141,"name":"Devon Lamb Thrush","orcid":null,"position":55,"is_corresponding":false},{"id":95720,"name":"Sabrina Toro","orcid":"0000-0002-4142-7153","position":56,"is_corresponding":false},{"id":1338687,"name":"Kezang Tshering","orcid":"0000-0001-9619-3625","position":57,"is_corresponding":false},{"id":49882,"name":"Nicole A. Vasilevsky","orcid":"0000-0001-5208-3432","position":58,"is_corresponding":false},{"id":1326549,"name":"Bess Wayburn","orcid":null,"position":59,"is_corresponding":false},{"id":894012,"name":"Ryan Webb","orcid":"0009-0003-2127-3550","position":60,"is_corresponding":false},{"id":995,"name":"Anne H. O’Donnell-Luria","orcid":"0000-0001-6418-9592","position":61,"is_corresponding":false},{"id":70735,"name":"Alison J. Coffey","orcid":"0000-0002-1338-8513","position":62,"is_corresponding":false},{"id":1339134,"name":"Eleanor C Broeren","orcid":null,"position":0,"is_corresponding":true}],"reference_count":35,"raw_metadata":null,"created_at":"2026-07-19T02:56:17.117043Z","pmid":"40496713","pmcid":"PMC12151239","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":61.1111,"fair_a":81.25,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":0.2857,"fair_rationale":{"fair_score":41.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":61.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"https://search.clinicalgenome.org/kb/gene-validity/","grounded":true,"rationale":"The only identifier for the dataset is a URL, not a persistent identifier scheme.","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":"Clinical Genome Resource website","grounded":true,"rationale":"The named host is a consortium website, not a curated data repository like GEO. [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":1.0,"verdict":"yes","evidence":"The data used in this publication are available in the Supplemental File and the online version of this article. The Clinical Genome Resource Syndromic Disorders Gene Curation Expert Panel makes all curations publicly available on the Clinical Genome Resource website ( https://search.clinicalgenome.org/kb/gene-validity/ ).","grounded":true,"rationale":"The statement points to a repository record (ClinGen website) with a persistent link.","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":"78 GDRs were classified as Definitive, 9 as Strong, 15 as Moderate, and 9 as Limited","grounded":true,"rationale":"The dataset's content is described in running prose, not 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 Clinical Genome Resource Syndromic Disorders Gene Curation Expert Panel makes all curations publicly available on the Clinical Genome Resource website ( https://search.clinicalgenome.org/kb/gene-validity/ ).","grounded":true,"rationale":"The dataset identifier appears only in the body text, not as a reference-list entry.","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":"makes all curations publicly available on the Clinical Genome Resource website","grounded":true,"rationale":"The text states the data are publicly available with no precondition.","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"makes all curations publicly available on the Clinical Genome Resource website","grounded":true,"rationale":"The paper uses the phrase 'publicly available' which is a natural-language synonym for open access.","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, 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":"makes all curations publicly available on the Clinical Genome Resource website","grounded":true,"rationale":"The paper states the data are available now but does not specify how long they will 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":40.0,"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":1.0,"verdict":"yes","evidence":"Human Phenotype Ontology (HPO)","grounded":true,"rationale":"The paper applies the HPO, a community-standard ontology, to describe phenotypes.","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., accession, DOI) is given for data the study depends on. [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":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 license is stated for the data; the CC BY 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":"curation is performed by SD-GCEP curators using ClinGen's Gene Curation Interface","grounded":true,"rationale":"The paper names a specific software tool used to produce the data.","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":0.5,"verdict":"partial","evidence":"Supplemental Table 2","grounded":true,"rationale":"Variable definitions live inside the article (Supplemental Table 2), not shipped with the data. [majority verdict 'partial' (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":"No version token or date pins the dataset 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"Code availability is not addressed.","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":"U24HD104591","grounded":true,"rationale":"An award number is given for the funding.","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 stated for the data; the CC BY license applies to the article only.","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"https://search.clinicalgenome.org/kb/gene-validity/","why":"The only identifier for the dataset is a URL, not a persistent identifier scheme.","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Clinical Genome Resource website","why":"The named host is a consortium website, not a curated data repository like GEO. [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"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 genomics / sequencing formats such as FASTQ, BAM or VCF.","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":"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":"Code availability is not addressed.","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 genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The Clinical Genome Resource Syndromic Disorders Gene Curation Expert Panel makes all curations publicly available on the Clinical Genome Resource website ( https://search.clinicalgenome.org/kb/gene-validity/ ).","why":"The dataset identifier appears only in the body text, not as a reference-list entry.","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 pins the dataset 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":"78 GDRs were classified as Definitive, 9 as Strong, 15 as Moderate, and 9 as Limited","why":"The dataset's content is described in running prose, not an itemised inventory. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Supplemental Table 2","why":"Variable definitions live inside the article (Supplemental Table 2), not shipped with the data. [majority verdict 'partial' (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. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive, and no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No identifier for an external resource (e.g., accession, DOI) is given for data the study depends on. [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":"partial","current":0.5,"evidence":"makes all curations publicly available on the Clinical Genome Resource website","why":"The paper states the data are available now but does not specify how long they will 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.","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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 genomics / sequencing formats such as FASTQ, BAM or VCF.","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":"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":"2026-07-20T13:53:56.162144Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}