{"doi":"10.1093/nar/gkad1051","title":"The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem","abstract":"In 2003, the Human Disease Ontology (DO, https://disease-ontology.org/) was established at Northwestern University. In the intervening 20 years, the DO has expanded to become a highly-utilized disease knowledge resource. Serving as the nomenclature and classification standard for human diseases, the DO provides a stable, etiology-based structure integrating mechanistic drivers of human disease. Over the past two decades the DO has grown from a collection of clinical vocabularies, into an expertly curated semantic resource of over 11300 common and rare diseases linking disease concepts through more than 37000 vocabulary cross mappings (v2023-08-08). Here, we introduce the recently launched DO Knowledgebase (DO-KB), which expands the DO's representation of the diseaseome and enhances the findability, accessibility, interoperability and reusability (FAIR) of disease data through a new SPARQL service and new Faceted Search Interface. The DO-KB is an integrated data system, built upon the DO's semantic disease knowledge backbone, with resources that expose and connect the DO's semantic knowledge with disease-related data across Open Linked Data resources. This update includes descriptions of efforts to assess the DO's global impact and improvements to data quality and content, with emphasis on changes in the last two years.","journal":"Nucleic Acids Research","year":2023,"id":319279,"datarank":1.522205812017459,"base_score":4.060443010546419,"endowment":4.060443010546419,"self_citation_contribution":0.6090664515819629,"citation_network_contribution":0.9131393604354963,"self_endowment_contribution":0.6090664515819629,"citer_contribution":0.9131393604354963,"corpus_percentile":86.37734973311673,"corpus_rank":1762,"citation_count":57,"citer_count":49,"citers_with_citation_signal":34,"citers_with_endowment":34,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9447,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":58.3333,"fair_percentile":72.8829104249465,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1027993,"name":"Claudia Sanchez-Beato Johnson","orcid":"0009-0003-9378-6419","position":1,"is_corresponding":false},{"id":59076,"name":"Michael Schor","orcid":"0000-0002-4493-7992","position":2,"is_corresponding":false},{"id":618854,"name":"Dustin Olley","orcid":"0000-0001-8685-0839","position":3,"is_corresponding":false},{"id":482467,"name":"Lance Nickel","orcid":"0000-0002-5836-3571","position":4,"is_corresponding":false},{"id":482466,"name":"Victor Felix","orcid":"0000-0002-9773-0629","position":5,"is_corresponding":false},{"id":70332,"name":"James B. Munro","orcid":"0000-0003-3067-6434","position":6,"is_corresponding":false},{"id":227448,"name":"Susan M. Bello","orcid":"0000-0003-4606-0597","position":7,"is_corresponding":false},{"id":389963,"name":"Cynthia F. Bearer","orcid":"0000-0003-4809-2250","position":8,"is_corresponding":false},{"id":619820,"name":"Richard Lichenstein","orcid":null,"position":9,"is_corresponding":false},{"id":618856,"name":"Katharine Bisordi","orcid":"0000-0001-7380-4817","position":10,"is_corresponding":false},{"id":1027994,"name":"Rima Koka","orcid":"0000-0002-0457-8489","position":11,"is_corresponding":false},{"id":618858,"name":"Carol L. Greene","orcid":"0000-0001-8219-8767","position":12,"is_corresponding":false},{"id":19861,"name":"Lynn M. Schriml","orcid":"0000-0001-8910-9851","position":13,"is_corresponding":false},{"id":618855,"name":"J. Allen Baron","orcid":"0000-0002-0593-3569","position":0,"is_corresponding":true}],"reference_count":14,"raw_metadata":null,"created_at":"2026-07-19T01:07:12.004111Z","pmid":"37953304","pmcid":"PMC10767934","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":44.4444,"fair_a":25.0,"fair_i":60.0,"fair_r":66.6667,"fair_zscore":0.9454,"fair_rationale":{"fair_score":58.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":44.44,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","grounded":false,"rationale":"The paper provides a DOI (10.5281/zenodo.10030384) for the data, which is a persistent identifier scheme. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","grounded":false,"rationale":"The paper names Zenodo, a curated repository listed in re3data, as a holder of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"Data availability: All data produced for this work is made available under the Creative Commons CC0 1.0 license (https://creativecommons.org). Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","grounded":false,"rationale":"The data-availability statement points to a repository (Zenodo) with a DOI, which is a repository record. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"The DO-KB is an integrated data system, built upon the DO’s semantic disease knowledge backbone, with resources that expose and connect the DO’s semantic knowledge with disease-related data across Open Linked Data resources.","grounded":true,"rationale":"The dataset is described in running prose, not as an itemized 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":0.0,"verdict":"no","evidence":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","grounded":false,"rationale":"The Zenodo DOI appears only in the body text (data availability statement), not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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":25.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All data produced for this work is made available under the Creative Commons CC0 1.0 license (https://creativecommons.org). Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","grounded":false,"rationale":"The text provides a direct route (GitHub and Zenodo) with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":0.0,"verdict":"no","evidence":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","grounded":false,"rationale":"The paper describes the access action (data available from GitHub and Zenodo) but does not label the access level with a standard vocabulary term. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 paper does not involve sensitive or 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":"No statement about how long the data will persist or when it becomes available. [majority verdict 'no' (3/4 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":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"OWL","grounded":false,"rationale":"The paper states the data is available in OWL format, an open community standard. [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":"the DO is an OBO Foundry (http://obofoundry.org/) ontology","grounded":false,"rationale":"The paper states that the DO (the data resource) is an OBO Foundry ontology, which is a community standard for ontology representation. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":1.0,"verdict":"yes","evidence":"http://purl.obolibrary.org/obo/PR_000000053","grounded":true,"rationale":"The paper includes a URI for a protein ontology term, which is a qualified reference to another resource. [majority verdict 'yes' (3/4 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":66.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Creative Commons CC0 1.0 license","grounded":true,"rationale":"The data is licensed under CC0, an open standard license.","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 DO-KB Faceted Search Interface is powered by Elasticsearch (https://www.elastic.co/elasticsearch/). This back-end service was chosen to optimize processing speed and enable advanced programmatic logical queries. To format the data for Elasticsearch, a new ‘OWL Flattener’ program was developed to extract terms and their associated logical statements from the DO OWL files, to arrange the DO terms in JSON key-value lists and to organize those terms into dynamic facets using Java and the Java OWL API package.","grounded":false,"rationale":"The paper names specific tools and software (Elasticsearch, OWL Flattener, Java OWL API) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 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":"No documentation object (README, codebook) is named as travelling with the data. [majority verdict 'no' (2/4 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":1.0,"verdict":"yes","evidence":"the DO (v2023-08-08) has expanded to include 11367 diseases","grounded":true,"rationale":"The paper gives a version token (v2023-08-08) for the DO data, which is the study's own dataset. [majority verdict 'yes' (3/4 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":0.5,"verdict":"partial","evidence":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","grounded":false,"rationale":"The paper provides a machine-resolvable locator (GitHub URL and Zenodo DOI) for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":1.0,"verdict":"yes","evidence":"U41 HG008735-01A1","grounded":true,"rationale":"The paper includes a grant number for the funding agency.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For 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":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","why":"The paper provides a DOI (10.5281/zenodo.10030384) for the data, which is a persistent identifier scheme. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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 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":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","why":"The paper names Zenodo, a curated repository listed in re3data, as a holder of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For 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":"All data produced for this work is made available under the Creative Commons CC0 1.0 license (https://creativecommons.org). Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","why":"The text provides a direct route (GitHub and Zenodo) with no stated precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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 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":"no","current":0.0,"evidence":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","why":"The Zenodo DOI appears only in the body text (data availability statement), not in the reference list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"OWL","why":"The paper states the data is available in OWL format, an open community standard. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","gain":4.17,"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":"partial","current":0.5,"evidence":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","why":"The paper provides a machine-resolvable locator (GitHub URL and Zenodo DOI) for the study's own code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data availability: All data produced for this work is made available under the Creative Commons CC0 1.0 license (https://creativecommons.org). Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","why":"The data-availability statement points to a repository (Zenodo) with a DOI, which is a repository record. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/4 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":"The DO-KB is an integrated data system, built upon the DO’s semantic disease knowledge backbone, with resources that expose and connect the DO’s semantic knowledge with disease-related data across Open Linked Data resources.","why":"The dataset is described in running prose, not as an itemized 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":"no","current":0.0,"evidence":"Data files and code are available from the project's GitHub repository ((https://github.com/DiseaseOntology/) and from Zenodo (https://doi.org/10.5281/zenodo.10030384).","why":"The paper describes the access action (data available from GitHub and Zenodo) but does not label the access level with a standard vocabulary term. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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 genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"the DO is an OBO Foundry (http://obofoundry.org/) ontology","why":"The paper states that the DO (the data resource) is an OBO Foundry ontology, which is a community standard for ontology representation. [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_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 DO-KB Faceted Search Interface is powered by Elasticsearch (https://www.elastic.co/elasticsearch/). This back-end service was chosen to optimize processing speed and enable advanced programmatic logical queries. To format the data for Elasticsearch, a new ‘OWL Flattener’ program was developed to extract terms and their associated logical statements from the DO OWL files, to arrange the DO terms in JSON key-value lists and to organize those terms into dynamic facets using Java and the Java OWL API package.","why":"The paper names specific tools and software (Elasticsearch, OWL Flattener, Java OWL API) used to produce the data. [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_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":"No documentation object (README, codebook) is named as travelling with the data. [majority verdict 'no' (2/4 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 paper does not involve sensitive or human-subject data, so no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No statement about how long the data will persist or when it becomes available. [majority verdict 'no' (3/4 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For 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).","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","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.","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."],"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":"2026-07-20T11:18:43.091775Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}