{"doi":"10.1371/journal.pone.0154556","title":"The Ontology for Biomedical Investigations","abstract":"The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.","journal":"PLOS ONE","year":2016,"id":11260,"datarank":6.7526523948024995,"base_score":5.968707559985366,"endowment":5.968707559985366,"self_citation_contribution":0.895306133997805,"citation_network_contribution":5.857346260804695,"self_endowment_contribution":0.895306133997805,"citer_contribution":5.857346260804695,"corpus_percentile":97.22286686779609,"corpus_rank":360,"citation_count":390,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.5145,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2016-04-29","fair_score":75.0,"fair_percentile":95.6282482421278,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":72912,"name":"Mathias Brochhausen","orcid":"0000-0003-1834-3856","position":2,"is_corresponding":false},{"id":90647,"name":"Bill Bug","orcid":null,"position":4,"is_corresponding":false},{"id":90648,"name":"Marcus C. Chibucos","orcid":"0000-0001-9586-0780","position":5,"is_corresponding":false},{"id":90649,"name":"Kevin Clancy","orcid":null,"position":6,"is_corresponding":false},{"id":2538,"name":"Mélanie Courtot","orcid":"0000-0002-9551-6370","position":7,"is_corresponding":false},{"id":90650,"name":"Dirk Derom","orcid":"0000-0001-7102-5932","position":8,"is_corresponding":false},{"id":74,"name":"Michel J. Dumontier","orcid":"0000-0003-4727-9435","position":9,"is_corresponding":false},{"id":90651,"name":"Liju Fan","orcid":null,"position":10,"is_corresponding":false},{"id":5918,"name":"Jennifer Fostel","orcid":"0000-0001-5858-4393","position":11,"is_corresponding":false},{"id":37090,"name":"Gilberto Fragoso","orcid":null,"position":12,"is_corresponding":false},{"id":6365,"name":"Frank Gibson","orcid":null,"position":13,"is_corresponding":false},{"id":90652,"name":"Yongqun He","orcid":"0000-0001-9189-9661","position":16,"is_corresponding":false},{"id":20918,"name":"Mervi Heiskanen","orcid":null,"position":17,"is_corresponding":false},{"id":90653,"name":"Mark Jensen","orcid":"0000-0001-9228-8838","position":19,"is_corresponding":false},{"id":52518,"name":"Yu Lin","orcid":"0000-0003-2620-0345","position":20,"is_corresponding":false},{"id":288,"name":"Allyson L. Lister","orcid":"0000-0002-7702-4495","position":21,"is_corresponding":false},{"id":6377,"name":"Phillip Lord","orcid":"0000-0002-4699-6769","position":22,"is_corresponding":false},{"id":19113,"name":"James Malone","orcid":"0000-0002-1615-2899","position":23,"is_corresponding":false},{"id":14811,"name":"Elisabetta Manduchi","orcid":"0000-0002-4110-3714","position":24,"is_corresponding":false},{"id":90654,"name":"Monnie McGee","orcid":"0000-0001-9150-7832","position":25,"is_corresponding":false},{"id":6383,"name":"Norman Morrison","orcid":"0000-0003-1604-1512","position":26,"is_corresponding":false},{"id":72076,"name":"James A. Overton","orcid":"0000-0001-5139-5557","position":27,"is_corresponding":false},{"id":2833,"name":"Helen Parkinson","orcid":"0000-0003-3035-4195","position":28,"is_corresponding":false},{"id":34766,"name":"Bjoern Peters","orcid":"0000-0002-8457-6693","position":29,"is_corresponding":false},{"id":5765,"name":"Philippe Rocca-Serra","orcid":null,"position":30,"is_corresponding":false},{"id":6389,"name":"Richard H. Scheuermann","orcid":"0000-0003-1355-892X","position":33,"is_corresponding":false},{"id":6390,"name":"Daniel Schober","orcid":"0000-0001-8014-6648","position":34,"is_corresponding":false},{"id":6391,"name":"Barry Smith","orcid":"0000-0003-1384-116X","position":35,"is_corresponding":false},{"id":6393,"name":"Christian J. Stoeckert","orcid":"0000-0002-5714-991X","position":37,"is_corresponding":false},{"id":90655,"name":"Carlo Torniai","orcid":null,"position":39,"is_corresponding":false},{"id":90656,"name":"Jessica A. Turner","orcid":"0000-0003-0076-8434","position":40,"is_corresponding":false},{"id":55655,"name":"Randi Vita","orcid":"0000-0001-8957-7612","position":41,"is_corresponding":false},{"id":5932,"name":"Patricia L. Whetzel","orcid":"0000-0002-3458-4839","position":42,"is_corresponding":false},{"id":78817,"name":"Jie Zheng","orcid":"0000-0002-6623-6839","position":43,"is_corresponding":false},{"id":6360,"name":"Ryan R. Brinkman","orcid":"0000-0002-9765-2990","position":44,"is_corresponding":false},{"id":6458,"name":"Matthew Brush","orcid":"0000-0002-1048-5019","position":45,"is_corresponding":false},{"id":6400,"name":"F. Gibson","orcid":"0000-0003-3382-1748","position":46,"is_corresponding":false},{"id":286,"name":"Alejandra Noemí González Beltrán","orcid":"0000-0003-3499-8262","position":47,"is_corresponding":false},{"id":4026,"name":"Melissa A Haendel","orcid":"0000-0001-9114-8737","position":48,"is_corresponding":false},{"id":35255,"name":"Tina Hernandez‐Boussard","orcid":"0000-0001-6553-3455","position":49,"is_corresponding":false},{"id":289,"name":"Rocca-Serra, Philippe","orcid":"0000-0001-9853-5668","position":51,"is_corresponding":false},{"id":290,"name":"Susanna‐Assunta Sansone","orcid":"0000-0001-5306-5690","position":52,"is_corresponding":false},{"id":14525,"name":"Larisa Soldatova","orcid":"0000-0001-6489-3029","position":53,"is_corresponding":false},{"id":5912,"name":"Chris Taylor","orcid":"0000-0002-9666-798X","position":54,"is_corresponding":false},{"id":59084,"name":"Anita Bandrowski","orcid":"0000-0002-5497-0243","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"27128319","pmcid":"PMC4851331","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":50.0,"fair_a":75.0,"fair_i":60.0,"fair_r":83.3333,"fair_zscore":1.6051,"fair_rationale":{"fair_score":75.0,"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":"The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl","grounded":true,"rationale":"The identifier is a PURL (web address) not a DOI, Handle, or other persistent identifier scheme. [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":"Releases of OBI are also uploaded to the National Center for Biomedical Ontology (NCBO) BioPortal and the Ontobee repository at http://www.ontobee.org/","grounded":false,"rationale":"The paper names NCBO BioPortal, a curated repository, as a holder of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"All relevant data are within the paper and its Supporting Information files.","grounded":true,"rationale":"The data availability statement points to the article itself, not a repository record (Colavizza category 2). [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":"The OBI 2015-10-20 release includes 2366 classes, 84 individuals, and 40 relations (owl:objectProperties) native to OBI plus 556 classes, 94 individuals, and 59 relations imported from 20 ontologies and the Relations Ontology (RO).","grounded":true,"rationale":"The dataset content is described in running prose, not as an itemised inventory or section. [majority verdict 'partial' (4/5 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 current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl","grounded":true,"rationale":"The dataset identifier appears only in 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":75.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"OBI is publicly and freely available under the Creative Commons Attribution (CC-by) 3.0 license.","grounded":true,"rationale":"The text states the data are publicly and freely 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":"OBI is publicly and freely available under the Creative Commons Attribution (CC-by) 3.0 license.","grounded":true,"rationale":"The paper explicitly labels the data as 'publicly and freely available' and states the license, which is an access-level label.","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 or human-subject, 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":0.0,"verdict":"no","evidence":"The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl","grounded":true,"rationale":"The paper states availability but does not commit to a retention period or permanent archival. [majority verdict 'no' (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":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"OBI is expressed in the OWL 2 Web Ontology Language (http://www.w3.org/TR/owl2-overview/), which is a World Wide Web Consortium (W3C; http://www.w3.org) ontology language developed for the semantic web.","grounded":false,"rationale":"The data format is OWL, an open W3C standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":1.0,"verdict":"yes","evidence":"OBI addresses the requirement for a cross-disciplinary standard for representing biomedical investigations.","grounded":true,"rationale":"OBI itself is a community standard ontology, and the paper explicitly states it as a standard. [majority verdict 'yes' (3/5 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":"No explicit identifier (DOI, accession, RRID) for an external resource is provided; only names and bibliographic references are given. [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":83.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"OBI is publicly and freely available under the Creative Commons Attribution (CC-by) 3.0 license.","grounded":true,"rationale":"The license is an open standard licence (CC BY 3.0).","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":"These include the comprehensive OWL Application Program Interface (API) Java library and the Protégé-OWL (http://protege.stanford.edu/overview/protege-owl.html) graphical editor that builds upon it.","grounded":false,"rationale":"The paper names specific tools (Protégé-OWL) used to produce the ontology. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Table 1 Example metadata for class OBI_0000795.","grounded":true,"rationale":"Variable definitions are provided inside the article (Table 1), not as a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 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":1.0,"verdict":"yes","evidence":"The OBI 2015-10-20 release includes 2366 classes","grounded":true,"rationale":"The paper provides a release date (2015-10-20) and a version number (1.0). [majority verdict 'yes' (3/5 passes agreed)]","anchors":["DataCite Metadata Schema 4.6 — the 'Version' property","RDA-R1.2-01M — provenance information (which version was used is provenance)","NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The current development version of OBI is available at http://purl.obolibrary.org/obo/obi/repository","grounded":true,"rationale":"A machine-resolvable URL for the code repository is given. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code'","FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear","FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"R01AI081062 to YH","grounded":true,"rationale":"Award numbers are provided for the funding. [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":"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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl","why":"The identifier is a PURL (web address) not a DOI, Handle, or other persistent identifier scheme. [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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Releases of OBI are also uploaded to the National Center for Biomedical Ontology (NCBO) BioPortal and the Ontobee repository at http://www.ontobee.org/","why":"The paper names NCBO BioPortal, a curated repository, as a holder of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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 chemistry / materials repository accession (e.g. from Zenodo, PubChem or the Cambridge Structural Database (CSD)) in the reference list.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl","why":"The dataset identifier appears only in body text, not as a reference-list entry. [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open chemistry / materials formats such as CIF or MOL.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"OBI is expressed in the OWL 2 Web Ontology Language (http://www.w3.org/TR/owl2-overview/), which is a World Wide Web Consortium (W3C; http://www.w3.org) ontology language developed for the semantic web.","why":"The data format is OWL, an open W3C standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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":"All relevant data are within the paper and its Supporting Information files.","why":"The data availability statement points to the article itself, not a repository record (Colavizza category 2). [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":"The OBI 2015-10-20 release includes 2366 classes, 84 individuals, and 40 relations (owl:objectProperties) native to OBI plus 556 classes, 94 individuals, and 59 relations imported from 20 ontologies and the Relations Ontology (RO).","why":"The dataset content is described in running prose, not as an itemised inventory or section. [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"essential","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":"These include the comprehensive OWL Application Program Interface (API) Java library and the Protégé-OWL (http://protege.stanford.edu/overview/protege-owl.html) graphical editor that builds upon it.","why":"The paper names specific tools (Protégé-OWL) used to produce the ontology. [downgraded to 'partial' — no verifiable quote from the paper] [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":"partial","current":0.5,"evidence":"Table 1 Example metadata for class OBI_0000795.","why":"Variable definitions are provided inside the article (Table 1), not as a separate documentation object shipped with the data. [majority verdict 'partial' (3/5 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 data are not sensitive or human-subject, 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 explicit identifier (DOI, accession, RRID) for an external resource is provided; only names and bibliographic references are given. [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":"no","current":0.0,"evidence":"The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl","why":"The paper states availability but does not commit to a retention period or permanent archival. [majority verdict 'no' (4/5 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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","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 chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","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 chemistry / materials repository accession (e.g. from Zenodo, PubChem or the Cambridge Structural Database (CSD)) 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 chemistry / materials formats such as CIF or MOL.","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."],"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":"2026-07-20T10:49:49.158289Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}