{"doi":"10.1093/nargab/lqae167","title":"New developments for the Quest for Orthologs benchmark service","abstract":"The Quest for Orthologs (QfO) orthology benchmark service (https://orthology.benchmarkservice.org) hosts a wide range of standardized benchmarks for orthology inference evaluation. It is supported and maintained by the QfO consortium, and is used to gather ortholog predictions and to examine strengths and weaknesses of newly developed and existing orthology inference methods. The web server allows different inference methods to be compared in a standardized way using the same proteome data. The benchmark results are useful for developing new methods and can help researchers to guide their choice of orthology method for applications in comparative genomics and phylogenetic analysis. We here present a new release of the Orthology Benchmark Service with a new benchmark based on feature architecture similarity as well as updated reference proteomes. We further provide a meta-analysis of the public predictions from 18 different orthology assignment methods to reveal how they relate in terms of ortholog predictions and benchmark performance. These results can guide users of orthologs to the best suited method for their purpose.","journal":"NAR Genomics and Bioinformatics","year":2024,"id":437521,"datarank":0.43301730259472704,"base_score":2.4849066497880004,"endowment":2.4849066497880004,"self_citation_contribution":0.37273599746820013,"citation_network_contribution":0.06028130512652691,"self_endowment_contribution":0.37273599746820013,"citer_contribution":0.06028130512652691,"corpus_percentile":56.9196255898507,"corpus_rank":5570,"citation_count":11,"citer_count":5,"citers_with_citation_signal":3,"citers_with_endowment":3,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9057,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":33.3333,"fair_percentile":47.93641088352186,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":302071,"name":"Yannis Nevers","orcid":"0000-0002-8604-2943","position":1,"is_corresponding":false},{"id":1247018,"name":"Vinh Tran","orcid":"0000-0001-6772-7595","position":2,"is_corresponding":false},{"id":103497,"name":"Dushyanth Jyothi","orcid":"0000-0002-0448-5303","position":3,"is_corresponding":false},{"id":57226,"name":"María Martin","orcid":"0000-0001-5454-2815","position":4,"is_corresponding":false},{"id":302068,"name":"Salvatore Cosentino","orcid":"0000-0002-1066-8659","position":5,"is_corresponding":false},{"id":376052,"name":"Sina Majidian","orcid":"0000-0001-5345-6982","position":6,"is_corresponding":false},{"id":658728,"name":"Marina Marcet‐Houben","orcid":"0000-0003-4838-187X","position":7,"is_corresponding":false},{"id":884924,"name":"Diego Fuentes","orcid":"0000-0002-9977-6786","position":8,"is_corresponding":false},{"id":850000,"name":"Emma Persson","orcid":"0000-0003-0532-8251","position":9,"is_corresponding":false},{"id":665842,"name":"Thomas Walsh","orcid":"0000-0002-9328-6671","position":10,"is_corresponding":false},{"id":302075,"name":"Odile Lecompte","orcid":"0000-0002-2005-460X","position":11,"is_corresponding":false},{"id":30341,"name":"Toni Gabaldón","orcid":"0000-0003-0019-1735","position":12,"is_corresponding":false},{"id":75693,"name":"Steven Kelly","orcid":"0000-0001-8583-5362","position":13,"is_corresponding":false},{"id":259031,"name":"Yanhui Hu","orcid":"0000-0003-1494-1402","position":14,"is_corresponding":false},{"id":302074,"name":"Wataru Iwasaki","orcid":"0000-0002-9169-9245","position":15,"is_corresponding":false},{"id":2485,"name":"Salvador Capella-Gutierrez","orcid":"0000-0002-0309-604X","position":16,"is_corresponding":false},{"id":3398,"name":"Christophe Dessimoz","orcid":"0000-0002-2170-853X","position":17,"is_corresponding":false},{"id":4067,"name":"Paul D. Thomas","orcid":"0000-0002-9074-3507","position":18,"is_corresponding":false},{"id":316672,"name":"Ingo Ebersberger","orcid":"0000-0001-8187-9253","position":19,"is_corresponding":false},{"id":54428,"name":"Erik L. L. Sonnhammer","orcid":"0000-0002-9015-5588","position":20,"is_corresponding":false},{"id":302066,"name":"Adrian Altenhoff","orcid":"0000-0001-7492-1273","position":0,"is_corresponding":true}],"reference_count":35,"raw_metadata":null,"created_at":"2026-07-19T02:00:34.490087Z","pmid":"39664814","pmcid":"PMC11632614","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":22.2222,"fair_a":50.0,"fair_i":40.0,"fair_r":33.3333,"fair_zscore":-0.0442,"fair_rationale":{"fair_score":33.33,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":22.22,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz . The predicted ortholog data are available at https://orthology. benchmarkservice.org/ proxy/ projects/ 2022/ .","grounded":false,"rationale":"The data are identified by web URLs, not by a persistent identifier scheme (DOI, Handle, ARK, or repository accession). [downgraded to 'no' — no verifiable quote from the paper]","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":"The QfO Reference Proteomes (https://www.ebi.ac.uk/ reference _ proteomes/) have been jointly designed for this task by the QfO consortium and UniProtKB","grounded":false,"rationale":"The named holder is the EBI reference proteomes resource, a curated repository registered in re3data/FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper]","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 The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz . The predicted ortholog data are available at https://orthology. benchmarkservice.org/ proxy/ projects/ 2022/ . These links are also found at https:// orthology.benchmarkservice.org/ .","grounded":false,"rationale":"The data-availability statement provides links to archived data in public repositories, corresponding to Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [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":0.0,"verdict":"no","evidence":"The QfO Reference Proteomes 2022 dataset comprises 78 species (48 Eukaryotes, 23 Bacteria and 7 Archaea) based on the UniProtKB 2022_02 release... In aggregate, this represents 1 383 730 protein sequences (988 778 canonical protein sequences and 394 952 isoforms).","grounded":false,"rationale":"The dataset content is described in running prose, not in an itemised inventory like a table or list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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":0.0,"verdict":"no","evidence":"The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz .","grounded":false,"rationale":"The dataset identifier (URL) appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","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":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz .","grounded":false,"rationale":"The data are stated to be available at a public FTP link with no precondition, embargo, or registration. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-A1.1-01D — 'Data is accessible through a free access protocol'","FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"These pairs are made freely available under the FAIR principle through the OpenEBench platform.","grounded":true,"rationale":"The paper states the data are 'freely available', which is a natural-language access-level label equivalent to 'open access'. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":"These pairs are made freely available under the FAIR principle through the OpenEBench platform.","grounded":true,"rationale":"Data are not sensitive or human-subject; no gatekeeper is mentioned, so the default is no gatekeeper.","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 used proteome data are available at https://ftp.ebi.ac.uk/pub/databases/reference_proteomes/previous_releases/qfo_release-2022_02_with_updated_UP000000437/QfO_release_2022_02_with_updated_UP000000437.tar.gz . The predicted ortholog data are available at https://orthology.benchmarkservice.org/proxy/projects/2022/ .","grounded":false,"rationale":"The paper states that the data are available now but makes no commitment to how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [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":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"the protein sequences as FASTA and SeqXML files, CDS sequences for most proteins as FASTA files, and, for an increasing number of species, genomic locus coordinates are available in the XML format.","grounded":true,"rationale":"FASTA, SeqXML, and XML are open, non-proprietary community-standard formats.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No data or metadata community standard (e.g., MIAME, MIxS, an ontology) is named for the data; only format names and database names appear. [majority verdict 'no' (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 identifier for an external resource (e.g., another dataset, reference genome build) is given in the text. [majority verdict 'no' (3/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":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 reuse license is named for the data; the CC BY 4.0 license applies to the article only, not to the data.","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":"based on the UniProtKB 2022_02 release","grounded":true,"rationale":"The paper names the specific database release (UniProtKB 2022_02) used to produce the reference proteomes, providing a versioned provenance. [majority verdict 'yes' (3/5 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object (README, data dictionary, codebook) is named as accompanying the data; variable definitions are not provided in the article. [majority verdict 'no' (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 version used in the present QfO benchmark (QfO Reference Proteomes 2022) comprises 78 species","grounded":true,"rationale":"The paper provides a version token ('QfO Reference Proteomes 2022') for the dataset.","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":"No locator for the study's own code is given; the paper describes a service but does not provide a code repository or DOI.","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":"European Union [ERC-2016-724173]","grounded":true,"rationale":"Specific award numbers (e.g., ERC-2016-724173) are provided for funders.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz . The predicted ortholog data are available at https://orthology. benchmarkservice.org/ proxy/ projects/ 2022/ .","why":"The data are identified by web URLs, not by a persistent identifier scheme (DOI, Handle, ARK, or repository accession). [downgraded to 'no' — no verifiable quote from the paper]","gain":16.67,"priority":"essential","scored":true},{"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 reuse license is named for the data; the CC BY 4.0 license applies to the article only, not to the data.","gain":16.67,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The QfO Reference Proteomes (https://www.ebi.ac.uk/ reference _ proteomes/) have been jointly designed for this task by the QfO consortium and UniProtKB","why":"The named holder is the EBI reference proteomes resource, a curated repository registered in re3data/FAIRsharing. [downgraded to 'partial' — no verifiable quote from the paper]","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz .","why":"The data are stated to be available at a public FTP link with no precondition, embargo, or registration. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz .","why":"The dataset identifier (URL) appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","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":"No locator for the study's own code is given; the paper describes a service but does not provide a code repository or DOI.","gain":8.33,"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 The used proteome data are available at https://ftp.ebi.ac.uk/ pub/ databases/ reference _ proteomes/ previous _ releases/ qfo _ release-2022 _ 02 _ with _ updated _ UP000000437/ QfO _ release _ 2022 _ 02 _ with _ updated _ UP000000437.tar.gz . The predicted ortholog data are available at https://orthology. benchmarkservice.org/ proxy/ projects/ 2022/ . These links are also found at https:// orthology.benchmarkservice.org/ .","why":"The data-availability statement provides links to archived data in public repositories, corresponding to Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [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":"no","current":0.0,"evidence":"The QfO Reference Proteomes 2022 dataset comprises 78 species (48 Eukaryotes, 23 Bacteria and 7 Archaea) based on the UniProtKB 2022_02 release... In aggregate, this represents 1 383 730 protein sequences (988 778 canonical protein sequences and 394 952 isoforms).","why":"The dataset content is described in running prose, not in an itemised inventory like a table or list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In proteomics, describe the data with mzML or MIAPE.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No data or metadata community standard (e.g., MIAME, MIxS, an ontology) is named for the data; only format names and database names appear. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No documentation object (README, data dictionary, codebook) is named as accompanying the data; variable definitions are not provided in the article. [majority verdict 'no' (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":"These pairs are made freely available under the FAIR principle through the OpenEBench platform.","why":"Data are not sensitive or human-subject; no gatekeeper is mentioned, so the default is no gatekeeper.","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., another dataset, reference genome build) is given in the text. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"The used proteome data are available at https://ftp.ebi.ac.uk/pub/databases/reference_proteomes/previous_releases/qfo_release-2022_02_with_updated_UP000000437/QfO_release_2022_02_with_updated_UP000000437.tar.gz . The predicted ortholog data are available at https://orthology.benchmarkservice.org/proxy/projects/2022/ .","why":"The paper states that the data are available now but makes no commitment to how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","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 proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the proteomics repository accession (e.g. from PRIDE (PXD accession) or ProteomeXchange) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T12:20:25.612451Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}