{"doi":"10.1093/nar/gkac330","title":"The Quest for Orthologs orthology benchmark service in 2022","abstract":"The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.","journal":"Nucleic Acids Research","year":2022,"id":234434,"datarank":1.9634801686159618,"base_score":4.59511985013459,"endowment":4.59511985013459,"self_citation_contribution":0.6892679775201885,"citation_network_contribution":1.274212191095773,"self_endowment_contribution":0.6892679775201885,"citer_contribution":1.274212191095773,"corpus_percentile":89.14674711843429,"corpus_rank":1404,"citation_count":98,"citer_count":47,"citers_with_citation_signal":39,"citers_with_endowment":39,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9424,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":37.5,"fair_percentile":50.687863038826045,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":230940,"name":"Tamsin E. M. Jones","orcid":"0000-0002-0027-0858","position":1,"is_corresponding":false},{"id":103497,"name":"Dushyanth Jyothi","orcid":"0000-0002-0448-5303","position":2,"is_corresponding":false},{"id":230941,"name":"Bethan Yates","orcid":"0000-0003-1658-1762","position":3,"is_corresponding":false},{"id":850487,"name":"Meritxell Ferret","orcid":null,"position":4,"is_corresponding":false},{"id":42549,"name":"Laura Portell-Silva","orcid":null,"position":5,"is_corresponding":false},{"id":302073,"name":"Laia Codó","orcid":"0000-0002-6797-8746","position":6,"is_corresponding":false},{"id":302068,"name":"Salvatore Cosentino","orcid":"0000-0002-1066-8659","position":7,"is_corresponding":false},{"id":658728,"name":"Marina Marcet‐Houben","orcid":"0000-0003-4838-187X","position":8,"is_corresponding":false},{"id":552275,"name":"Anna Vlasova","orcid":"0000-0002-4241-2674","position":9,"is_corresponding":false},{"id":849998,"name":"Laetitia Poidevin","orcid":"0000-0002-6750-3732","position":10,"is_corresponding":false},{"id":849999,"name":"Arnaud Kress","orcid":"0000-0002-7616-8876","position":11,"is_corresponding":false},{"id":480879,"name":"Mark Hickman","orcid":"0000-0001-8183-2076","position":12,"is_corresponding":false},{"id":850000,"name":"Emma Persson","orcid":"0000-0003-0532-8251","position":13,"is_corresponding":false},{"id":850001,"name":"Ivana Piližota","orcid":"0000-0003-2365-8748","position":14,"is_corresponding":false},{"id":105338,"name":"Cristina Guijarro-Clarke","orcid":"0000-0002-1568-4797","position":15,"is_corresponding":false},{"id":302066,"name":"Adrian Altenhoff","orcid":"0000-0001-7492-1273","position":16,"is_corresponding":false},{"id":850488,"name":"Elspeth A Bruford","orcid":null,"position":17,"is_corresponding":false},{"id":3398,"name":"Christophe Dessimoz","orcid":"0000-0002-2170-853X","position":19,"is_corresponding":false},{"id":316672,"name":"Ingo Ebersberger","orcid":"0000-0001-8187-9253","position":20,"is_corresponding":false},{"id":75694,"name":"David Emms","orcid":"0000-0002-9065-8978","position":21,"is_corresponding":false},{"id":30341,"name":"Toni Gabaldón","orcid":"0000-0003-0019-1735","position":22,"is_corresponding":false},{"id":302069,"name":"Natasha Glover","orcid":"0000-0003-1811-4340","position":23,"is_corresponding":false},{"id":259031,"name":"Yanhui Hu","orcid":"0000-0003-1494-1402","position":26,"is_corresponding":false},{"id":302074,"name":"Wataru Iwasaki","orcid":"0000-0002-9169-9245","position":27,"is_corresponding":false},{"id":850489,"name":"Tamsin E M Jones","orcid":null,"position":28,"is_corresponding":false},{"id":302075,"name":"Odile Lecompte","orcid":"0000-0002-2005-460X","position":31,"is_corresponding":false},{"id":658720,"name":"Benjamin Linard","orcid":"0000-0002-5555-898X","position":32,"is_corresponding":false},{"id":57226,"name":"María Martin","orcid":"0000-0001-5454-2815","position":34,"is_corresponding":false},{"id":299002,"name":"David S. Roos","orcid":"0000-0001-6725-4089","position":39,"is_corresponding":false},{"id":850490,"name":"Erik Sonhammer","orcid":null,"position":40,"is_corresponding":false},{"id":4067,"name":"Paul D. Thomas","orcid":"0000-0002-9074-3507","position":41,"is_corresponding":false},{"id":105369,"name":"David Thybert","orcid":"0000-0001-7806-7318","position":42,"is_corresponding":false},{"id":850002,"name":"Klaas Vandepoele","orcid":"0000-0003-4790-2725","position":43,"is_corresponding":false},{"id":2485,"name":"Salvador Capella-Gutierrez","orcid":"0000-0002-0309-604X","position":46,"is_corresponding":false},{"id":850003,"name":"Asier Gonzalez‐Uriarte","orcid":"0000-0002-4159-6096","position":49,"is_corresponding":false},{"id":302067,"name":"Javier Garrayo-Ventas","orcid":"0000-0003-0015-1573","position":50,"is_corresponding":false},{"id":850004,"name":"Dmitry Repchevsky","orcid":"0000-0001-6415-0532","position":52,"is_corresponding":false},{"id":302072,"name":"Vicky Sundesha","orcid":"0000-0001-7667-6435","position":53,"is_corresponding":false},{"id":54428,"name":"Erik L. L. Sonnhammer","orcid":"0000-0002-9015-5588","position":56,"is_corresponding":false},{"id":78836,"name":"Elspeth A. Bruford","orcid":"0000-0002-8380-5247","position":63,"is_corresponding":false},{"id":302071,"name":"Yannis Nevers","orcid":"0000-0002-8604-2943","position":0,"is_corresponding":true}],"reference_count":37,"raw_metadata":null,"created_at":"2026-07-19T00:21:36.529874Z","pmid":"35552456","pmcid":"PMC9252809","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":33.3333,"fair_a":43.75,"fair_i":40.0,"fair_r":41.6667,"fair_zscore":0.1208,"fair_rationale":{"fair_score":37.5,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":33.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"Public benchmark results for the latest release are available on the orthology benchmarking service website (https://orthology.benchmarkservice.org) under the 'Public results' section, 'QfO Benchmark release 2020' subsection.","grounded":false,"rationale":"The strongest identifier given is a web URL (https://orthology.benchmarkservice.org), which is not a persistent identifier scheme (DOI, Handle, ARK, accession). 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[downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/3 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 are available for download in various formats: 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":false,"rationale":"The dataset contents are described in running prose, but there is no itemized inventory (section, table, or list) of files or variables. [downgraded to 'no' — no verifiable quote from the paper]","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":"Public benchmark results for the latest release are available on the orthology benchmarking service website (https://orthology.benchmarkservice.org) under the 'Public results' section, 'QfO Benchmark release 2020' subsection. Public orthologous pair predictions can be downloaded from the EUDAT platform through links under the 'Public projects'.","grounded":false,"rationale":"The dataset identifier (URL) appears only in the body text, not in the reference list. 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[downgraded to 'partial' — no verifiable quote from the paper]","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; no gatekeeper is named or needed.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.5,"verdict":"partial","evidence":"B2SHARE is the repository service for sharing research data of the EUDAT Data Collaborative Infrastructure (https://eudat.eu/), one of the largest e-infrastructures in Europe offering permanent storage capacity","grounded":false,"rationale":"The paper states that EUDAT B2SHARE provides permanent storage capacity, implying long-term persistence of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/3 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":40.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","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":false,"rationale":"FASTA, XML, and SeqXML are open, non-proprietary formats. [downgraded to 'partial' — no verifiable quote from the paper]","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":"community efforts will be directed into facilitating the adoption of the OrthoXML (37) format for orthogroups or gene tree inference provider as a common format to describe the nature of these relations.","grounded":false,"rationale":"OrthoXML is a community standard for orthology data, named in the paper. 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[majority verdict 'yes' (2/3 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 genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Public benchmark results for the latest release are available on the orthology benchmarking service website (https://orthology.benchmarkservice.org) under the 'Public results' section, 'QfO Benchmark release 2020' subsection.","why":"The strongest identifier given is a web URL (https://orthology.benchmarkservice.org), which is not a persistent identifier scheme (DOI, Handle, ARK, 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. 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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":"Public benchmark results for the latest release are available on the orthology benchmarking service website (https://orthology.benchmarkservice.org) under the 'Public results' section, 'QfO Benchmark release 2020' subsection. Public orthologous pair predictions can be downloaded from the EUDAT platform through links under the 'Public projects'.","why":"The data are stated to be publicly available with no precondition (no registration, embargo, or request required). [downgraded to 'partial' — no verifiable quote from the paper]","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":"Public benchmark results for the latest release are available on the orthology benchmarking service website (https://orthology.benchmarkservice.org) under the 'Public results' section, 'QfO Benchmark release 2020' subsection. 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Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"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.","why":"FASTA, XML, and SeqXML are open, non-proprietary formats. [downgraded to 'partial' — no verifiable quote from the paper]","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":"Public benchmark results for the latest release are available on the orthology benchmarking service website (https://orthology.benchmarkservice.org) under the ‘Public results’ section, ‘QfO Benchmark release 2020’ subsection. Public orthologous pair predictions can be downloaded from the EUDAT platform through links under the ‘Public projects’.","why":"The Data Availability statement points to a repository (EUDAT) and a website, which is a link to archived data in a public repository (Colavizza category 3). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/3 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 are available for download in various formats: 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.","why":"The dataset contents are described in running prose, but there is no itemized inventory (section, table, or list) of files or variables. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Public benchmark results for the latest release are available on the orthology benchmarking service website (https://orthology.benchmarkservice.org) under the 'Public results' section, 'QfO Benchmark release 2020' subsection. Public orthologous pair predictions can be downloaded from the EUDAT platform through links under the 'Public projects'.","why":"The paper labels the data as 'Public', which is a natural-language synonym for 'openly/publicly available' as per the rubric. [downgraded to 'partial' — no verifiable quote from the paper]","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":"community efforts will be directed into facilitating the adoption of the OrthoXML (37) format for orthogroups or gene tree inference provider as a common format to describe the nature of these relations.","why":"OrthoXML is a community standard for orthology data, named in the paper. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/3 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":"BBH (13) and RSD (14), two naive methods for inferring one-to-one orthologs, were generally outperformed by the publicly available orthology inference algorithms","why":"The paper names specific methods and tools (BBH, RSD, OMA Groups, etc.) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/3 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. For sensitive/human genomics / sequencing data, use a controlled-access repository such as dbGaP or EGA.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive or human-subject; no gatekeeper is named or needed.","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":"based on the UniProtKB 2020_04 release","why":"The paper gives a specific database release identifier (UniProtKB 2020_04) for a resource not produced by this study. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"B2SHARE is the repository service for sharing research data of the EUDAT Data Collaborative Infrastructure (https://eudat.eu/), one of the largest e-infrastructures in Europe offering permanent storage capacity","why":"The paper states that EUDAT B2SHARE provides permanent storage capacity, implying long-term persistence of the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/3 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).","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.","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.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"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":"2026-07-20T11:06:13.280932Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}