{"doi":"10.1093/nar/gkad1025","title":"The Reactome Pathway Knowledgebase 2024","abstract":"The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Here we review progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways. Finally, we briefly discuss issues involved in making Reactome more fully interoperable with other related resources such as the Gene Ontology and maintaining the resulting community resource network.","journal":"Nucleic Acids Research","year":2023,"id":314637,"datarank":4.503670328176398,"base_score":7.232733136177615,"endowment":7.232733136177615,"self_citation_contribution":1.0849099704266423,"citation_network_contribution":3.418760357749756,"self_endowment_contribution":1.0849099704266423,"citer_contribution":3.418760357749756,"corpus_percentile":95.12647946159201,"corpus_rank":631,"citation_count":1383,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9504,"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":75.0,"fair_percentile":95.6282482421278,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":993607,"name":"Deidre Beavers","orcid":"0000-0002-4259-7453","position":1,"is_corresponding":false},{"id":1015124,"name":"Patrick Conley","orcid":null,"position":2,"is_corresponding":false},{"id":614234,"name":"Chuqiao Gong","orcid":"0000-0001-8674-1739","position":3,"is_corresponding":false},{"id":531513,"name":"Marc Gillespie","orcid":"0000-0002-5766-1702","position":4,"is_corresponding":false},{"id":79929,"name":"Johannes Griss","orcid":"0000-0003-2206-9511","position":5,"is_corresponding":false},{"id":614242,"name":"Robin Haw","orcid":"0000-0002-2013-7835","position":6,"is_corresponding":false},{"id":614229,"name":"Bijay Jassal","orcid":"0000-0002-5039-5405","position":7,"is_corresponding":false},{"id":103863,"name":"Lisa Matthews","orcid":"0000-0001-5707-3065","position":8,"is_corresponding":false},{"id":614237,"name":"Bruce May","orcid":"0000-0001-5193-0855","position":9,"is_corresponding":false},{"id":13919,"name":"Robert Petryszak","orcid":"0000-0001-6333-2182","position":10,"is_corresponding":false},{"id":614236,"name":"Eliot Ragueneau","orcid":"0000-0002-7876-6503","position":11,"is_corresponding":false},{"id":614231,"name":"Karen Rothfels","orcid":"0000-0002-0705-7048","position":12,"is_corresponding":false},{"id":614233,"name":"Cristoffer Sevilla","orcid":"0000-0002-8570-4650","position":13,"is_corresponding":false},{"id":614238,"name":"Veronica Shamovsky","orcid":"0000-0002-2187-2241","position":14,"is_corresponding":false},{"id":95758,"name":"Ralf Stephan","orcid":"0000-0002-4650-631X","position":15,"is_corresponding":false},{"id":1013597,"name":"Krishna Kumar Tiwari","orcid":"0000-0002-3699-0937","position":16,"is_corresponding":false},{"id":614235,"name":"Thawfeek Varusai","orcid":"0000-0002-7864-5971","position":17,"is_corresponding":false},{"id":616425,"name":"Joel Weiser","orcid":null,"position":18,"is_corresponding":false},{"id":14465,"name":"A. Jordan Wright","orcid":"0000-0002-8317-6727","position":19,"is_corresponding":false},{"id":614243,"name":"Guanming Wu","orcid":"0000-0001-8196-1177","position":20,"is_corresponding":false},{"id":14310,"name":"Lincoln Stein","orcid":"0000-0002-1983-4588","position":21,"is_corresponding":false},{"id":5922,"name":"Henning Hermjakob","orcid":"0000-0001-8479-0262","position":22,"is_corresponding":false},{"id":57223,"name":"Peter D’Eustachio","orcid":"0000-0002-5494-626X","position":23,"is_corresponding":false},{"id":614230,"name":"M Orlic-Milacic","orcid":"0000-0002-3218-5631","position":0,"is_corresponding":true}],"reference_count":28,"raw_metadata":null,"created_at":"2026-07-19T01:06:02.898877Z","pmid":"37941124","pmcid":"PMC10767911","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":83.3333,"fair_a":81.25,"fair_i":80.0,"fair_r":41.6667,"fair_zscore":1.6051,"fair_rationale":{"fair_score":75.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":83.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)","grounded":true,"rationale":"The paper provides a DOI for its own dataset (Zenodo), which is a persistent identifier scheme. [majority verdict 'yes' (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":1.0,"verdict":"yes","evidence":"We have created Zenodo packages for the versions of our software and data discussed in the article","grounded":true,"rationale":"Zenodo is a named data repository, and the data are deposited there. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"We have created Zenodo packages for the versions of our software and data discussed in the article: … Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)","grounded":false,"rationale":"The statement points to a repository record with a persistent identifier (Zenodo DOI). [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":1.0,"verdict":"yes","evidence":"Table 1. Reactome content, version 78 (9/2021) versus 86 (9/2023)","grounded":true,"rationale":"The paper includes an itemised inventory (Table 1) listing the dataset's content types and counts.","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":"Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)","grounded":true,"rationale":"The dataset identifier appears only in the body text (Data availability section), not as a reference-list entry.","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":81.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"All Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ).","grounded":true,"rationale":"The text gives a direct download route with no stated precondition. [majority verdict 'yes' (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":"Reactome is open-source and open-access.","grounded":true,"rationale":"The paper explicitly labels the data as open-access in the Data availability section.","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 human-subject data; no gatekeeper is mentioned.","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":"All Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ).","grounded":true,"rationale":"Only availability timing (now) is stated; no persistence commitment is given. [majority verdict 'partial' (3/5 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":80.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Data dump of version 86, both Neo4j and MySQL database","grounded":true,"rationale":"The paper names Neo4j and MySQL database formats for the data dump, which are not in the open/community-standard list (CSV, JSON, etc.). [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":"Processes are systematically described in molecular detail to generate an ordered network of molecular transformations, resulting in an extended version of a classic metabolic map ( 4 ) generally compliant with the SBGN process description standard ( 5 ).","grounded":true,"rationale":"The paper names multiple community standards (SBGN, Gene Ontology, ChEBI, RHEA, etc.) applied to the data.","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":"The 11148 protein gene products now annotated in Reactome are 56.2% of the 19 831 protein-coding genes predicted in the current (GRCh38.p14) human genome assembly","grounded":true,"rationale":"The paper gives the assembly identifier GRCh38.p14 for an external resource (the human genome assembly). [majority verdict 'yes' (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":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No specific license is named for the data; the CC-BY license applies to the article, not the dataset.","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":0.0,"verdict":"no","evidence":"The Reactome Knowledgebase, … provides manually curated molecular details of a broad range of normal and disease-related biological processes.","grounded":false,"rationale":"The production method is described generically (manual curation) without naming specific instruments or software versions. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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. Reactome content, version 78 (9/2021) versus 86 (9/2023)","grounded":true,"rationale":"The paper includes a table inside the article that defines the dataset's content, but no separate documentation object is named to accompany 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":"Reactome (version 86—September 2023)","grounded":true,"rationale":"The paper gives a version token (version 86) for the data.","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":"All software is available from our GitHub repositories ( https://github.com/reactome and https://github.com/reactome-pwp ), under terms that allow for free reuse and redistribution.","grounded":true,"rationale":"The paper gives a machine-resolvable locator (GitHub URLs) for the study's own code. [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":"The development of Reactome is supported by grants from the National Institutes of Health [U41HG003751, U24HG012198, U24HG011851, U54GM114833, U01CA239069]","grounded":true,"rationale":"The paper provides specific grant numbers (award identifiers) for the funding.","anchors":["DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award","Crossref Funder Registry — canonical funder identifiers for funding metadata","RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco"],"scored":true,"signal":null}]}},"actions":[{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No specific license is named for the data; the CC-BY license applies to the article, not the dataset.","gain":16.67,"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":"partial","current":0.5,"evidence":"Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)","why":"The dataset identifier appears only in the body text (Data availability section), not as a reference-list entry.","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 genomics / sequencing formats such as FASTQ, BAM or VCF.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data dump of version 86, both Neo4j and MySQL database","why":"The paper names Neo4j and MySQL database formats for the data dump, which are not in the open/community-standard list (CSV, JSON, etc.). [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":"We have created Zenodo packages for the versions of our software and data discussed in the article: … Reactome Data 86: 10.5281/zenodo.10018440 (Data dump of version 86, both Neo4j and MySQL database)","why":"The statement points to a repository record with a persistent identifier (Zenodo DOI). [downgraded to 'partial' — no verifiable quote from the paper] [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":"no","current":0.0,"evidence":"The Reactome Knowledgebase, … provides manually curated molecular details of a broad range of normal and disease-related biological processes.","why":"The production method is described generically (manual curation) without naming specific instruments or software versions. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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. Reactome content, version 78 (9/2021) versus 86 (9/2023)","why":"The paper includes a table inside the article that defines the dataset's content, but no separate documentation object is named to accompany 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. 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 human-subject data; no gatekeeper is mentioned.","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":"All Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ).","why":"Only availability timing (now) is stated; no persistence commitment is given. [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","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.","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.","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."],"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":"2026-07-20T10:46:23.093503Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}