{"doi":"10.1093/nar/gkaf1223","title":"The Reactome Knowledgebase 2026","abstract":"The Reactome Knowledgebase (https://reactome.org) is a freely accessible, expert-curated, open-source, and open-data resource that describes human biology in molecular detail. It spans normal physiology as well as disease mechanisms, including the impact of genetic variation and drug action. Reactome content is continuously expanded and revised, with automated workflows now monitoring retracted publications to maintain data integrity. To meet the needs of a growing user base, Reactome has launched a redesigned Angular-based interface with enhanced accessibility, modular architecture, and a hierarchy of visualization tools: ReacFoam for global pathway overviews, enhanced high-level diagrams for intuitive navigation, and redesigned entity level views (ELVs) enriched with chemical structures, animated protein models, and a new \"compare mode\" to contrast normal and disease states. New analysis tools support multi-omics integration and customizable visualizations. Recent innovations include the React-to-me chatbot for natural language interaction, community-driven tutorials, and an open Figma icon library. Reactome's sustainability and compliance with FAIR data principles were recently recognized with CoreTrustSeal certification and its designation as a Global Core Biodata and ELIXIR resource, reinforcing its role as a trusted global knowledgebase.","journal":"Nucleic Acids Research","year":2025,"id":509521,"datarank":0.5902251044632622,"base_score":3.4965075614664802,"endowment":3.4965075614664802,"self_citation_contribution":0.5244761342199721,"citation_network_contribution":0.06574897024329007,"self_endowment_contribution":0.5244761342199721,"citer_contribution":0.06574897024329007,"corpus_percentile":66.65119517289395,"corpus_rank":4312,"citation_count":32,"citer_count":29,"citers_with_citation_signal":4,"citers_with_endowment":4,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9516,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":41.6667,"fair_percentile":54.173035768878016,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":614234,"name":"Chuqiao Gong","orcid":"0000-0001-8674-1739","position":1,"is_corresponding":false},{"id":1364415,"name":"Pierre Sinquin","orcid":null,"position":2,"is_corresponding":false},{"id":614233,"name":"Cristoffer Sevilla","orcid":"0000-0002-8570-4650","position":3,"is_corresponding":false},{"id":993607,"name":"Deidre Beavers","orcid":"0000-0002-4259-7453","position":4,"is_corresponding":false},{"id":1225367,"name":"Alexander Grentner","orcid":"0009-0006-2960-7107","position":5,"is_corresponding":false},{"id":79929,"name":"Johannes Griss","orcid":"0000-0003-2206-9511","position":6,"is_corresponding":false},{"id":687265,"name":"Gregory Hogue","orcid":null,"position":7,"is_corresponding":false},{"id":1161509,"name":"Nancy T. Li","orcid":"0000-0002-2663-5245","position":8,"is_corresponding":false},{"id":103863,"name":"Lisa Matthews","orcid":"0000-0001-5707-3065","position":9,"is_corresponding":false},{"id":614237,"name":"Bruce May","orcid":"0000-0001-5193-0855","position":10,"is_corresponding":false},{"id":614230,"name":"M Orlic-Milacic","orcid":"0000-0002-3218-5631","position":11,"is_corresponding":false},{"id":1363649,"name":"Helia Mohammadi","orcid":"0009-0001-9112-5559","position":12,"is_corresponding":false},{"id":13919,"name":"Robert Petryszak","orcid":"0000-0001-6333-2182","position":13,"is_corresponding":false},{"id":614231,"name":"Karen Rothfels","orcid":"0000-0002-0705-7048","position":14,"is_corresponding":false},{"id":614238,"name":"Veronica Shamovsky","orcid":"0000-0002-2187-2241","position":15,"is_corresponding":false},{"id":95758,"name":"Ralf Stephan","orcid":"0000-0002-4650-631X","position":16,"is_corresponding":false},{"id":1013597,"name":"Krishna Kumar Tiwari","orcid":"0000-0002-3699-0937","position":17,"is_corresponding":false},{"id":616425,"name":"Joel Weiser","orcid":null,"position":18,"is_corresponding":false},{"id":49664,"name":"Adam Wright","orcid":"0000-0002-5719-4024","position":19,"is_corresponding":false},{"id":531513,"name":"Marc Gillespie","orcid":"0000-0002-5766-1702","position":20,"is_corresponding":false},{"id":614243,"name":"Guanming Wu","orcid":"0000-0001-8196-1177","position":21,"is_corresponding":false},{"id":14310,"name":"Lincoln Stein","orcid":"0000-0002-1983-4588","position":22,"is_corresponding":false},{"id":5922,"name":"Henning Hermjakob","orcid":"0000-0001-8479-0262","position":23,"is_corresponding":false},{"id":57223,"name":"Peter D’Eustachio","orcid":"0000-0002-5494-626X","position":24,"is_corresponding":false},{"id":614236,"name":"Eliot Ragueneau","orcid":"0000-0002-7876-6503","position":0,"is_corresponding":true}],"reference_count":20,"raw_metadata":null,"created_at":"2026-07-19T02:47:24.513904Z","pmid":"41251150","pmcid":"PMC12807730","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":66.6667,"fair_a":62.5,"fair_i":40.0,"fair_r":50.0,"fair_zscore":0.2857,"fair_rationale":{"fair_score":41.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":66.67,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ) and from Zenodo ( https://zenodo.org/records/15731221 )","grounded":true,"rationale":"The paper gives a web URL (zenodo.org/records/15731221) rather than a persistent identifier string such as a DOI or Handle. 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[downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":62.5,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ) and from Zenodo ( https://zenodo.org/records/15731221 ), under terms that allow free reuse and redistribution.","grounded":false,"rationale":"The route to the data is given with no precondition; the data are freely available now. [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":"The Reactome Knowledgebase ( https://reactome.org ) is a freely accessible, expert-curated, open-source, and open-data resource","grounded":true,"rationale":"The abstract explicitly labels the data as 'freely accessible' and 'open-data', which is a natural-language equivalent of the open-access level. [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":null,"grounded":false,"rationale":"The data are not sensitive human-subject data; no gatekeeper is named because none is 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":1.0,"verdict":"yes","evidence":"Reactome was awarded CoreTrustSeal certification, independently validating our sustainability, transparency, governance, and commitment to longterm preservation.","grounded":true,"rationale":"The paper asserts a commitment to long-term preservation through CoreTrustSeal certification, which is a persistence commitment.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper states 'various formats' but does not name any specific file format token for the data.","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":"resulting in an extended version of a classic metabolic map generally compliant with the SBGN process description standard","grounded":true,"rationale":"SBGN is a community standard for biological pathway diagrams, registered in FAIRsharing. 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[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":50.0,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data availability statement mentions 'free reuse and redistribution' but does not name a standard open license (e.g., CC0, CC BY). 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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":"All Reactome data are available in various formats from our downloads page ( https://reactome.org/download-data ) and from Zenodo ( https://zenodo.org/records/15731221 )","why":"The paper gives a web URL (zenodo.org/records/15731221) rather than a persistent identifier string such as a DOI or Handle. [majority verdict 'partial' (3/5 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. 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[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 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":"from Zenodo (https://zenodo.org/records/15731221)","why":"The dataset identifier (Zenodo URL) appears only in the body text of the Data availability section, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. 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[majority verdict 'no' (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.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For genomics / sequencing data, deposit in GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. 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Cite the genomics / sequencing repository accession (e.g. from GEO (GSE accession), SRA (SRP/SRR) or ENA/BioProject (PRJEB/PRJNA)) in the reference list."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:33:47.750472Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}