{"doi":"10.1093/nar/gkaf1126","title":"OmniPath: integrated knowledgebase for multi-omics analysis","abstract":"Analysis and interpretation of omics data largely benefit from the use of prior knowledge. However, this knowledge is fragmented across resources and often is not directly accessible for analytical methods. We developed OmniPath (https://omnipathdb.org/), a database combining diverse molecular knowledge from 168 resources. It covers causal protein-protein, gene regulatory, microRNA, and enzyme-post-translational modification interactions, cell-cell communication, protein complexes, and information about the function, localization, structure, and many other aspects of biomolecules. It prioritizes literature curated data, and complements it with predictions and large scale databases. To enable interactive browsing of this large corpus of knowledge, we developed OmniPath Explorer, which also includes a large language model agent that has direct access to the database. Python and R/Bioconductor client packages and a Cytoscape plugin create easy access to customized prior knowledge for omics analysis environments, such as scverse. OmniPath can be broadly used for the analysis of bulk, single-cell, and spatial multi-omics data, especially for mechanistic and causal modeling.","journal":"Nucleic Acids Research","year":2025,"id":5242,"datarank":0.43307503463116986,"base_score":2.772588722239781,"endowment":2.772588722239781,"self_citation_contribution":0.41588830833596724,"citation_network_contribution":0.01718672629520264,"self_endowment_contribution":0.41588830833596724,"citer_contribution":0.01718672629520264,"corpus_percentile":56.942832830509786,"corpus_rank":5567,"citation_count":15,"citer_count":14,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9404,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-11-18","fair_score":66.6667,"fair_percentile":86.48731274839498,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":52608,"name":"Jonathan Schaul","orcid":"0009-0000-2718-0636","position":1,"is_corresponding":false},{"id":17167,"name":"Nicolàs Palacio‐Escat","orcid":"0000-0002-7022-1437","position":2,"is_corresponding":false},{"id":52609,"name":"Balázs Bohár","orcid":"0000-0002-3033-5448","position":3,"is_corresponding":false},{"id":52610,"name":"Yunfan Bai","orcid":"0000-0003-0479-2108","position":4,"is_corresponding":false},{"id":52611,"name":"Francesco Ceccarelli","orcid":"0000-0002-5995-5077","position":5,"is_corresponding":false},{"id":52612,"name":"Elif Çevrim","orcid":"0000-0001-7797-8080","position":6,"is_corresponding":false},{"id":52613,"name":"Macabe Daley","orcid":"0000-0002-8026-7068","position":7,"is_corresponding":false},{"id":52614,"name":"Melih Darcan","orcid":"0009-0002-7620-6286","position":8,"is_corresponding":false},{"id":48976,"name":"Daniel Dimitrov","orcid":"0000-0002-5197-2112","position":9,"is_corresponding":false},{"id":52615,"name":"Tunca Doğan","orcid":"0000-0002-1298-9763","position":10,"is_corresponding":false},{"id":52616,"name":"Daniel Domingo-Fernández","orcid":"0000-0002-2046-6145","position":11,"is_corresponding":false},{"id":52617,"name":"Aurelien Dugourd","orcid":"0000-0002-0714-028X","position":12,"is_corresponding":false},{"id":17170,"name":"Attila Gábor","orcid":"0000-0002-0776-1182","position":13,"is_corresponding":false},{"id":52618,"name":"Lejla Potari-Gul","orcid":"0000-0001-9972-9149","position":14,"is_corresponding":false},{"id":52619,"name":"Benjamin A. Hall","orcid":"0000-0003-0355-2946","position":15,"is_corresponding":false},{"id":52620,"name":"Charles Tapley Hoyt","orcid":"0000-0003-4423-4370","position":16,"is_corresponding":false},{"id":17168,"name":"Olga Ivanova","orcid":"0000-0002-9111-4593","position":17,"is_corresponding":false},{"id":2916,"name":"Michal Klein","orcid":"0000-0002-2433-6380","position":18,"is_corresponding":false},{"id":52621,"name":"Toby Lawrence","orcid":"0009-0000-9576-0376","position":19,"is_corresponding":false},{"id":52622,"name":"Diego Mañanes","orcid":"0000-0001-7247-6794","position":20,"is_corresponding":false},{"id":12428,"name":"Costas Mitsopoulos","orcid":"0000-0002-9116-5921","position":21,"is_corresponding":false},{"id":52623,"name":"Sophia Müller-Dott","orcid":"0000-0002-9710-1865","position":22,"is_corresponding":false},{"id":17169,"name":"Márton Ölbei","orcid":"0000-0002-4903-6237","position":23,"is_corresponding":false},{"id":52624,"name":"Christina Schmidt","orcid":"0000-0002-3867-0881","position":24,"is_corresponding":false},{"id":52625,"name":"Bünyamin Şen","orcid":"0000-0002-0853-4731","position":25,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":26,"is_corresponding":false},{"id":52626,"name":"Atabey Ünlü","orcid":"0000-0003-0078-6069","position":27,"is_corresponding":false},{"id":52627,"name":"Erva Ulusoy","orcid":"0000-0002-2643-0362","position":28,"is_corresponding":false},{"id":17165,"name":"Alberto Valdeolivas","orcid":"0000-0001-5482-9023","position":29,"is_corresponding":false},{"id":17171,"name":"Tamás Korcsmáros","orcid":"0000-0003-1717-996X","position":30,"is_corresponding":false},{"id":12565,"name":"Julio Saez-Rodriguez","orcid":"0000-0002-8552-8976","position":31,"is_corresponding":false},{"id":17164,"name":"Dénes Türei","orcid":"0000-0002-7249-9379","position":0,"is_corresponding":true}],"reference_count":49,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"41251164","pmcid":"PMC12807778","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":50.0,"fair_a":56.25,"fair_i":60.0,"fair_r":66.6667,"fair_zscore":1.2752,"fair_rationale":{"fair_score":66.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"OmniPath data is available at https://omnipathdb.org/","grounded":true,"rationale":"The paper provides a web URL, not a persistent identifier from a recognized scheme such as DOI, Handle, or repository accession.","anchors":["RDA-F1-01D 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[majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"OmniPath data is available at https://omnipathdb.org/","grounded":true,"rationale":"The dataset identifier (URL) appears only in body text, not in the reference list.","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":56.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"OmniPath data is available at https://omnipathdb.org/ and by the web app at https://explore.omnipathdb.org/ , under the licenses of the constituting resources.","grounded":true,"rationale":"The text gives a URL with no precondition for access.","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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not explicitly label the data's access level, but describes the access action (available at a URL) from which it can be inferred. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (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, so no gatekeeper 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":0.5,"verdict":"partial","evidence":"OmniPath data is available at https://omnipathdb.org/","grounded":true,"rationale":"The paper states current availability but does not commit to a retention period or permanent archival. [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":60.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The web service serves data in tabular or JSON format","grounded":true,"rationale":"JSON is an open, community-standard format.","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":"The Gene Ontology [36] tree","grounded":false,"rationale":"The paper references standard vocabularies like Gene Ontology but does not state that the data itself complies with a specific community standard. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 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":1.0,"verdict":"yes","evidence":"10.1093/nar/gkac883","grounded":true,"rationale":"The paper includes DOIs for source databases (e.g., SIGNOR 3.0) that the data derives from. [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":66.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"OmniPath data is available at https://omnipathdb.org/ and by the web app at https://explore.omnipathdb.org/ , under the licenses of the constituting resources.","grounded":true,"rationale":"The data license is given as the licenses of the constituting resources, which is not a standard open license (e.g., CC0, CC BY). [majority verdict 'partial' (3/5 passes agreed)]","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":"The pypath package is responsible for resource-specific parsing and compiling the combined databases.","grounded":true,"rationale":"The paper names a specific software tool (pypath) used to produce the data. 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[majority verdict 'no' (3/5 passes agreed)]","gain":4.17,"priority":"useful","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). 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[majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","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 chemistry / materials repository accession (e.g. from Zenodo, PubChem or the Cambridge Structural Database (CSD)) in the reference list.","Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset."],"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":"2026-07-20T12:05:01.246202Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}