{"doi":"10.1093/bioinformatics/btr260","title":"Molecular signatures database (MSigDB) 3.0","abstract":"<jats:title>Abstract</jats:title>\n               <jats:p>Motivation: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets.</jats:p>\n               <jats:p>Results: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental signatures from publications, enhanced annotations and upgrades to the web site.</jats:p>\n               <jats:p>Availability and Implementation: MSigDB is freely available for non-commercial use at http://www.broadinstitute.org/msigdb.</jats:p>\n               <jats:p>Contact:  gsea@broadinstitute.org</jats:p>","journal":"Bioinformatics","year":2011,"id":12022,"datarank":10.895689888267231,"base_score":8.967249182852276,"endowment":8.967249182852276,"self_citation_contribution":1.3450873774278416,"citation_network_contribution":9.55060251083939,"self_endowment_contribution":1.3450873774278416,"citer_contribution":9.55060251083939,"corpus_percentile":99.05623887986386,"corpus_rank":123,"citation_count":7841,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9591,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2011-05-05","fair_score":59.1667,"fair_percentile":45.1,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":16653,"name":"Aravind Subramanian","orcid":null,"position":1,"is_corresponding":false},{"id":20428,"name":" Helga Thorvaldsdottir","orcid":null,"position":3,"is_corresponding":false},{"id":32013,"name":"Pablo Tamayo","orcid":"0000-0002-9360-4668","position":4,"is_corresponding":false},{"id":25136,"name":"Jill P. 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Pinchback","orcid":null,"position":6,"is_corresponding":false},{"id":28642,"name":"Arthur Liberzon","orcid":null,"position":0,"is_corresponding":true}],"reference_count":13,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"21546393","pmcid":"PMC3106198","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":100.0,"fair_a":70.0,"fair_i":50.0,"fair_r":16.6667,"fair_zscore":null,"fair_rationale":{"fair_score":59.17,"has_llm":false,"dimensions":{"F":{"name":"Findable","score":100.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=25, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"OpenAlex id present","rationale":null}]},"A":{"name":"Accessible","score":70.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":0.5,"signal":"files/OA location present but not flagged OA","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"7 OA location(s)","rationale":null}]},"I":{"name":"Interoperable","score":50.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"linked_datasets=25, datacite=25","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null}]},"R":{"name":"Reusable","score":16.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null}]}},"suggestions":["Attach a clear, open reuse license (e.g. CC-BY or CC0).","Reference data using standard accessions (e.g. GEO, PDB, ClinicalTrials.gov).","Maintain explicit versioning for the dataset.","Make the paper/data Open Access or deposit the files in an open repository."],"model":null,"agent_version":"fair_agent_v3","fulltext_source":"oa_pdf"},"fair_model":null,"fair_agent_version":"fair_agent_v3","fair_fulltext_source":"oa_pdf","fair_has_llm":false,"fair_computed_at":"2026-07-06T03:31:49.023864Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}