{"doi":"10.1093/nar/gkw377","title":"Enrichr: a comprehensive gene set enrichment analysis web server 2016 update","abstract":"Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.","journal":"Nucleic Acids Research","year":2016,"id":8931,"datarank":15.915227705769535,"base_score":9.308917935337178,"endowment":9.308917935337178,"self_citation_contribution":1.3963376903005769,"citation_network_contribution":14.518890015468958,"self_endowment_contribution":1.3963376903005769,"citer_contribution":14.518890015468958,"corpus_percentile":88.8527257933279,"corpus_rank":138,"citation_count":11578,"citer_count":191,"citers_with_citation_signal":191,"citers_with_endowment":191,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9285,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2016-05-03","fair_score":39.375,"fair_percentile":20.030782761653473,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":66716,"name":"Matthew R. Jones","orcid":"0000-0002-4822-157X","position":1,"is_corresponding":false},{"id":76154,"name":"Andrew D. Rouillard","orcid":"0000-0002-3502-7161","position":2,"is_corresponding":false},{"id":76155,"name":"Nicolas F. Fernandez","orcid":null,"position":3,"is_corresponding":false},{"id":76156,"name":"Qiaonan Duan","orcid":null,"position":4,"is_corresponding":false},{"id":76157,"name":"Zichen Wang","orcid":"0000-0002-1415-1286","position":5,"is_corresponding":false},{"id":64661,"name":"Simon Koplev","orcid":"0000-0002-8586-5614","position":6,"is_corresponding":false},{"id":64662,"name":"Sherry L. Jenkins","orcid":"0000-0003-1730-0977","position":7,"is_corresponding":false},{"id":64660,"name":"Kathleen M. Jagodnik","orcid":"0000-0002-2755-2097","position":8,"is_corresponding":false},{"id":76158,"name":"Alexander Lachmann","orcid":"0000-0002-1982-7652","position":9,"is_corresponding":false},{"id":76159,"name":"Michael G. McDermott","orcid":null,"position":10,"is_corresponding":false},{"id":76160,"name":"Caroline D. Monteiro","orcid":null,"position":11,"is_corresponding":false},{"id":76161,"name":"Gregory W. Gundersen","orcid":null,"position":12,"is_corresponding":false},{"id":76163,"name":"Nicolas Fernandez","orcid":"0000-0001-7979-2941","position":14,"is_corresponding":false},{"id":60353,"name":"Avi Ma’ayan","orcid":"0000-0002-6904-1017","position":15,"is_corresponding":false},{"id":76153,"name":"Maxim V. Kuleshov","orcid":"0000-0002-7812-7752","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"27141961","pmcid":"PMC4987924","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by-nc","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":52.5,"fair_a":55.0,"fair_i":25.0,"fair_r":25.0,"fair_zscore":-0.5279,"fair_rationale":{"fair_score":39.38,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"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=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.25,"signal":null,"rationale":"The paper provides a URL to the web server and mentions downloadable libraries, but does not include structured, machine-readable metadata (e.g., schema.org, JSON-LD) for the data or code."}]},"A":{"name":"Accessible","score":55.0,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper states the tool is freely available at a URL and libraries are downloadable, but does not specify a clear, persistent access protocol (e.g., DOI, repository) for the underlying data or code."}]},"I":{"name":"Interoperable","score":25.0,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","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},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper uses standard gene symbols and mentions formats like BED and BioPAX, but does not explicitly state use of standard vocabularies or identifiers for all data, nor provide a formal data model."}]},"R":{"name":"Reusable","score":25.0,"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},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.333,"signal":null,"rationale":"The paper includes a CC-BY-NC license and mentions downloadable libraries, but lacks a formal data-availability statement, persistent identifiers for datasets, and detailed reproducibility instructions for the analysis."}]}},"suggestions":["Provide a formal data-availability statement with a persistent identifier (e.g., DOI) for the gene set libraries and code.","Include structured, machine-readable metadata (e.g., JSON-LD) in the paper or associated repository to improve findability.","Specify standard vocabularies and identifiers (e.g., using identifiers.org) for all gene sets and annotations to enhance interoperability.","Add a clear protocol for accessing the exact version of the data and code used in the paper, including a license for the code.","Provide detailed reproducibility instructions, including software versions and parameters, for the benchmarking and fuzzy enrichment analyses."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:24:54.243933Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}