{"doi":"10.1371/journal.pbio.1001046","title":"A User's Guide to the Encyclopedia of DNA Elements (ENCODE)","abstract":"The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.","journal":"PLoS Biology","year":2011,"id":9630,"datarank":12.638295136539273,"base_score":7.375255778009754,"endowment":7.375255778009754,"self_citation_contribution":1.1062883667014631,"citation_network_contribution":11.53200676983781,"self_endowment_contribution":1.1062883667014631,"citer_contribution":11.53200676983781,"corpus_percentile":99.4739692117274,"corpus_rank":69,"citation_count":1595,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9376,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2011-04-19","fair_score":84.1667,"fair_percentile":90.2,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":19871,"name":"The ENCODE Project Consortium","orcid":null,"position":0,"is_corresponding":true}],"reference_count":121,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"21526222","pmcid":"PMC3079585","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":100.0,"fair_a":70.0,"fair_i":100.0,"fair_r":66.6667,"fair_zscore":0.2955,"fair_rationale":{"fair_score":84.17,"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":"35 OA location(s)","rationale":null}]},"I":{"name":"Interoperable","score":100.0,"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":1.0,"signal":"accessions=3, trials=0","rationale":null}]},"R":{"name":"Reusable","score":66.67,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"open license (cc-by)","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":["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":"epmc_xml"},"fair_model":null,"fair_agent_version":"fair_agent_v3","fair_fulltext_source":"epmc_xml","fair_has_llm":false,"fair_computed_at":"2026-07-05T07:02:36.568467Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}