{"id":"https://openalex.org/W2042881722","doi":"https://doi.org/10.1093/nar/gki081","title":"Rfam: annotating non-coding RNAs in complete genomes","display_name":"Rfam: annotating non-coding RNAs in complete genomes","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W2042881722","doi":"https://doi.org/10.1093/nar/gki081","mag":"2042881722","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608160"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki081","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki081","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D121/7622063/gki081.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D121/7622063/gki081.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001502247","display_name":"Sam Griffiths\u2010Jones","orcid":"https://orcid.org/0000-0001-6043-807X"},"institutions":[{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"S. Griffiths-Jones","raw_affiliation_strings":["The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. sgj@sanger.ac.uk",", The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. sgj@sanger.ac.uk","institution_ids":["https://openalex.org/I2802476451"]},{"raw_affiliation_string":", The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK,","institution_ids":["https://openalex.org/I2802476451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5001502247"],"corresponding_institution_ids":["https://openalex.org/I2802476451"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":82.3014,"has_fulltext":true,"cited_by_count":1753,"citation_normalized_percentile":{"value":0.99975991,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"33","issue":"Database issue","first_page":"D121","last_page":"D124"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991000294685364,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7015222311019897},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.573081910610199},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4929037094116211},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.47116217017173767},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.45845526456832886},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.44639384746551514},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.3298039138317108},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27417314052581787},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11637696623802185}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7015222311019897},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.573081910610199},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4929037094116211},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.47116217017173767},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.45845526456832886},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.44639384746551514},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.3298039138317108},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27417314052581787},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11637696623802185},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030561","descriptor_name":"Databases, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1093/nar/gki081","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki081","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D121/7622063/gki081.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15608160","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608160","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/9a2dc90d-9763-4044-8f77-83218425fe92","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/9a2dc90d-9763-4044-8f77-83218425fe92","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Griffiths-Jones, S, Moxon, S, Marshall, M, Khanna, A, Eddy, S R & Bateman, A 2005, 'Rfam: Annotating non-coding RNAs in complete genomes', Nucleic acids research., vol. 33, pp. D121-D124. https://doi.org/10.1093/nar/gki081","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:digitalcommons.wustl.edu:open_access_pubs-1160","is_oa":true,"landing_page_url":"https://digitalcommons.wustl.edu/open_access_pubs/159","pdf_url":"https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=1160&context=open_access_pubs","source":{"id":"https://openalex.org/S4306400764","display_name":"Digital Commons@Becker (Washington University School of Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I204465549","host_organization_name":"Washington University in St. Louis","host_organization_lineage":["https://openalex.org/I204465549"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Open Access Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:540035","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/540035","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/9a2dc90d-9763-4044-8f77-83218425fe92","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/rfam-annotating-noncoding-rnas-in-complete-genomes(9a2dc90d-9763-4044-8f77-83218425fe92).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Griffiths-Jones, S, Moxon, S, Marshall, M, Khanna, A, Eddy, S R & Bateman, A 2005, 'Rfam: Annotating non-coding RNAs in complete genomes', Nucleic acids research., vol. 33, pp. D121-D124. https://doi.org/10.1093/nar/gki081","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:ueaeprints.uea.ac.uk:60007","is_oa":false,"landing_page_url":"https://ueaeprints.uea.ac.uk/id/eprint/60007/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400384","display_name":"UEA Digital Repository (University of East Anglia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1118541","host_organization_name":"University of East Anglia","host_organization_lineage":["https://openalex.org/I1118541"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/nar/gki081","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki081","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D121/7622063/gki081.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6000000238418579,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W1972708527","https://openalex.org/W1996146264","https://openalex.org/W2024799598","https://openalex.org/W2064345118","https://openalex.org/W2065225159","https://openalex.org/W2090415636","https://openalex.org/W2093417734","https://openalex.org/W2103973742","https://openalex.org/W2120242947","https://openalex.org/W2141885858","https://openalex.org/W2149941588","https://openalex.org/W2151464048","https://openalex.org/W2158381555","https://openalex.org/W2158714788","https://openalex.org/W2159850373","https://openalex.org/W2168148721","https://openalex.org/W2168909179","https://openalex.org/W4210400672","https://openalex.org/W4292239814"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W2079327011","https://openalex.org/W2147993839","https://openalex.org/W2058984380","https://openalex.org/W2900182103","https://openalex.org/W1988125422","https://openalex.org/W4365136234","https://openalex.org/W3183769948","https://openalex.org/W2010385783","https://openalex.org/W2600828970"],"abstract_inverted_index":{"Rfam":[0,20,100],"is":[1,101],"a":[2,59],"comprehensive":[3],"collection":[4],"of":[5,28,31,38,52,54,66,75,80],"non-coding":[6],"RNA":[7],"(ncRNA)":[8],"families,":[9,34],"represented":[10],"by":[11],"multiple":[12,55],"sequence":[13,33],"alignments":[14],"and":[15,26,35,108],"profile":[16],"stochastic":[17],"context-free":[18],"grammars.":[19],"aims":[21],"to":[22,84],"facilitate":[23],"the":[24,49,90,98,104],"identification":[25],"classification":[27],"new":[29],"members":[30],"known":[32],"distributes":[36],"annotation":[37],"ncRNAs":[39],"in":[40,71,89],"over":[41],"200":[42],"complete":[43],"genome":[44],"sequences.":[45],"The":[46],"data":[47],"provide":[48],"first":[50],"glimpses":[51],"conservation":[53],"ncRNA":[56],"families":[57,68,82],"across":[58],"wide":[60],"taxonomic":[61],"range.":[62],"A":[63],"small":[64],"number":[65],"large":[67,78],"are":[69,92],"essential":[70],"all":[72],"three":[73],"kingdoms":[74],"life,":[76],"with":[77,95],"numbers":[79],"smaller":[81],"specific":[83],"certain":[85],"taxa.":[86],"Recent":[87],"improvements":[88],"database":[91],"discussed,":[93],"together":[94],"challenges":[96],"for":[97],"future.":[99],"available":[102],"on":[103],"Web":[105],"at":[106],"http://www.sanger.ac.uk/Software/Rfam/":[107],"http://rfam.wustl.edu/.":[109]},"counts_by_year":[{"year":2026,"cited_by_count":58},{"year":2025,"cited_by_count":117},{"year":2024,"cited_by_count":144},{"year":2023,"cited_by_count":101},{"year":2022,"cited_by_count":116},{"year":2021,"cited_by_count":85},{"year":2020,"cited_by_count":76},{"year":2019,"cited_by_count":44},{"year":2018,"cited_by_count":32},{"year":2017,"cited_by_count":49},{"year":2016,"cited_by_count":49},{"year":2015,"cited_by_count":60},{"year":2014,"cited_by_count":57},{"year":2013,"cited_by_count":79},{"year":2012,"cited_by_count":65}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-10-10T00:00:00"}