{"id":"https://openalex.org/W4320301318","doi":"https://doi.org/10.1093/nar/gkr1065","title":"The Pfam protein families database","display_name":"The Pfam protein families database","publication_year":2011,"publication_date":"2011-11-29","ids":{"openalex":"https://openalex.org/W4320301318","doi":"https://doi.org/10.1093/nar/gkr1065"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkr1065","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1065","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkr1065","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056369160","display_name":"Marco Punta","orcid":"https://orcid.org/0000-0002-0050-0676"},"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":"M. Punta","raw_affiliation_strings":["Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. mp13@sanger.ac.uk"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. mp13@sanger.ac.uk","institution_ids":["https://openalex.org/I2802476451"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079459718","display_name":"Penny Coggill","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"P. C. Coggill","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040135675","display_name":"Ruth Y. Eberhardt","orcid":"https://orcid.org/0000-0001-6152-1369"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. Y. Eberhardt","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024885643","display_name":"Jaina Mistry","orcid":"https://orcid.org/0000-0003-2479-5322"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Mistry","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024838105","display_name":"John Tate","orcid":"https://orcid.org/0000-0002-8315-6574"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Tate","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047131485","display_name":"Chris Boursnell","orcid":"https://orcid.org/0000-0002-3494-4451"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"C. Boursnell","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108830374","display_name":"Ningze Pang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"N. Pang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036688931","display_name":"Sofia K. Forslund","orcid":"https://orcid.org/0000-0003-4285-6993"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"K. Forslund","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112736972","display_name":"Goran Ceric","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"G. Ceric","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084167899","display_name":"Jody Clements","orcid":"https://orcid.org/0000-0003-3932-8188"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"J. Clements","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021930729","display_name":"Andreas Heger","orcid":"https://orcid.org/0000-0001-7720-0447"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Heger","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064498279","display_name":"Liisa Holm","orcid":"https://orcid.org/0000-0002-7807-2966"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"L. Holm","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032432650","display_name":"Erik L. L. Sonnhammer","orcid":"https://orcid.org/0000-0002-9015-5588"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"E. L. L. Sonnhammer","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020118397","display_name":"Sean R. Eddy","orcid":"https://orcid.org/0000-0001-6676-4706"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"S. R. Eddy","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059430118","display_name":"Alex Bateman","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Bateman","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5104045098","display_name":"ROBERT FINN","orcid":"https://orcid.org/0000-0001-8626-2148"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"R. D. Finn","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":16,"corresponding_author_ids":["https://openalex.org/A5056369160"],"corresponding_institution_ids":["https://openalex.org/I2802476451"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":221.079,"has_fulltext":false,"cited_by_count":3771,"citation_normalized_percentile":{"value":0.99998361,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"40","issue":"D1","first_page":"D290","last_page":"D301"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9837999939918518,"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/uniprot","display_name":"UniProt","score":0.9566203355789185},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5868567824363708},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5698820948600769},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.46933713555336},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43898671865463257},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.42433464527130127},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3443465530872345},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.28904080390930176},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21377602219581604},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.19315865635871887}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.9566203355789185},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5868567824363708},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5698820948600769},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.46933713555336},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43898671865463257},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.42433464527130127},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3443465530872345},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.28904080390930176},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21377602219581604},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.19315865635871887},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkr1065","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1065","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"pmh:oai:edoc.mdc-berlin.de:17330","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400224","display_name":"MDC Repository (Max-Delbrueck-Center for Molecular Medicine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I149899117","host_organization_name":"Max Planck Society","host_organization_lineage":["https://openalex.org/I149899117"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:helda.helsinki.fi:10138/162477","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/162477","pdf_url":"http://hdl.handle.net/10138/162477","source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1022.6396","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1022.6396","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/40/D1/D290.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1027.7589","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1027.7589","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/early/2011/11/29/nar.gkr1065.full.pdf","raw_type":"text"},{"id":"pmh:oai:open-archive.highwire.org:nar:40/D1/D290","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/40/D1/D290","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/nar/gkr1065","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkr1065","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":[{"id":"https://metadata.un.org/sdg/4","score":0.6600000262260437,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G6955215639","display_name":null,"funder_award_id":"BB/F010435/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1569186605","https://openalex.org/W1965186869","https://openalex.org/W1980589790","https://openalex.org/W1982307380","https://openalex.org/W1994547959","https://openalex.org/W1996112765","https://openalex.org/W2007745123","https://openalex.org/W2023270883","https://openalex.org/W2024708232","https://openalex.org/W2026523507","https://openalex.org/W2050028106","https://openalex.org/W2051711006","https://openalex.org/W2064795263","https://openalex.org/W2069458148","https://openalex.org/W2076048958","https://openalex.org/W2085277871","https://openalex.org/W2104265053","https://openalex.org/W2108376182","https://openalex.org/W2108929776","https://openalex.org/W2116423958","https://openalex.org/W2116824254","https://openalex.org/W2119936798","https://openalex.org/W2130682154","https://openalex.org/W2136280642","https://openalex.org/W2141885858","https://openalex.org/W2149477647","https://openalex.org/W2155744824","https://openalex.org/W4210623056","https://openalex.org/W4211208250","https://openalex.org/W4256395558"],"related_works":["https://openalex.org/W2102027645","https://openalex.org/W2107785922","https://openalex.org/W2059359052","https://openalex.org/W2035528219","https://openalex.org/W2402478170","https://openalex.org/W2946410450","https://openalex.org/W2999847357","https://openalex.org/W2901823680","https://openalex.org/W2157190239","https://openalex.org/W341177065"],"abstract_inverted_index":{"Pfam":[0,22,94,103,118,150],"is":[1,23],"a":[2,183],"widely":[3],"used":[4],"database":[5],"of":[6,19,66,80,85,129,132,145,159,169,172,174,187],"protein":[7,16],"families,":[8],"currently":[9],"containing":[10],"more":[11],"than":[12],"13,000":[13],"manually":[14,161],"curated":[15,162],"families":[17,62,87,95,188],"as":[18,125,179],"release":[20],"26.0.":[21],"available":[24],"via":[25],"servers":[26],"in":[27],"the":[28,31,53,67,78,83,89,102,117,126,149,155,170],"UK":[29],"(http://pfam.sanger.ac.uk/),":[30],"USA":[32],"(http://pfam.janelia.org/)":[33],"and":[34,63,100,104,109,120,157],"Sweden":[35],"(http://pfam.sbc.su.se/).":[36],"Here,":[37],"we":[38,57,75,137,153,166],"report":[39],"on":[40],"changes":[41],"that":[42,142],"have":[43,58,76],"occurred":[44],"since":[45],"our":[46,86],"2010":[47],"NAR":[48],"paper":[49],"(release":[50],"24.0).":[51],"Over":[52],"last":[54],"2":[55],"years,":[56],"generated":[59],"1840":[60],"new":[61,122],"increased":[64],"coverage":[65],"UniProt":[68],"Knowledgebase":[69],"(UniProtKB)":[70],"to":[71,88,96,107,115,148],"nearly":[72],"80%.":[73],"Notably,":[74],"taken":[77],"step":[79],"opening":[81],"up":[82],"annotation":[84],"Wikipedia":[90,98,105],"community,":[91],"by":[92],"linking":[93],"relevant":[97],"pages":[99],"encouraging":[101],"communities":[106],"improve":[108,116],"expand":[110],"those":[111],"pages.":[112],"We":[113],"continue":[114],"website":[119],"add":[121],"visualizations,":[123],"such":[124],"'sunburst'":[127],"representation":[128],"taxonomic":[130],"distribution":[131],"families.":[133],"In":[134],"this":[135],"work":[136],"additionally":[138],"address":[139],"two":[140],"topics":[141],"will":[143],"be":[144],"particular":[146],"interest":[147],"community.":[151],"First,":[152],"explain":[154],"definition":[156],"use":[158],"family-specific,":[160],"gathering":[163],"thresholds.":[164],"Second,":[165],"discuss":[167],"some":[168],"features":[171],"domains":[173],"unknown":[175],"function":[176],"(also":[177],"known":[178],"DUFs),":[180],"which":[181],"constitute":[182],"rapidly":[184],"growing":[185],"class":[186],"within":[189],"Pfam.":[190]},"counts_by_year":[{"year":2026,"cited_by_count":22},{"year":2025,"cited_by_count":72},{"year":2024,"cited_by_count":123},{"year":2023,"cited_by_count":102},{"year":2022,"cited_by_count":168},{"year":2021,"cited_by_count":183},{"year":2020,"cited_by_count":184},{"year":2019,"cited_by_count":162},{"year":2018,"cited_by_count":174},{"year":2017,"cited_by_count":214},{"year":2016,"cited_by_count":267},{"year":2015,"cited_by_count":385},{"year":2014,"cited_by_count":711},{"year":2013,"cited_by_count":604},{"year":2012,"cited_by_count":304}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}
