{"id":"https://openalex.org/W2096039184","doi":"https://doi.org/10.1093/nar/gki007","title":"ProtoNet 4.0: A hierarchical classification of one million protein sequences","display_name":"ProtoNet 4.0: A hierarchical classification of one million protein sequences","publication_year":2004,"publication_date":"2004-12-17","ids":{"openalex":"https://openalex.org/W2096039184","doi":"https://doi.org/10.1093/nar/gki007","mag":"2096039184","pmid":"https://pubmed.ncbi.nlm.nih.gov/15608180"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki007","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D216/7621418/gki007.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","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":"hybrid","oa_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D216/7621418/gki007.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033160755","display_name":"N. Kaplan","orcid":"https://orcid.org/0000-0001-9940-1987"},"institutions":[{"id":"https://openalex.org/I197251160","display_name":"Hebrew University of Jerusalem","ror":"https://ror.org/03qxff017","country_code":"IL","type":"education","lineage":["https://openalex.org/I197251160"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"N. Kaplan","raw_affiliation_strings":["Department of Biological Chemistry, Institute of Life Sciences and School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel. kaplann@cc.huji.ac.il","Department of Biological Chemistry, Institute of Life Sciences and School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel"],"affiliations":[{"raw_affiliation_string":"Department of Biological Chemistry, Institute of Life Sciences and School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel. kaplann@cc.huji.ac.il","institution_ids":["https://openalex.org/I197251160"]},{"raw_affiliation_string":"Department of Biological Chemistry, Institute of Life Sciences and School of Computer Science and Engineering, The Hebrew University of Jerusalem, Israel","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5033160755"],"corresponding_institution_ids":["https://openalex.org/I197251160"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.2912,"has_fulltext":true,"cited_by_count":64,"citation_normalized_percentile":{"value":0.87780766,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"33","issue":"Database issue","first_page":"D216","last_page":"D218"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987999796867371,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983999729156494,"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":0.9495622515678406},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5017642974853516},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.43907666206359863},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43190521001815796}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.9495622515678406},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5017642974853516},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.43907666206359863},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43190521001815796}],"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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/nar/gki007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki007","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D216/7621418/gki007.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:15608180","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15608180","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:ink.library.smu.edu.sg:sis_research-1088","is_oa":true,"landing_page_url":"https://ink.library.smu.edu.sg/sis_research/89","pdf_url":null,"source":{"id":"https://openalex.org/S4377196871","display_name":"Institutional Knowledge (InK) - Institutional Knowledge at Singapore Management University (Singapore Management University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79891267","host_organization_name":"Singapore Management University","host_organization_lineage":["https://openalex.org/I79891267"],"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":"http://dx.doi.org/10.1093/nar/gki007","raw_type":"Journal Article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.582.7295","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.582.7295","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/33/suppl_1/D216.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.59.5509","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.59.5509","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.huji.ac.il/~kaplann/KaplanNAR2005.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.76.6797","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.76.6797","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cs.huji.ac.il/~nati/PAPERS/pnet4.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:163472","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC539961","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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"},{"id":"pmh:oai:pubmedcentral.nih.gov:539961","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/539961","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"}],"best_oa_location":{"id":"doi:10.1093/nar/gki007","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki007","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_1/D216/7621418/gki007.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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2096039184.pdf","grobid_xml":"https://content.openalex.org/works/W2096039184.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2108401170","https://openalex.org/W2108491719","https://openalex.org/W2108758729","https://openalex.org/W2111973517","https://openalex.org/W2130687290","https://openalex.org/W2135144811","https://openalex.org/W2146585102","https://openalex.org/W2148853951","https://openalex.org/W2158714788","https://openalex.org/W2628074563","https://openalex.org/W4319780061"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2061542922"],"abstract_inverted_index":{"ProtoNet":[0,14,73,101],"is":[1,102],"an":[2],"automatic":[3],"hierarchical":[4],"classification":[5],"of":[6,20,53,56,71,78,84],"the":[7,13,18,41,54,57,72,79],"protein":[8],"sequence":[9],"space.":[10],"In":[11,31],"2004,":[12],"(version":[15],"4.0)":[16],"presents":[17],"analysis":[19,37],"over":[21],"one":[22],"million":[23],"proteins":[24],"merged":[25],"from":[26],"SwissProt":[27],"and":[28,36],"TrEMBL":[29],"databases.":[30],"addition":[32],"to":[33,39,75,95],"rich":[34],"visualization":[35],"tools":[38],"navigate":[40],"clustering":[42],"hierarchy,":[43],"we":[44],"incorporated":[45],"several":[46],"improvements":[47],"that":[48,64],"allow":[49],"a":[50,69],"simplified":[51],"view":[52],"scaffold":[55],"proteins.":[58],"An":[59],"unsupervised,":[60],"biologically":[61],"valid":[62],"method":[63],"was":[65,87],"developed":[66],"resulted":[67],"in":[68],"condensation":[70],"hierarchy":[74],"only":[76],"12%":[77],"clusters.":[80],"A":[81],"large":[82],"portion":[83],"these":[85],"clusters":[86],"automatically":[88],"assigned":[89],"high":[90],"confidence":[91],"biological":[92],"names":[93],"according":[94],"their":[96],"correspondence":[97],"with":[98],"functional":[99],"annotations.":[100],"available":[103],"at:":[104],"http://www.protonet.cs.huji.ac.il.":[105]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
