{"id":"https://openalex.org/W2083184875","doi":"https://doi.org/10.1093/nar/gkn193","title":"FFPred: an integrated feature-based function prediction server for vertebrate proteomes","display_name":"FFPred: an integrated feature-based function prediction server for vertebrate proteomes","publication_year":2008,"publication_date":"2008-05-08","ids":{"openalex":"https://openalex.org/W2083184875","doi":"https://doi.org/10.1093/nar/gkn193","mag":"2083184875"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkn193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn193","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W297/7623970/gkn193.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":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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/nar/article-pdf/36/suppl_2/W297/7623970/gkn193.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044132842","display_name":"Anna Lobley","orcid":"https://orcid.org/0000-0002-5365-2526"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"A. E. Lobley","raw_affiliation_strings":["Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom","Department of Computer Science, University College London, London, WC1E 6BT, UNITED KINGDOM"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]},{"raw_affiliation_string":"Department of Computer Science, University College London, London, WC1E 6BT, UNITED KINGDOM","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002637452","display_name":"Timothy Nugent","orcid":"https://orcid.org/0000-0003-2201-2769"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"T. Nugent","raw_affiliation_strings":["Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053149072","display_name":"Christine Orengo","orcid":"https://orcid.org/0000-0002-7141-8936"},"institutions":[{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"C. A. Orengo","raw_affiliation_strings":["Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108445457","display_name":"D. T. Jones","orcid":null},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I4210157240","display_name":"Institute of Structural and Molecular Biology","ror":"https://ror.org/05wsetc54","country_code":"GB","type":"facility","lineage":["https://openalex.org/I124357947","https://openalex.org/I124357947","https://openalex.org/I4210157240","https://openalex.org/I45129253","https://openalex.org/I98259816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"D. T. Jones","raw_affiliation_strings":["Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University College London and 2 Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, United Kingdom","institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044132842"],"corresponding_institution_ids":["https://openalex.org/I4210157240","https://openalex.org/I45129253"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.93,"has_fulltext":true,"cited_by_count":65,"citation_normalized_percentile":{"value":0.85508806,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"Web Server","first_page":"W297","last_page":"W302"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9994999766349792,"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":0.9991999864578247,"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/annotation","display_name":"Annotation","score":0.6588480472564697},{"id":"https://openalex.org/keywords/server","display_name":"Server","score":0.6109493374824524},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5712378621101379},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5349280834197998},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.49389010667800903},{"id":"https://openalex.org/keywords/upload","display_name":"Upload","score":0.4799404740333557},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.4486718475818634},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.4365326762199402},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.43066826462745667},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37880080938339233},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3759986460208893},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3535720705986023},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34335485100746155},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.08512836694717407}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6588480472564697},{"id":"https://openalex.org/C93996380","wikidata":"https://www.wikidata.org/wiki/Q44127","display_name":"Server","level":2,"score":0.6109493374824524},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5712378621101379},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5349280834197998},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.49389010667800903},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.4799404740333557},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.4486718475818634},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.4365326762199402},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.43066826462745667},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37880080938339233},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3759986460208893},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3535720705986023},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34335485100746155},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.08512836694717407},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/nar/gkn193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn193","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W297/7623970/gkn193.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":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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2447771","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2447771","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkn193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkn193","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_2/W297/7623970/gkn193.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":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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/17","display_name":"Partnerships for the goals","score":0.4000000059604645}],"awards":[{"id":"https://openalex.org/G4447653093","display_name":null,"funder_award_id":"Network","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G6982995691","display_name":null,"funder_award_id":"LHSG-CT-2003-503265","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2083184875.pdf","grobid_xml":"https://content.openalex.org/works/W2083184875.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1966243465","https://openalex.org/W1976952616","https://openalex.org/W2023557647","https://openalex.org/W2024228937","https://openalex.org/W2056983531","https://openalex.org/W2085176241","https://openalex.org/W2100320834","https://openalex.org/W2103017472","https://openalex.org/W2107415275","https://openalex.org/W2108491719","https://openalex.org/W2115595474","https://openalex.org/W2118286367","https://openalex.org/W2121265934","https://openalex.org/W2134789671","https://openalex.org/W2154139219","https://openalex.org/W2165797737"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2944823289","https://openalex.org/W2358755282","https://openalex.org/W3037018281","https://openalex.org/W2972592048","https://openalex.org/W2070735207"],"abstract_inverted_index":{"One":[0],"of":[1,4,17,47,87,186,191],"the":[2,5,184,192],"challenges":[3],"post-genomic":[6],"era":[7],"is":[8,175],"to":[9,64,140,179],"provide":[10],"accurate":[11],"function":[12,25,66,134,197],"annotations":[13,34],"for":[14,103,189],"large":[15],"volumes":[16],"data":[18],"resulting":[19],"from":[20,76],"genome":[21],"sequencing":[22],"projects.":[23],"Most":[24],"prediction":[26,67,135,158],"servers":[27,136],"utilize":[28],"methods":[29,43],"that":[30,44],"transfer":[31],"existing":[32],"database":[33],"between":[35,194],"orthologous":[36],"sequences.":[37,56],"In":[38],"contrast,":[39],"there":[40],"are":[41,45,82],"few":[42],"independent":[46],"homology":[48],"and":[49,53,98,144,148,152,167,196],"can":[50],"annotate":[51,141],"distant":[52,142],"orphan":[54,145],"protein":[55,69,116,146],"The":[57,80,107],"FFPred":[58,128],"server":[59],"adopts":[60],"a":[61,85],"machinelearning":[62],"approach":[63],"perform":[65],"in":[68,137],"feature":[70,73],"space":[71],"using":[72],"characteristics":[74],"predicted":[75],"amino":[77,165],"acid":[78,166],"sequence.":[79],"features":[81,195],"scanned":[83],"against":[84],"library":[86,110],"support":[88],"vector":[89],"machines":[90],"representing":[91],"over":[92,132],"300":[93],"Gene":[94],"Ontology":[95],"(GO)":[96],"classes":[97],"probabilistic":[99],"confidence":[100],"scores":[101],"returned":[102],"each":[104],"annotation":[105,169],"term.":[106],"GO":[108],"term":[109],"has":[111],"been":[112],"modelled":[113],"on":[114,183],"human":[115],"annotations;":[117],"however,":[118],"benchmark":[119],"performance":[120,124],"testing":[121],"showed":[122],"robust":[123],"across":[125],"higher":[126],"eukaryotes.":[127],"offers":[129],"important":[130],"advantages":[131],"traditional":[133],"its":[138],"ability":[139],"homologues":[143],"sequences,":[147],"achieves":[149],"greater":[150],"coverage":[151],"classification":[153],"accuracy":[154],"than":[155],"other":[156],"feature-based":[157],"servers.":[159],"A":[160],"user":[161],"may":[162],"upload":[163],"an":[164],"receive":[168],"predictions":[170],"via":[171],"email.":[172],"Feature":[173],"information":[174],"provided":[176],"as":[177],"easy":[178],"interpret":[180],"graphics":[181],"displayed":[182],"sequence":[185],"interest,":[187],"allowing":[188],"back-interpretation":[190],"associations":[193],"classes.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-21T08:13:44.787528","created_date":"2016-06-24T00:00:00"}
