{"id":"https://openalex.org/W2143250705","doi":"https://doi.org/10.1093/bioinformatics/btu851","title":"PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment","display_name":"PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment","publication_year":2015,"publication_date":"2015-01-08","ids":{"openalex":"https://openalex.org/W2143250705","doi":"https://doi.org/10.1093/bioinformatics/btu851","mag":"2143250705","pmid":"https://pubmed.ncbi.nlm.nih.gov/25653249"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu851","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu851","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110295182","display_name":"Patrik Koskinen","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Patrik Koskinen","raw_affiliation_strings":["1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030987435","display_name":"Petri T\u00f6r\u00f6nen","orcid":"https://orcid.org/0000-0003-4764-9790"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Petri T\u00f6r\u00f6nen","raw_affiliation_strings":["1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063152758","display_name":"Jussi Nokso-Koivisto","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jussi Nokso-Koivisto","raw_affiliation_strings":["1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064498279","display_name":"Liisa Holm","orcid":"https://orcid.org/0000-0002-7807-2966"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Liisa Holm","raw_affiliation_strings":["1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland and 2Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5110295182"],"corresponding_institution_ids":["https://openalex.org/I133731052"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":8.5849,"has_fulltext":false,"cited_by_count":155,"citation_normalized_percentile":{"value":0.98340361,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"31","issue":"10","first_page":"1544","last_page":"1552"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7465000152587891,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7465000152587891,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.1940000057220459,"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":0.03400000184774399,"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":0.8482130169868469},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7978686094284058},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7527284622192383},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6337403655052185},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.44889524579048157},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4006202220916748},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3815620243549347},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2681131064891815},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21985509991645813},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13562139868736267},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12479463219642639},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.11938545107841492}],"concepts":[{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.8482130169868469},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7978686094284058},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7527284622192383},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6337403655052185},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.44889524579048157},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4006202220916748},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3815620243549347},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2681131064891815},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21985509991645813},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13562139868736267},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12479463219642639},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.11938545107841492},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu851","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu851","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25653249","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25653249","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/10/1544","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/10/1544","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":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1647729745","https://openalex.org/W1700503930","https://openalex.org/W1841334989","https://openalex.org/W1969423031","https://openalex.org/W1974116356","https://openalex.org/W1975589113","https://openalex.org/W1975970608","https://openalex.org/W1991570251","https://openalex.org/W1996351562","https://openalex.org/W2011025549","https://openalex.org/W2054118996","https://openalex.org/W2060797027","https://openalex.org/W2084168100","https://openalex.org/W2102814386","https://openalex.org/W2107251251","https://openalex.org/W2113505030","https://openalex.org/W2117486996","https://openalex.org/W2121343862","https://openalex.org/W2121984048","https://openalex.org/W2124410686","https://openalex.org/W2130253098","https://openalex.org/W2135046866","https://openalex.org/W2141148930","https://openalex.org/W2141925828","https://openalex.org/W2142428670","https://openalex.org/W2146389940","https://openalex.org/W2146638336","https://openalex.org/W2151937508","https://openalex.org/W2158714788","https://openalex.org/W2161418621","https://openalex.org/W2167318540","https://openalex.org/W2169059428","https://openalex.org/W2171674404","https://openalex.org/W2328649201","https://openalex.org/W6636975626","https://openalex.org/W6677458394"],"related_works":["https://openalex.org/W2102027645","https://openalex.org/W2107785922","https://openalex.org/W2035528219","https://openalex.org/W2402478170","https://openalex.org/W2946410450","https://openalex.org/W2901823680","https://openalex.org/W2161189461","https://openalex.org/W2972635466","https://openalex.org/W2803517106","https://openalex.org/W2106830745"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"The":[2,148,160,183],"last":[3],"decade":[4],"has":[5],"seen":[6],"a":[7,17,19,63,104,124],"remarkable":[8],"growth":[9,14],"in":[10,110,141],"protein":[11,24,38,88],"databases.":[12],"This":[13],"comes":[15],"at":[16,201,211],"price:":[18],"growing":[20],"number":[21],"of":[22,31,58,103,163],"submitted":[23,33],"sequences":[25,32],"lack":[26],"functional":[27,69,105],"annotation.":[28,106],"Approximately":[29],"32%":[30],"to":[34,55,99,134],"the":[35,49,101,154,164,173,179,193],"most":[36],"comprehensive":[37],"database":[39,168],"UniProtKB":[40],"are":[41,53,190,209],"labelled":[42],"as":[43],"\u2018Unknown":[44],"protein\u2019":[45],"or":[46],"alike.":[47],"Also":[48],"functionally":[50],"annotated":[51],"parts":[52],"reported":[54],"contain":[56],"30\u201340%":[57],"errors.":[59],"Here,":[60],"we":[61,118,130],"introduce":[62],"high-throughput":[64],"tool":[65],"for":[66,169,178],"more":[67],"reliable":[68],"annotation":[70],"called":[71],"Protein":[72],"ANNotation":[73],"with":[74,96,123],"Z-score":[75],"(PANNZER).":[76],"PANNZER":[77,90,149,165,194,197],"predicts":[78],"Gene":[79],"Ontology":[80],"(GO)":[81],"classes":[82],"and":[83,146,172,188],"free":[84,111],"text":[85,112],"descriptions":[86],"about":[87],"functionality.":[89],"uses":[91],"weighted":[92],"k-nearest":[93],"neighbour":[94],"methods":[95,122],"statistical":[97],"testing":[98],"maximize":[100],"reliability":[102],"Results:":[107],"Our":[108],"results":[109,189],"description":[113],"line":[114],"prediction":[115,129],"show":[116,131],"that":[117,138],"outperformed":[119],"all":[120],"competing":[121],"clear":[125,132],"margin.":[126],"In":[127],"GO":[128],"improvement":[133],"our":[135],"older":[136],"method":[137],"performed":[139],"well":[140],"CAFA":[142],"2011":[143],"challenge.":[144],"Availability":[145],"implementation:":[147],"program":[150],"was":[151],"developed":[152],"using":[153],"Python":[155],"programming":[156],"language":[157],"(Version":[158],"2.6).":[159],"stand-alone":[161],"installation":[162],"requires":[166],"MySQL":[167],"data":[170,208],"storage":[171],"BLAST":[174],"(BLASTALL":[175],"v.2.2.21)":[176],"tools":[177],"sequence":[180],"similarity":[181],"search.":[182],"tutorial,":[184],"evaluation":[185],"test":[186],"sets":[187],"available":[191,200,210],"on":[192],"web":[195],"site.":[196],"is":[198],"freely":[199],"http://ekhidna.biocenter.helsinki.fi/pannzer.":[202],"Contact:":[203],"patrik.koskinen@helsinki.fi":[204],"Supplementary":[205,207],"information:":[206],"Bioinformatics":[212],"online.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":14},{"year":2018,"cited_by_count":19},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":13},{"year":2015,"cited_by_count":14}],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2025-10-10T00:00:00"}