{"id":"https://openalex.org/W2426363820","doi":"https://doi.org/10.1093/bioinformatics/btw366","title":"NegGOA: negative GO annotations selection using ontology structure","display_name":"NegGOA: negative GO annotations selection using ontology structure","publication_year":2016,"publication_date":"2016-06-17","ids":{"openalex":"https://openalex.org/W2426363820","doi":"https://doi.org/10.1093/bioinformatics/btw366","mag":"2426363820","pmid":"https://pubmed.ncbi.nlm.nih.gov/27318205"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw366","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw366","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2996/25072589/btw366.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2996/25072589/btw366.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101990230","display_name":"Guangyuan Fu","orcid":"https://orcid.org/0000-0002-1960-0546"},"institutions":[{"id":"https://openalex.org/I142108993","display_name":"Southwest University","ror":"https://ror.org/01kj4z117","country_code":"CN","type":"education","lineage":["https://openalex.org/I142108993"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangyuan Fu","raw_affiliation_strings":["1 College of Computer and Information Science, Southwest University, Chongqing 400715, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 College of Computer and Information Science, Southwest University, Chongqing 400715, China","institution_ids":["https://openalex.org/I142108993"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100384767","display_name":"Jun Wang","orcid":"https://orcid.org/0000-0002-5890-0365"},"institutions":[{"id":"https://openalex.org/I142108993","display_name":"Southwest University","ror":"https://ror.org/01kj4z117","country_code":"CN","type":"education","lineage":["https://openalex.org/I142108993"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["1 College of Computer and Information Science, Southwest University, Chongqing 400715, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 College of Computer and Information Science, Southwest University, Chongqing 400715, China","institution_ids":["https://openalex.org/I142108993"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028694889","display_name":"Bo Yang","orcid":"https://orcid.org/0000-0003-1927-8419"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Yang","raw_affiliation_strings":["2 Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027082940","display_name":"Guoxian Yu","orcid":"https://orcid.org/0000-0002-1667-6705"},"institutions":[{"id":"https://openalex.org/I142108993","display_name":"Southwest University","ror":"https://ror.org/01kj4z117","country_code":"CN","type":"education","lineage":["https://openalex.org/I142108993"]},{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guoxian Yu","raw_affiliation_strings":["1 College of Computer and Information Science, Southwest University, Chongqing 400715, China","2 Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 College of Computer and Information Science, Southwest University, Chongqing 400715, China","institution_ids":["https://openalex.org/I142108993"]},{"raw_affiliation_string":"2 Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China","institution_ids":["https://openalex.org/I194450716"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5027082940"],"corresponding_institution_ids":["https://openalex.org/I142108993","https://openalex.org/I194450716"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.5881,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.9307204,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"32","issue":"19","first_page":"2996","last_page":"3004"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9118000268936157,"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":0.9118000268936157,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0471000000834465,"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":0.02449999935925007,"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/computer-science","display_name":"Computer science","score":0.7543163299560547},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.7317940592765808},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.614920973777771},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5820830464363098},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5395208597183228},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5227577686309814},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5186718702316284},{"id":"https://openalex.org/keywords/negative-selection","display_name":"Negative selection","score":0.5038461089134216},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.49527421593666077},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.42239853739738464},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.4040827751159668},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.398580402135849},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39704790711402893},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33763229846954346},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16212984919548035},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15932196378707886},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12462759017944336},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.08793464303016663},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08646512031555176}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7543163299560547},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.7317940592765808},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.614920973777771},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5820830464363098},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5395208597183228},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5227577686309814},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5186718702316284},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.5038461089134216},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.49527421593666077},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.42239853739738464},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4040827751159668},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.398580402135849},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39704790711402893},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33763229846954346},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16212984919548035},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15932196378707886},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12462759017944336},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.08793464303016663},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08646512031555176},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","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},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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},{"descriptor_ui":"D051379","descriptor_name":"Mice","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":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","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":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw366","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw366","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2996/25072589/btw366.pdf","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:27318205","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27318205","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:32/19/2996","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/19/2996","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/bioinformatics/btw366","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw366","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/19/2996/25072589/btw366.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1984806465","display_name":null,"funder_award_id":"CYS16070","funder_id":"https://openalex.org/F4320335872","funder_display_name":"Chongqing Graduate Student Research Innovation Project"},{"id":"https://openalex.org/G2758728005","display_name":null,"funder_award_id":"XDJK2016B009","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G381237529","display_name":null,"funder_award_id":"XDJK2016B009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4372538537","display_name":null,"funder_award_id":"61402378","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5139603256","display_name":null,"funder_award_id":"XDJK2016D021","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5258682401","display_name":null,"funder_award_id":"2362015XK07","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G73025078","display_name":null,"funder_award_id":"2362015XK07","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321550","display_name":"Chongqing Science and Technology Commission","ror":"https://ror.org/05w9erc61"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320335872","display_name":"Chongqing Graduate Student Research Innovation Project","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2426363820.pdf","grobid_xml":"https://content.openalex.org/works/W2426363820.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1590721879","https://openalex.org/W1647729745","https://openalex.org/W1880262756","https://openalex.org/W1895597370","https://openalex.org/W1965887320","https://openalex.org/W1972881673","https://openalex.org/W1975414584","https://openalex.org/W1993760308","https://openalex.org/W2001004762","https://openalex.org/W2012336263","https://openalex.org/W2045729458","https://openalex.org/W2057119643","https://openalex.org/W2069313265","https://openalex.org/W2076743129","https://openalex.org/W2084168100","https://openalex.org/W2103017472","https://openalex.org/W2108892946","https://openalex.org/W2117235735","https://openalex.org/W2117486996","https://openalex.org/W2120688086","https://openalex.org/W2121893605","https://openalex.org/W2122872449","https://openalex.org/W2123958887","https://openalex.org/W2124649441","https://openalex.org/W2125282516","https://openalex.org/W2129026672","https://openalex.org/W2145189015","https://openalex.org/W2147461734","https://openalex.org/W2153499010","https://openalex.org/W2165858555","https://openalex.org/W2166985665","https://openalex.org/W2169059428","https://openalex.org/W2169896388","https://openalex.org/W4252684946","https://openalex.org/W6639619044"],"related_works":["https://openalex.org/W3132344302","https://openalex.org/W2094822546","https://openalex.org/W1969080446","https://openalex.org/W4388708026","https://openalex.org/W3108941781","https://openalex.org/W2082380079","https://openalex.org/W2134206588","https://openalex.org/W2084200259","https://openalex.org/W1797688090","https://openalex.org/W1977065177"],"abstract_inverted_index":{"MOTIVATION:":[0],"Predicting":[1],"the":[2,10,14,21,59,100,114,143,161,185,197],"biological":[3],"functions":[4,198],"of":[5,9,23,39,71,81,94,103,113,142,150,153,160,199,229],"proteins":[6,62,72,200,230],"is":[7,88,223],"one":[8],"key":[11],"challenges":[12],"in":[13,201],"post-genomic":[15],"era.":[16],"Computational":[17],"models":[18],"have":[19],"demonstrated":[20],"utility":[22],"applying":[24],"machine":[25],"learning":[26],"methods":[27,34],"to":[28,134,156,195],"predict":[29,196],"protein":[30,87,105,115,155],"function.":[31,50],"Most":[32],"prediction":[33,193],"explicitly":[35],"require":[36],"a":[37,48,65,86,104,118,129,154],"set":[38],"negative":[40,101,136,158,168,187],"examples-proteins":[41],"that":[42,61,174],"are":[43,73,243,253],"known":[44],"not":[45],"carrying":[46],"out":[47,64],"particular":[49,66],"However,":[51],"Gene":[52],"Ontology":[53],"(GO)":[54],"almost":[55],"always":[56],"only":[57],"provides":[58],"knowledge":[60],"carry":[63],"function,":[67],"and":[68,85,148,172,205,240],"functional":[69],"annotations":[70,147,152,228],"incomplete.":[74],"GO":[75,83,121],"structurally":[76],"organizes":[77],"more":[78],"than":[79,181,212,231],"tens":[80],"thousands":[82],"terms":[84],"annotated":[89],"with":[90,166],"several":[91],"(or":[92],"dozens)":[93],"these":[95,98,213,232],"terms.":[96],"For":[97],"reasons,":[99],"examples":[102,112,159,169,188],"can":[106],"greatly":[107],"help":[108],"distinguishing":[109],"true":[110],"positive":[111],"from":[116,226],"such":[117],"large":[119],"candidate":[120],"space.":[122],"RESULTS:":[123],"In":[124,220],"this":[125],"paper,":[126],"we":[127],"present":[128],"novel":[130],"approach":[131],"(called":[132],"NegGOA)":[133],"select":[135],"examples.":[137],"Specifically,":[138],"NegGOA":[139,165,175,207,222],"takes":[140],"advantage":[141],"ontology":[144],"structure,":[145],"available":[146,244,254],"potentiality":[149],"additional":[151],"choose":[157],"protein.":[162],"We":[163,183],"compare":[164],"other":[167],"selection":[170],"algorithms":[171,215],"find":[173],"produces":[176],"much":[177],"fewer":[178],"false":[179],"negatives":[180],"them.":[182],"incorporate":[184],"selected":[186],"into":[189],"an":[190],"efficient":[191],"function":[192],"model":[194],"Yeast,":[202],"Human,":[203],"Mouse":[204],"Fly.":[206],"also":[208],"demonstrates":[209],"improved":[210],"accuracy":[211],"comparing":[214,233],"across":[216],"various":[217],"evaluation":[218],"metrics.":[219],"addition,":[221],"less":[224],"suffered":[225],"incomplete":[227],"methods.":[234],"AVAILABILITY":[235],"AND":[236],"IMPLEMENTATION:":[237],"The":[238],"Matlab":[239],"R":[241],"codes":[242],"at":[245,255],"https://sites.google.com/site/guoxian85/neggoa":[246],"CONTACT:":[247],"gxyu@swu.edu.cn":[248],"SUPPLEMENTARY":[249],"INFORMATION:":[250],"Supplementary":[251],"data":[252],"Bioinformatics":[256],"online.":[257]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}