{"id":"https://openalex.org/W2171649066","doi":"https://doi.org/10.1093/bib/bbt012","title":"Data construction for phosphorylation site prediction","display_name":"Data construction for phosphorylation site prediction","publication_year":2013,"publication_date":"2013-03-29","ids":{"openalex":"https://openalex.org/W2171649066","doi":"https://doi.org/10.1093/bib/bbt012","mag":"2171649066","pmid":"https://pubmed.ncbi.nlm.nih.gov/23543354"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbt012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt012","pdf_url":"https://academic.oup.com/bib/article-pdf/15/5/839/17488289/bbt012.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/15/5/839/17488289/bbt012.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008815742","display_name":"Haipeng Gong","orcid":null},"institutions":[{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haipeng Gong","raw_affiliation_strings":["Haipeng Gong received the BS degree in software engineering from Dalian University of Technology, China, in 2011. He is currently working towards the MS degree in the School of Software at Dalian University of Technology. His research interests include data mining and computational proteomics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Haipeng Gong received the BS degree in software engineering from Dalian University of Technology, China, in 2011. He is currently working towards the MS degree in the School of Software at Dalian University of Technology. His research interests include data mining and computational proteomics","institution_ids":["https://openalex.org/I4210092944"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100320548","display_name":"Xiaoqing Liu","orcid":"https://orcid.org/0000-0003-0982-4615"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqing Liu","raw_affiliation_strings":["Xiaoqing Liu is currently working towards the BS degree in the School of Software at Dalian University of Technology. She is one of the students recommended for admission for MS degree in the School of Software at Dalian University of Technology. Her research interests include bioinformatics and data mining"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xiaoqing Liu is currently working towards the BS degree in the School of Software at Dalian University of Technology. She is one of the students recommended for admission for MS degree in the School of Software at Dalian University of Technology. Her research interests include bioinformatics and data mining","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011120737","display_name":"Jun Wu","orcid":"https://orcid.org/0000-0002-2693-7112"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Wu","raw_affiliation_strings":["Jun Wu is currently working towards the BS degree in the School of Software at Dalian University of Technology. He is one of the students recommended for admission for MS degree in the School of Software at Dalian University of Technology. His research interests include bioinformatics and data mining"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jun Wu is currently working towards the BS degree in the School of Software at Dalian University of Technology. He is one of the students recommended for admission for MS degree in the School of Software at Dalian University of Technology. His research interests include bioinformatics and data mining","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009588567","display_name":"Zengyou He","orcid":"https://orcid.org/0000-0001-9526-8816"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK"],"is_corresponding":true,"raw_author_name":"Zengyou He","raw_affiliation_strings":["received the BS, MS and PhD degrees in computer science from Harbin Institute of Technology, China, in 2000, 2002 and 2006, respectively. He was a research associate in the Department of Electronic and Computer Engineering at the Hong Kong University of Science and Technology from February 2007 to February 2010. Since March 2010, he has been an associate professor in the School of Software at Dalian University of Technology. His research interests include data mining and computational mass spectrometry. Corresponding author. Zengyou He, School of Software, Dalian University of Technology, DaLian, LiaoNing, 116621, China. Tel.: +86-411-87571630"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"received the BS, MS and PhD degrees in computer science from Harbin Institute of Technology, China, in 2000, 2002 and 2006, respectively. He was a research associate in the Department of Electronic and Computer Engineering at the Hong Kong University of Science and Technology from February 2007 to February 2010. Since March 2010, he has been an associate professor in the School of Software at Dalian University of Technology. His research interests include data mining and computational mass spectrometry. Corresponding author. Zengyou He, School of Software, Dalian University of Technology, DaLian, LiaoNing, 116621, China. Tel.: +86-411-87571630","institution_ids":["https://openalex.org/I27357992","https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009588567"],"corresponding_institution_ids":["https://openalex.org/I27357992","https://openalex.org/I889458895"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.885,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.74729044,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"15","issue":"5","first_page":"839","last_page":"855"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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":0.9983000159263611,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9976000189781189,"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/generalization","display_name":"Generalization","score":0.8174577951431274},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7483453154563904},{"id":"https://openalex.org/keywords/categorization","display_name":"Categorization","score":0.6767711639404297},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5653060078620911},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5352998375892639},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.5110403299331665},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.5039297938346863},{"id":"https://openalex.org/keywords/test-data","display_name":"Test data","score":0.49975109100341797},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4514172077178955},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.4503549039363861},{"id":"https://openalex.org/keywords/test","display_name":"Test (biology)","score":0.4160110056400299},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4053216278553009},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09428420662879944}],"concepts":[{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.8174577951431274},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7483453154563904},{"id":"https://openalex.org/C94124525","wikidata":"https://www.wikidata.org/wiki/Q912550","display_name":"Categorization","level":2,"score":0.6767711639404297},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5653060078620911},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5352998375892639},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.5110403299331665},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.5039297938346863},{"id":"https://openalex.org/C16910744","wikidata":"https://www.wikidata.org/wiki/Q7705759","display_name":"Test data","level":2,"score":0.49975109100341797},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4514172077178955},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4503549039363861},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.4160110056400299},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4053216278553009},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09428420662879944},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbt012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt012","pdf_url":"https://academic.oup.com/bib/article-pdf/15/5/839/17488289/bbt012.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23543354","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23543354","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.724.4696","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.724.4696","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://gs1.dlut.edu.cn/newVersion/Files/dsxx/1795.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbt012","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbt012","pdf_url":"https://academic.oup.com/bib/article-pdf/15/5/839/17488289/bbt012.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171649066.pdf"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1565746575","https://openalex.org/W1588644033","https://openalex.org/W1970039616","https://openalex.org/W1972676371","https://openalex.org/W1984875564","https://openalex.org/W1985085054","https://openalex.org/W1995989434","https://openalex.org/W2021177388","https://openalex.org/W2022446852","https://openalex.org/W2038163496","https://openalex.org/W2043794217","https://openalex.org/W2068181796","https://openalex.org/W2076573118","https://openalex.org/W2082637975","https://openalex.org/W2096699854","https://openalex.org/W2098963498","https://openalex.org/W2102025585","https://openalex.org/W2103404876","https://openalex.org/W2104244040","https://openalex.org/W2107201292","https://openalex.org/W2123812510","https://openalex.org/W2126101541","https://openalex.org/W2130277691","https://openalex.org/W2133990480","https://openalex.org/W2134129243","https://openalex.org/W2138573001","https://openalex.org/W2144864517","https://openalex.org/W2145275914","https://openalex.org/W2150541721","https://openalex.org/W2151031196","https://openalex.org/W2155239883","https://openalex.org/W2158714788","https://openalex.org/W2162172965","https://openalex.org/W2167350014","https://openalex.org/W2170678561","https://openalex.org/W2418657672","https://openalex.org/W2502654571","https://openalex.org/W4214553437","https://openalex.org/W6681614728"],"related_works":["https://openalex.org/W4250128246","https://openalex.org/W2933653026","https://openalex.org/W2786391746","https://openalex.org/W3132346564","https://openalex.org/W2914559142","https://openalex.org/W2891480213","https://openalex.org/W4226059458","https://openalex.org/W4381430104","https://openalex.org/W209733029","https://openalex.org/W2991483587"],"abstract_inverted_index":{"Protein":[0],"phosphorylation":[1,24,36,97],"is":[2,39,54,108],"one":[3,51],"of":[4,57,96,104,115,222],"the":[5,55,72,94,112,126,230],"most":[6,139],"pervasive":[7],"post-translational":[8],"modifications,":[9],"regulating":[10],"diverse":[11],"cellular":[12],"processes":[13],"in":[14,34,47,93,119,203,213],"various":[15],"organisms.":[16],"As":[17],"mass":[18],"spectrometry-based":[19],"experimental":[20,148,158],"approaches":[21],"for":[22,63,110,138,150],"identifying":[23],"events":[25],"are":[26,184,235],"resource-intensive,":[27],"many":[28],"computational":[29],"methods":[30,76,92,166,182,198],"have":[31,199],"been":[32],"proposed,":[33],"which":[35,132,237],"site":[37,98],"prediction":[38,99,113,155,172],"formulated":[40],"as":[41],"a":[42,116],"classification":[43],"problem.":[44],"They":[45],"differ":[46],"several":[48],"ways,":[49],"and":[50,60,77,153,193,236],"crucial":[52],"issue":[53],"construction":[56,75,91,130,165,181,197,240],"training":[58,128,238],"data":[59,62,74,90,106,129,164,180,196,234,239],"test":[61,105,179,233],"unbiased":[64,109,185,232],"performance":[65,114,137,202],"evaluation.":[66],"In":[67],"this":[68],"article,":[69],"we":[70,145],"categorize":[71],"existing":[73],"try":[78],"to":[79,87,169,188],"answer":[80,142],"three":[81],"questions:":[82],"(i)":[83,162],"Is":[84],"it":[85],"equivalent":[86],"use":[88],"different":[89,120,163,171,178,189,195,200,204],"assessment":[95],"algorithms?":[100],"(ii)":[101,174],"What":[102],"kind":[103,221],"set":[107],"assessing":[111],"trained":[117],"algorithm":[118,225],"real":[121,190,205],"world":[122,191,206],"scenarios?":[123,140],"(iii)":[124,194],"Among":[125],"summarized":[127],"methods,":[131],"one(s)":[133],"has":[134],"better":[135],"generalization":[136,201,245],"To":[141],"these":[143],"questions,":[144],"conduct":[146],"comprehensive":[147],"studies":[149],"both":[151],"non-kinase-specific":[152],"kinase-specific":[154],"tasks.":[156],"The":[157],"results":[159],"show":[160],"that:":[161],"can":[167,176,242],"lead":[168],"significantly":[170],"performance;":[173],"there":[175],"be":[177],"that":[183],"with":[186],"respect":[187],"scenarios;":[192],"scenarios.":[207],"Therefore,":[208],"when":[209],"developing":[210],"new":[211],"algorithms":[212],"future":[214],"research,":[215],"people":[216],"should":[217],"concentrate":[218],"on":[219],"what":[220,229],"scenario":[223],"their":[224],"will":[226],"work":[227],"for,":[228],"corresponding":[231],"method":[241],"generate":[243],"best":[244],"performance.":[246]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2025-10-10T00:00:00"}
