{"id":"https://openalex.org/W1541995035","doi":"https://doi.org/10.1186/1471-2164-16-s2-s4","title":"Integrating experimental and literature protein-protein interaction data for protein complex prediction","display_name":"Integrating experimental and literature protein-protein interaction data for protein complex prediction","publication_year":2015,"publication_date":"2015-01-21","ids":{"openalex":"https://openalex.org/W1541995035","doi":"https://doi.org/10.1186/1471-2164-16-s2-s4","mag":"1541995035","pmid":"https://pubmed.ncbi.nlm.nih.gov/25708571"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2164-16-s2-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-16-s2-s4","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-16-S2-S4","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Genomics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-16-S2-S4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046020427","display_name":"Yijia Zhang","orcid":"https://orcid.org/0000-0002-5843-4675"},"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":true,"raw_author_name":"Yijia Zhang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023931221","display_name":"Hongfei Lin","orcid":"https://orcid.org/0000-0003-0872-7688"},"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":"Hongfei Lin","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051597671","display_name":"Zhihao Yang","orcid":"https://orcid.org/0000-0001-6186-2024"},"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":"Zhihao Yang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100370523","display_name":"Jian Wang","orcid":"https://orcid.org/0000-0002-9849-7558"},"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":"Jian Wang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology Dalian, Liaoning, China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5046020427"],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":{"value":2690,"currency":"USD","value_usd":2690},"apc_paid":{"value":2690,"currency":"USD","value_usd":2690},"fwci":1.3772,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.79862277,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"16","issue":"S2","first_page":"S4","last_page":"S4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9883000254631042,"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":0.9883000254631042,"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":0.0052999998442828655,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0007999999797903001,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.6976028680801392},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.6539312601089478},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6291927099227905},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.6114053130149841},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.6085354089736938},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.550406277179718},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.4213225543498993},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3831297755241394},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32718294858932495},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24797376990318298},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1711938977241516}],"concepts":[{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.6976028680801392},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.6539312601089478},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6291927099227905},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.6114053130149841},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.6085354089736938},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.550406277179718},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.4213225543498993},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3831297755241394},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32718294858932495},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24797376990318298},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1711938977241516},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":"D011642","descriptor_name":"Publications","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2164-16-s2-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-16-s2-s4","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-16-S2-S4","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Genomics","raw_type":"journal-article"},{"id":"pmid:25708571","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25708571","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":"BMC genomics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4331718","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4331718","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Genomics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2164-16-s2-s4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2164-16-s2-s4","pdf_url":"https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/1471-2164-16-S2-S4","source":{"id":"https://openalex.org/S28614077","display_name":"BMC Genomics","issn_l":"1471-2164","issn":["1471-2164"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Genomics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.6899999976158142,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1541995035.pdf","grobid_xml":"https://content.openalex.org/works/W1541995035.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1967822181","https://openalex.org/W1973346243","https://openalex.org/W1986214964","https://openalex.org/W1987363726","https://openalex.org/W1994505288","https://openalex.org/W2004917988","https://openalex.org/W2050721857","https://openalex.org/W2069074200","https://openalex.org/W2082565035","https://openalex.org/W2084619201","https://openalex.org/W2090422756","https://openalex.org/W2091254101","https://openalex.org/W2103017472","https://openalex.org/W2103316358","https://openalex.org/W2107067224","https://openalex.org/W2108102049","https://openalex.org/W2116117181","https://openalex.org/W2121844933","https://openalex.org/W2136850043","https://openalex.org/W2140280811","https://openalex.org/W2160429376","https://openalex.org/W2163107094","https://openalex.org/W2164928285","https://openalex.org/W2165533101","https://openalex.org/W2167883838"],"related_works":["https://openalex.org/W3132344302","https://openalex.org/W2094822546","https://openalex.org/W4388708026","https://openalex.org/W1969080446","https://openalex.org/W3108941781","https://openalex.org/W2065048840","https://openalex.org/W2082380079","https://openalex.org/W2134206588","https://openalex.org/W1797688090","https://openalex.org/W1977065177"],"abstract_inverted_index":{"BACKGROUND:":[0],"Accurate":[1],"determination":[2],"of":[3,22,29,49,60,130,134,174,184],"protein":[4,30,50,73,117,144,175,199],"complexes":[5,31,51,118,145],"is":[6,96,124],"crucial":[7],"for":[8,72,115],"understanding":[9],"cellular":[10],"organization":[11],"and":[12,43,102,111,136,186],"function.":[13],"High-throughput":[14],"experimental":[15,67],"techniques":[16],"have":[17],"generated":[18],"a":[19,81,112],"large":[20,58],"amount":[21],"protein-protein":[23],"interaction":[24],"(PPI)":[25],"data,":[26,69],"allowing":[27],"prediction":[28,48,201],"from":[32,90,119],"PPI":[33,61,68,88,101,109,122,139,158,167,189],"networks.":[34],"However,":[35],"the":[36,91,120,131,172],"high-throughput":[37,66,100,135,185],"data":[38,62,89,95,105,168,190,195],"often":[39],"includes":[40],"false":[41,44],"positives":[42],"negatives,":[45],"making":[46],"accurate":[47],"difficult.":[52],"METHOD:":[53],"The":[54,160],"biomedical":[55,92,137,165,187],"literature":[56,138,166,188],"contains":[57],"quantities":[59],"that,":[63],"along":[64,191],"with":[65,99,192],"are":[70,146],"valuable":[71],"complex":[74,176,200],"prediction.":[75],"In":[76],"this":[77,150],"study,":[78],"we":[79],"employ":[80],"natural":[82],"language":[83],"processing":[84],"technique":[85],"to":[86,154,196],"extract":[87],"literature.":[93],"This":[94,126],"subsequently":[97],"integrated":[98],"gene":[103,193],"ontology":[104,194],"by":[106,149],"constructing":[107],"attributed":[108,121],"networks,":[110],"novel":[113],"method":[114,127,151,180],"predicting":[116],"networks":[123],"proposed.":[125],"allows":[128],"calculation":[129],"relative":[132],"contribution":[133],"data.":[140],"RESULTS:":[141],"Many":[142],"well-characterized":[143],"accurately":[147],"predicted":[148],"when":[152],"apply":[153],"two":[155],"different":[156],"yeast":[157],"datasets.":[159],"results":[161],"show":[162],"that":[163],"(i)":[164],"can":[169],"effectively":[170],"improve":[171],"performance":[173],"prediction;":[177],"(ii)":[178],"our":[179],"makes":[181],"good":[182],"use":[183],"achieve":[197],"state-of-the-art":[198],"capabilities.":[202]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":4}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
