{"id":"https://openalex.org/W1981854862","doi":"https://doi.org/10.4018/jcmam.2010072003","title":"Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval","display_name":"Classification Systems for Bacterial Protein-Protein Interaction Document Retrieval","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W1981854862","doi":"https://doi.org/10.4018/jcmam.2010072003","mag":"1981854862"},"language":"en","primary_location":{"id":"doi:10.4018/jcmam.2010072003","is_oa":false,"landing_page_url":"https://doi.org/10.4018/jcmam.2010072003","pdf_url":null,"source":{"id":"https://openalex.org/S141528356","display_name":"International Journal of Computational Models and Algorithms in Medicine","issn_l":"1947-3133","issn":["1947-3133","1947-3141"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Computational Models and Algorithms in Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5101585391","display_name":"Hongfang Liu","orcid":"https://orcid.org/0000-0003-2570-3741"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hongfang Liu","raw_affiliation_strings":["Georgetown University Medical Center, USA"],"affiliations":[{"raw_affiliation_string":"Georgetown University Medical Center, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028161578","display_name":"Manabu Torii","orcid":"https://orcid.org/0000-0002-4825-0696"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manabu Torii","raw_affiliation_strings":["Georgetown University Medical Center, USA"],"affiliations":[{"raw_affiliation_string":"Georgetown University Medical Center, USA","institution_ids":["https://openalex.org/I2799903593","https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042529505","display_name":"Guixian Xu","orcid":"https://orcid.org/0000-0001-8815-479X"},"institutions":[{"id":"https://openalex.org/I145897649","display_name":"Minzu University of China","ror":"https://ror.org/0044e2g62","country_code":"CN","type":"education","lineage":["https://openalex.org/I145897649"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guixian Xu","raw_affiliation_strings":["Minzu University of China, China"],"affiliations":[{"raw_affiliation_string":"Minzu University of China, China","institution_ids":["https://openalex.org/I145897649"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059160677","display_name":"Johannes B. Goll","orcid":"https://orcid.org/0000-0002-9968-4080"},"institutions":[{"id":"https://openalex.org/I1301553790","display_name":"J. Craig Venter Institute","ror":"https://ror.org/049r1ts75","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1301553790"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Johannes Goll","raw_affiliation_strings":["The J. Craig Venter Institute, USA"],"affiliations":[{"raw_affiliation_string":"The J. Craig Venter Institute, USA","institution_ids":["https://openalex.org/I1301553790"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101585391"],"corresponding_institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0623771,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"1","issue":"1","first_page":"34","last_page":"44"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.992900013923645,"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":0.992900013923645,"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":0.9797000288963318,"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"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9771000146865845,"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":0.8365263938903809},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6537173986434937},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.6025211811065674},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.5132584571838379},{"id":"https://openalex.org/keywords/binary-classification","display_name":"Binary classification","score":0.4655189514160156},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.44045305252075195},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34398967027664185},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29569804668426514},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.137874573469162}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8365263938903809},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6537173986434937},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.6025211811065674},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.5132584571838379},{"id":"https://openalex.org/C66905080","wikidata":"https://www.wikidata.org/wiki/Q17005494","display_name":"Binary classification","level":3,"score":0.4655189514160156},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.44045305252075195},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34398967027664185},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29569804668426514},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.137874573469162},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.4018/jcmam.2010072003","is_oa":false,"landing_page_url":"https://doi.org/10.4018/jcmam.2010072003","pdf_url":null,"source":{"id":"https://openalex.org/S141528356","display_name":"International Journal of Computational Models and Algorithms in Medicine","issn_l":"1947-3133","issn":["1947-3133","1947-3141"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Computational Models and Algorithms in Medicine","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:igg:jcmam0:v:1:y:2010:i:1:p:34-44","is_oa":false,"landing_page_url":"http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/jcmam.2010072003","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.49000000953674316}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1534477342","https://openalex.org/W1551909886","https://openalex.org/W1560724230","https://openalex.org/W1576520375","https://openalex.org/W1965895350","https://openalex.org/W2023450550","https://openalex.org/W2023639956","https://openalex.org/W2053724458","https://openalex.org/W2055271333","https://openalex.org/W2058165281","https://openalex.org/W2098049402","https://openalex.org/W2102162073","https://openalex.org/W2103333826","https://openalex.org/W2109410256","https://openalex.org/W2123958887","https://openalex.org/W2131547811","https://openalex.org/W2135401299","https://openalex.org/W2143516113","https://openalex.org/W2149684865","https://openalex.org/W2161732286","https://openalex.org/W2167277498","https://openalex.org/W2285627996","https://openalex.org/W2435251607","https://openalex.org/W2613161123","https://openalex.org/W3120421331","https://openalex.org/W3142980988","https://openalex.org/W4230674625","https://openalex.org/W4241931738","https://openalex.org/W6634442568","https://openalex.org/W6674674938"],"related_works":["https://openalex.org/W1557094818","https://openalex.org/W2183246718","https://openalex.org/W2099261052","https://openalex.org/W3209204065","https://openalex.org/W2105707930","https://openalex.org/W1755711892","https://openalex.org/W4226316650","https://openalex.org/W4382934300","https://openalex.org/W2121061354","https://openalex.org/W4285388059"],"abstract_inverted_index":{"Protein-protein":[0],"interaction":[1],"(PPI)":[2],"networks":[3,17],"are":[4,42,51,121,126,184],"essential":[5],"to":[6,21,62,90,130,143,209],"understand":[7],"the":[8,46,63,71,105,113,124,193,202,205,210,216],"fundamental":[9],"processes":[10],"governing":[11],"cell":[12],"biology.":[13],"Recently,":[14],"studying":[15],"PPI":[16,81,171],"becomes":[18],"possible":[19],"due":[20],"advances":[22],"in":[23,45,54],"experimental":[24],"high-throughput":[25,34],"genomics":[26],"and":[27,36,49,96,111,123,152,174,215],"proteomics":[28],"technologies.":[29],"Many":[30],"interactions":[31,38],"from":[32,39,169,189],"such":[33,69,132],"studies":[35,41],"most":[37],"small-scale":[40],"reported":[43],"only":[44],"scientific":[47],"literature":[48],"thus":[50],"not":[52],"accessible":[53],"a":[55,150,161,175],"readily":[56],"analyzable":[57],"format.":[58],"This":[59],"has":[60],"led":[61],"birth":[64],"of":[65,80,163,178,182,195,204,207,212,218],"manual":[66,78],"curation":[67,79],"initiatives":[68],"as":[70,115],"International":[72],"Molecular":[73],"Exchange":[74],"Consortium":[75],"(IMEx).":[76],"The":[77],"knowledge":[82,99,172],"can":[83,156,166,186],"be":[84,157,167,187],"accelerated":[85],"by":[86,200],"text":[87],"mining":[88],"systems":[89],"retrieve":[91],"PPI-relevant":[92,98,119],"articles":[93,120],"(article":[94],"retrieval)":[95],"extract":[97],"(information":[100],"extraction).":[101],"In":[102,128],"this":[103],"article,":[104],"authors":[106],"focus":[107],"on":[108],"article":[109],"retrieval":[110],"define":[112],"task":[114],"binary":[116],"classification":[117],"where":[118,160],"positives":[122,208],"others":[125],"negatives.":[127],"order":[129],"build":[131],"classifier,":[133],"an":[134,145],"annotated":[135,146,154],"corpus":[136,147,155],"is":[137,140],"needed.":[138],"It":[139],"very":[141],"expensive":[142],"obtain":[144],"manually":[148],"but":[149],"noisy":[151],"imbalanced":[153],"obtained":[158],"automatically,":[159],"collection":[162],"positive":[164],"documents":[165,180,214],"retrieved":[168,188],"existing":[170],"bases":[173],"large":[176],"number":[177,206,211,217],"unlabeled":[179,213],"(most":[181],"them":[183],"negatives)":[185],"PubMed.":[190],"They":[191],"compared":[192],"performance":[194],"several":[196],"machine":[197],"learning":[198],"algorithms":[199],"varying":[201],"ratio":[203],"features":[219],"used.":[220]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
