{"id":"https://openalex.org/W2148282068","doi":"https://doi.org/10.1093/bioinformatics/btk016","title":"BioContrasts: extracting and exploiting protein\u2013protein contrastive relations from biomedical literature","display_name":"BioContrasts: extracting and exploiting protein\u2013protein contrastive relations from biomedical literature","publication_year":2005,"publication_date":"2005-12-20","ids":{"openalex":"https://openalex.org/W2148282068","doi":"https://doi.org/10.1093/bioinformatics/btk016","mag":"2148282068","pmid":"https://pubmed.ncbi.nlm.nih.gov/16368768"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btk016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/597/48838938/bioinformatics_22_5_597.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/22/5/597/48838938/bioinformatics_22_5_597.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050571650","display_name":"Jung\u2010Jae Kim","orcid":"https://orcid.org/0000-0001-6024-0047"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jung-jae Kim","raw_affiliation_strings":["Computer Science Division & AITrc, Korea Advanced Institute of Science and Technology 1 \u00a0 1 \u00a0 \u00a0 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701 South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Division & AITrc, Korea Advanced Institute of Science and Technology 1 \u00a0 1 \u00a0 \u00a0 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701 South Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100429699","display_name":"Zhuo Zhang","orcid":"https://orcid.org/0000-0002-0013-432X"},"institutions":[{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Zhuo Zhang","raw_affiliation_strings":["Knowledge Discovery Department, Institute for Infocomm Research 2 \u00a0 2 \u00a0 \u00a0 21 Heng Mui Keng Terrace, Singapore 119613, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Knowledge Discovery Department, Institute for Infocomm Research 2 \u00a0 2 \u00a0 \u00a0 21 Heng Mui Keng Terrace, Singapore 119613, Singapore","institution_ids":["https://openalex.org/I3005327000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100641120","display_name":"Jong Cheol Park","orcid":"https://orcid.org/0000-0002-8859-5111"},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jong C. Park","raw_affiliation_strings":["Computer Science Division & AITrc, Korea Advanced Institute of Science and Technology 1 \u00a0 1 \u00a0 \u00a0 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701 South Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Division & AITrc, Korea Advanced Institute of Science and Technology 1 \u00a0 1 \u00a0 \u00a0 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701 South Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090171111","display_name":"See-Kiong Ng","orcid":"https://orcid.org/0000-0001-6565-7511"},"institutions":[{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"See-Kiong Ng","raw_affiliation_strings":["Knowledge Discovery Department, Institute for Infocomm Research 2 \u00a0 2 \u00a0 \u00a0 21 Heng Mui Keng Terrace, Singapore 119613, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Knowledge Discovery Department, Institute for Infocomm Research 2 \u00a0 2 \u00a0 \u00a0 21 Heng Mui Keng Terrace, Singapore 119613, Singapore","institution_ids":["https://openalex.org/I3005327000"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5090171111"],"corresponding_institution_ids":["https://openalex.org/I3005327000"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.474,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.62219154,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"22","issue":"5","first_page":"597","last_page":"605"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9794999957084656,"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":0.9794999957084656,"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":0.010999999940395355,"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":0.0012000000569969416,"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":0.723863959312439},{"id":"https://openalex.org/keywords/contrastive-analysis","display_name":"Contrastive analysis","score":0.6107804179191589},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5140131711959839},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4715041220188141},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3679850697517395},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.35669785737991333}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.723863959312439},{"id":"https://openalex.org/C2777629044","wikidata":"https://www.wikidata.org/wiki/Q614959","display_name":"Contrastive analysis","level":2,"score":0.6107804179191589},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5140131711959839},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4715041220188141},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3679850697517395},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.35669785737991333},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003628","descriptor_name":"Database Management Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010506","descriptor_name":"Periodicals as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btk016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/597/48838938/bioinformatics_22_5_597.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:16368768","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16368768","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":"Evaluation Study"},{"id":"pmh:oai:koasas.kaist.ac.kr:10203/3131","is_oa":false,"landing_page_url":"http://hdl.handle.net/10203/3131","pdf_url":null,"source":{"id":"https://openalex.org/S4306402435","display_name":"KAIST Institutional Repository (KAIST)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I157485424","host_organization_name":"Korea Advanced Institute of Science and Technology","host_organization_lineage":["https://openalex.org/I157485424"],"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":{"id":"doi:10.1093/bioinformatics/btk016","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btk016","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/5/597/48838938/bioinformatics_22_5_597.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":[],"funders":[{"id":"https://openalex.org/F4320322348","display_name":"Korea Science and Engineering Foundation","ror":"https://ror.org/013aysd81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2148282068.pdf","grobid_xml":"https://content.openalex.org/works/W2148282068.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W108101778","https://openalex.org/W117665274","https://openalex.org/W136846643","https://openalex.org/W642409479","https://openalex.org/W1493557141","https://openalex.org/W1527927437","https://openalex.org/W1972895912","https://openalex.org/W2038721957","https://openalex.org/W2039612385","https://openalex.org/W2045412364","https://openalex.org/W2061327015","https://openalex.org/W2079611736","https://openalex.org/W2117400858","https://openalex.org/W2127241285","https://openalex.org/W2130687290","https://openalex.org/W2142237411","https://openalex.org/W2152183901","https://openalex.org/W2152653671","https://openalex.org/W2161062388","https://openalex.org/W3088539955","https://openalex.org/W6677437730","https://openalex.org/W6678664594","https://openalex.org/W6782969257"],"related_works":["https://openalex.org/W2945865340","https://openalex.org/W4294495400","https://openalex.org/W2972340244","https://openalex.org/W1834428557","https://openalex.org/W3204019825","https://openalex.org/W2394697227","https://openalex.org/W4306855854","https://openalex.org/W1979243875","https://openalex.org/W3192129151","https://openalex.org/W2399786155"],"abstract_inverted_index":{"MOTIVATION:":[0],"Contrasts":[1],"are":[2,29,47,107,168,207],"useful":[3,75],"conceptual":[4],"vehicles":[5],"for":[6,38,81,103,181],"learning":[7],"processes":[8],"and":[9,26,72,94],"exploratory":[10],"research":[11],"of":[12,30,125,129,142,157,166,187],"the":[13,31,42,53,79,96,110,185],"unknown.":[14],"For":[15],"example,":[16],"contrastive":[17,45,76,89,114,130,143,164],"information":[18,46,77,90,97,106,167],"between":[19,159],"proteins":[20],"can":[21,178,192],"reveal":[22],"what":[23],"similarities,":[24],"divergences":[25],"relations":[27],"there":[28,57],"two":[32],"proteins,":[33],"leading":[34],"to":[35,49,98,146,152],"invaluable":[36],"insights":[37],"better":[39],"understanding":[40],"about":[41],"proteins.":[43],"Such":[44],"found":[48],"be":[50,179,193],"reported":[51,61],"in":[52,63,100,109],"biomedical":[54,65],"literature.":[55],"However,":[56],"have":[58],"been":[59],"no":[60],"attempts":[62],"current":[64],"text":[66,111],"mining":[67],"work":[68],"that":[69,177],"systematically":[70],"extract":[71],"present":[73],"such":[74,117,183],"from":[78,91,135],"literature":[80],"exploitation.":[82,104],"RESULTS:":[83],"Our":[84],"BioContrasts":[85,191],"system":[86],"extracts":[87],"protein-protein":[88],"MEDLINE":[92,138],"abstracts":[93,112],"presents":[95],"biologists":[99],"a":[101,172],"web-application":[102],"Contrastive":[105],"identified":[108],"with":[113],"negation":[115],"patterns":[116],"as":[118,184],"'A":[119],"but":[120],"not":[121],"B'.":[122],"A":[123],"total":[124],"799":[126],"169":[127],"pairs":[128],"expressions":[131],"were":[132,150],"successfully":[133],"extracted":[134],"2.5":[136],"million":[137],"abstracts.":[139],"Using":[140],"grounding":[141],"protein":[144,161],"names":[145],"Swiss-Prot":[147,160],"entries,":[148],"we":[149],"able":[151],"produce":[153],"41":[154],"471":[155],"pieces":[156,165],"contrasts":[158],"entries.":[162],"These":[163],"then":[169],"presented":[170],"via":[171],"user-friendly":[173],"interactive":[174],"web":[175],"portal":[176],"exploited":[180],"applications":[182],"refinement":[186],"biological":[188],"pathways.":[189],"AVAILABILITY:":[190],"accessed":[194],"at":[195,201,209],"http://biocontrasts.i2r.a-star.edu.sg.":[196],"It":[197],"is":[198],"also":[199],"mirrored":[200],"http://biocontrasts.biopathway.org.":[202],"SUPPLEMENTARY":[203],"INFORMATION:":[204],"Supplementary":[205],"materials":[206],"available":[208],"Bioinformatics":[210],"online.":[211]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
