{"id":"https://openalex.org/W1999665498","doi":"https://doi.org/10.1109/bibm.2012.6392739","title":"PPIExtractor: A protein-protein interaction Extractor for biomédical literature","display_name":"PPIExtractor: A protein-protein interaction Extractor for biomédical literature","publication_year":2012,"publication_date":"2012-10-01","ids":{"openalex":"https://openalex.org/W1999665498","doi":"https://doi.org/10.1109/bibm.2012.6392739","mag":"1999665498"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2012.6392739","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392739","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"},"type":"conference-paper","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/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, China","College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042620633","display_name":"Zhehuan Zhao","orcid":"https://orcid.org/0000-0002-5001-1352"},"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":"Zhehuan Zhao","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China","College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100718350","display_name":"Yanpeng Li","orcid":"https://orcid.org/0000-0003-3365-6092"},"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":"Yanpeng Li","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China","College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086780706","display_name":"Yuncui Hu","orcid":null},"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":"Yuncui Hu","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China","College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","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, China","College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China 116023#TAB#","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9890999794006348,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9688000082969666,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/computer-science","display_name":"Computer science","score":0.7647275924682617},{"id":"https://openalex.org/keywords/extractor","display_name":"Extractor","score":0.7527146339416504},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.525146484375},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5081708431243896},{"id":"https://openalex.org/keywords/convolution","display_name":"Convolution (computer science)","score":0.4641161561012268},{"id":"https://openalex.org/keywords/feature-extraction","display_name":"Feature extraction","score":0.45832693576812744},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4558623135089874},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.44961613416671753},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4220707416534424},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4163752794265747},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4127150774002075},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37527307868003845},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3280867338180542},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20935392379760742},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.13365983963012695},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11396041512489319},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.10073328018188477}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7647275924682617},{"id":"https://openalex.org/C117978034","wikidata":"https://www.wikidata.org/wiki/Q5422192","display_name":"Extractor","level":2,"score":0.7527146339416504},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.525146484375},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5081708431243896},{"id":"https://openalex.org/C45347329","wikidata":"https://www.wikidata.org/wiki/Q5166604","display_name":"Convolution (computer science)","level":3,"score":0.4641161561012268},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.45832693576812744},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4558623135089874},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.44961613416671753},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4220707416534424},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4163752794265747},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4127150774002075},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37527307868003845},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3280867338180542},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20935392379760742},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.13365983963012695},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11396041512489319},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.10073328018188477},{"id":"https://openalex.org/C21880701","wikidata":"https://www.wikidata.org/wiki/Q2144042","display_name":"Process engineering","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2012.6392739","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2012.6392739","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE International Conference on Bioinformatics and Biomedicine","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.7200000286102295,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W86561409","https://openalex.org/W1559664142","https://openalex.org/W1973406306","https://openalex.org/W1980127292","https://openalex.org/W1981805898","https://openalex.org/W1981933378","https://openalex.org/W1987818105","https://openalex.org/W1990794790","https://openalex.org/W1996699506","https://openalex.org/W2062163602","https://openalex.org/W2064030835","https://openalex.org/W2071993998","https://openalex.org/W2103017472","https://openalex.org/W2103316358","https://openalex.org/W2108010925","https://openalex.org/W2114361266","https://openalex.org/W2115880858","https://openalex.org/W2122904379","https://openalex.org/W2126690563","https://openalex.org/W2127713198","https://openalex.org/W2129113459","https://openalex.org/W2132288458","https://openalex.org/W2138627627","https://openalex.org/W2141605886","https://openalex.org/W2144255051","https://openalex.org/W2166111585","https://openalex.org/W2169250301","https://openalex.org/W3140879122","https://openalex.org/W6603577330","https://openalex.org/W6679091061"],"related_works":["https://openalex.org/W3082848404","https://openalex.org/W1979583797","https://openalex.org/W2016864125","https://openalex.org/W2372254676","https://openalex.org/W2080135837","https://openalex.org/W2793679056","https://openalex.org/W3145050838","https://openalex.org/W4283332091","https://openalex.org/W2393154870","https://openalex.org/W4237873526"],"abstract_inverted_index":{"Knowledge":[0],"about":[1],"protein-protein":[2],"interactions":[3],"(PPIs)":[4],"unveils":[5],"the":[6,51,73],"molecular":[7],"mechanisms":[8],"of":[9],"biological":[10],"processes.":[11],"In":[12],"this":[13],"paper,":[14],"we":[15],"present":[16],"a":[17,34,86],"PPI":[18,74],"extraction":[19],"system,":[20],"termed":[21],"PPIExtractor,":[22],"which":[23],"automatically":[24],"extracts":[25],"PPIs":[26],"from":[27],"biomedical":[28],"text":[29],"and":[30,64,70],"visualizes":[31,72],"them.":[32],"Given":[33],"Medline":[35],"record":[36],"dataset,":[37],"PPIExtractor":[38,80,94],"first":[39],"applies":[40],"Feature":[41],"Coupling":[42],"Generalization":[43],"(FCG)":[44],"to":[45,56,67,91],"tag":[46],"protein":[47],"names,":[48],"next":[49],"uses":[50],"extended":[52],"semantic":[53],"similarity-based":[54],"method":[55],"normalize":[57],"them,":[58],"then":[59],"combines":[60],"feature-based,":[61],"convolution":[62],"tree":[63],"graph":[65],"kernels":[66],"extract":[68],"PPIs,":[69],"finally":[71],"network.":[75],"Experimental":[76],"evaluations":[77],"show":[78],"that":[79],"can":[81],"achieve":[82],"state-of-the-art":[83],"performance":[84],"on":[85],"DIP":[87],"subset":[88],"with":[89],"respect":[90],"comparable":[92],"evaluations.":[93],"is":[95],"freely":[96],"available":[97],"for":[98],"academic":[99],"purposes":[100],"at:":[101],"http://202.118.75.18:8080/PPIExtractor/.":[102]},"counts_by_year":[{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}