{"id":"https://openalex.org/W1575390247","doi":"https://doi.org/10.1109/cibcb.2004.1393960","title":"Extracting and mining protein-protein interaction network from biomedical literature","display_name":"Extracting and mining protein-protein interaction network from biomedical literature","publication_year":2005,"publication_date":"2005-03-21","ids":{"openalex":"https://openalex.org/W1575390247","doi":"https://doi.org/10.1109/cibcb.2004.1393960","mag":"1575390247"},"language":"en","primary_location":{"id":"doi:10.1109/cibcb.2004.1393960","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2004.1393960","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IGARSS 2004. 2004 IEEE International Geoscience and Remote Sensing (IEEE Cat. No.04CH37612)","raw_type":"proceedings-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/A5101569679","display_name":"Xiaohua Hu","orcid":"https://orcid.org/0000-0002-4777-3022"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xiaohua Hu","raw_affiliation_strings":["College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","College of Information Science & Technology, Drexel University, Philadelphia, PA, USA"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]},{"raw_affiliation_string":"College of Information Science & Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011662726","display_name":"Illhoi Yoo","orcid":"https://orcid.org/0000-0003-2536-3660"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I. Yoo","raw_affiliation_strings":["College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","College of Information Science & Technology, Drexel University, Philadelphia, PA, USA"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]},{"raw_affiliation_string":"College of Information Science & Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112014361","display_name":"Il-Yeol Song","orcid":null},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I.-Y. Song","raw_affiliation_strings":["College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","College of Information Science & Technology, Drexel University, Philadelphia, PA, USA"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]},{"raw_affiliation_string":"College of Information Science & Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045749444","display_name":"Min Song","orcid":"https://orcid.org/0000-0003-3255-1600"},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Song","raw_affiliation_strings":["College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","College of Information Science & Technology, Drexel University, Philadelphia, PA, USA"],"affiliations":[{"raw_affiliation_string":"College of Information Science and Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]},{"raw_affiliation_string":"College of Information Science & Technology, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101142357","display_name":"Jianchao Han","orcid":null},"institutions":[{"id":"https://openalex.org/I127339247","display_name":"California State University System","ror":"https://ror.org/020qm1538","country_code":"US","type":"education","lineage":["https://openalex.org/I127339247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jianchao Han","raw_affiliation_strings":["Department of Computer Science, California State University, USA","The California State University"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, California State University, USA","institution_ids":["https://openalex.org/I127339247"]},{"raw_affiliation_string":"The California State University","institution_ids":["https://openalex.org/I127339247"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026169909","display_name":"Mark S. Lechner","orcid":null},"institutions":[{"id":"https://openalex.org/I72816309","display_name":"Drexel University","ror":"https://ror.org/04bdffz58","country_code":"US","type":"education","lineage":["https://openalex.org/I72816309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Lechner","raw_affiliation_strings":["Department of Bioscience & BioTech, Drexel University, Philadelphia, PA, USA","Drexel University"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience & BioTech, Drexel University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I72816309"]},{"raw_affiliation_string":"Drexel University","institution_ids":["https://openalex.org/I72816309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101569679"],"corresponding_institution_ids":["https://openalex.org/I72816309"],"apc_list":null,"apc_paid":null,"fwci":1.519,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.80317537,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"244","last_page":"251"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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":0.996399998664856,"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":0.9948999881744385,"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":0.7531687021255493},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6878800392150879},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5807744860649109},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5737789273262024},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.5174863338470459},{"id":"https://openalex.org/keywords/vertex","display_name":"Vertex (graph theory)","score":0.47990477085113525},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4735088646411896},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.42294448614120483},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4185054302215576},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3601808547973633},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3224947452545166},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3142632246017456},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30680686235427856},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15853580832481384},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.14778602123260498},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12124812602996826}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7531687021255493},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6878800392150879},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5807744860649109},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5737789273262024},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.5174863338470459},{"id":"https://openalex.org/C80899671","wikidata":"https://www.wikidata.org/wiki/Q1304193","display_name":"Vertex (graph theory)","level":3,"score":0.47990477085113525},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4735088646411896},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.42294448614120483},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4185054302215576},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3601808547973633},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3224947452545166},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3142632246017456},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30680686235427856},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15853580832481384},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.14778602123260498},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12124812602996826},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/cibcb.2004.1393960","is_oa":false,"landing_page_url":"https://doi.org/10.1109/cibcb.2004.1393960","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IGARSS 2004. 2004 IEEE International Geoscience and Remote Sensing (IEEE Cat. No.04CH37612)","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.706.6346","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.706.6346","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.cis.drexel.edu/faculty/song/publications/CIBCB2004_Best_Paper_Award.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.5099999904632568}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1528914253","https://openalex.org/W1592053870","https://openalex.org/W1670263352","https://openalex.org/W1981086745","https://openalex.org/W2003004389","https://openalex.org/W2008620264","https://openalex.org/W2040615703","https://openalex.org/W2043909051","https://openalex.org/W2065769502","https://openalex.org/W2103931177","https://openalex.org/W2109070394","https://openalex.org/W2122510385","https://openalex.org/W2124634352","https://openalex.org/W2130687290","https://openalex.org/W2136850043","https://openalex.org/W2148512362","https://openalex.org/W2152183901","https://openalex.org/W2155320925","https://openalex.org/W2161466446","https://openalex.org/W2162340487","https://openalex.org/W2167869241","https://openalex.org/W2175110005","https://openalex.org/W3103071483","https://openalex.org/W3143219376","https://openalex.org/W4236521339","https://openalex.org/W4256647194","https://openalex.org/W6635275303","https://openalex.org/W6678794661","https://openalex.org/W6793127252"],"related_works":["https://openalex.org/W4229728790","https://openalex.org/W2800059693","https://openalex.org/W2066232588","https://openalex.org/W4377086792","https://openalex.org/W2767490506","https://openalex.org/W1987705964","https://openalex.org/W1841073402","https://openalex.org/W2106286319","https://openalex.org/W2069244164","https://openalex.org/W3087302704"],"abstract_inverted_index":{"We":[0],"present":[1],"a":[2,41,62,71],"biomedical":[3,26,55,163],"literature":[4,27,164],"data":[5],"mining":[6,161],"system":[7,154],"SPIE-DM":[8,31,145],"(Scalable":[9],"and":[10,14,19,43,115,125,160],"Portable":[11],"Information":[12],"Extraction":[13],"Data":[15],"Mining)":[16],"to":[17,48,76,99,133],"extract":[18,49],"mine":[20,77],"the":[21,50,54,78,85,101,108,111,119,123],"protein-protein":[22,51,59,79],"interaction":[23,52,80],"network":[24,64,86,113],"from":[25,53,162],"such":[28],"as":[29],"MedLine.":[30],"consists":[32],"of":[33,110,122,144],"two":[34],"phases:":[35],"in":[36,84],"phase":[37,67],"1,":[38],"we":[39,69],"develop":[40],"scalable":[42],"portable":[44],"ie":[45],"method":[46,74],"(SPIE)":[47],"literature.":[56],"These":[57],"extracted":[58],"interactions":[60],"form":[61],"scale-free":[63,112],"graph.":[65],"In":[66],"2,":[68],"apply":[70],"novel":[72],"clustering":[73,105],"SFCluster":[75],"network.":[81],"The":[82,104,142],"clusters":[83,137],"graph":[87],"represent":[88],"some":[89],"potential":[90],"protein":[91,102],"complexes,":[92],"which":[93],"are":[94],"very":[95,156],"important":[96],"for":[97,158],"biologist":[98],"study":[100],"functionality.":[103],"algorithm":[106],"considers":[107],"characteristics":[109],"graphs":[114],"is":[116,155],"based":[117],"on":[118,146],"local":[120],"density":[121,140],"vertex":[124],"its":[126],"neighborhood":[127],"functions":[128],"that":[129,152],"can":[130],"be":[131],"used":[132],"find":[134],"more":[135],"meaningful":[136],"at":[138],"different":[139],"levels.":[141],"experiments":[143],"around":[147],"1600":[148],"chromatin":[149],"proteins":[150],"indicate":[151],"our":[153],"promising":[157],"extracting":[159],"databases.":[165]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}