{"id":"https://openalex.org/W2018788394","doi":"https://doi.org/10.1108/07378830911007637","title":"Direct use of information extraction from scientific text for modeling and simulation in the life sciences","display_name":"Direct use of information extraction from scientific text for modeling and simulation in the life sciences","publication_year":2009,"publication_date":"2009-11-20","ids":{"openalex":"https://openalex.org/W2018788394","doi":"https://doi.org/10.1108/07378830911007637","mag":"2018788394"},"language":"en","primary_location":{"id":"doi:10.1108/07378830911007637","is_oa":false,"landing_page_url":"https://doi.org/10.1108/07378830911007637","pdf_url":null,"source":{"id":"https://openalex.org/S143568823","display_name":"Library Hi Tech","issn_l":"0737-8831","issn":["0737-8831","2054-166X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319811","host_organization_name":"Emerald Publishing Limited","host_organization_lineage":["https://openalex.org/P4310319811"],"host_organization_lineage_names":["Emerald Publishing Limited"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Library Hi Tech","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/A5017224802","display_name":"Martin Hofman\u2010Apitius","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Hofman\u2010Apitius","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060985142","display_name":"Erfan Younesi","orcid":"https://orcid.org/0000-0001-8793-2692"},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erfan Younesi","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090051941","display_name":"Vinod Kasam","orcid":null},"institutions":[{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Vinod Kasam","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210098248"],"apc_list":null,"apc_paid":null,"fwci":0.135,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.53461281,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"27","issue":"4","first_page":"505","last_page":"519"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9995999932289124,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9973000288009644,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9954000115394592,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8235030174255371},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7213547825813293},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.6075151562690735},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5610349178314209},{"id":"https://openalex.org/keywords/digital-library","display_name":"Digital library","score":0.5321654081344604},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.4981822967529297},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4720737934112549},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.43227261304855347},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3375723958015442},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.21644484996795654},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.13687261939048767},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.12415367364883423},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.10951906442642212}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8235030174255371},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7213547825813293},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.6075151562690735},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5610349178314209},{"id":"https://openalex.org/C513874922","wikidata":"https://www.wikidata.org/wiki/Q212805","display_name":"Digital library","level":3,"score":0.5321654081344604},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.4981822967529297},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4720737934112549},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.43227261304855347},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3375723958015442},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.21644484996795654},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.13687261939048767},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.12415367364883423},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.10951906442642212},{"id":"https://openalex.org/C164913051","wikidata":"https://www.wikidata.org/wiki/Q482","display_name":"Poetry","level":2,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C124952713","wikidata":"https://www.wikidata.org/wiki/Q8242","display_name":"Literature","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1108/07378830911007637","is_oa":false,"landing_page_url":"https://doi.org/10.1108/07378830911007637","pdf_url":null,"source":{"id":"https://openalex.org/S143568823","display_name":"Library Hi Tech","issn_l":"0737-8831","issn":["0737-8831","2054-166X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319811","host_organization_name":"Emerald Publishing Limited","host_organization_lineage":["https://openalex.org/P4310319811"],"host_organization_lineage_names":["Emerald Publishing Limited"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Library Hi Tech","raw_type":"journal-article"},{"id":"pmh:oai:fraunhofer.de:N-118808","is_oa":false,"landing_page_url":"http://publica.fraunhofer.de/documents/N-118808.html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400801","display_name":"Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Fraunhofer SCAI","raw_type":"Conference Paper"},{"id":"pmh:oai:publica.fraunhofer.de:publica/364053","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/364053","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"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":"conference paper"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W121221959","https://openalex.org/W1895993106","https://openalex.org/W1985849948","https://openalex.org/W1989684700","https://openalex.org/W1994306321","https://openalex.org/W2018100041","https://openalex.org/W2033591223","https://openalex.org/W2035530476","https://openalex.org/W2037324626","https://openalex.org/W2040022066","https://openalex.org/W2051554764","https://openalex.org/W2056254608","https://openalex.org/W2057626690","https://openalex.org/W2066669827","https://openalex.org/W2068403353","https://openalex.org/W2069719501","https://openalex.org/W2082853993","https://openalex.org/W2083045667","https://openalex.org/W2091257550","https://openalex.org/W2096080855","https://openalex.org/W2100681757","https://openalex.org/W2106289940","https://openalex.org/W2106901334","https://openalex.org/W2107889007","https://openalex.org/W2125838338","https://openalex.org/W2132773777","https://openalex.org/W2138689719","https://openalex.org/W2141869602","https://openalex.org/W2147880316","https://openalex.org/W2154947819","https://openalex.org/W2156779720","https://openalex.org/W2165742252","https://openalex.org/W2211458005","https://openalex.org/W2287834700","https://openalex.org/W2310083561","https://openalex.org/W2397228500","https://openalex.org/W3200692722"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2040022066","https://openalex.org/W1966944120","https://openalex.org/W1514912413","https://openalex.org/W2168979046","https://openalex.org/W2607044197","https://openalex.org/W2023322671","https://openalex.org/W1986386500","https://openalex.org/W2935815612","https://openalex.org/W2513700792"],"abstract_inverted_index":{"Purpose":[0],"The":[1,131,180,257],"purpose":[2],"of":[3,22,44,69,90,99,108,126,133,146,166,174,216,225,268,291],"this":[4],"paper":[5,56,102],"is":[6,141,161,236],"to":[7,38,49,58,72,79,104,189,207],"demonstrate":[8],"how":[9,109],"the":[10,55,84,95,144,164,171,175,197,223,265,279],"information":[11,218],"extracted":[12,111],"from":[13,112,219],"scientific":[14,91,113,292],"text":[15,61,220],"can":[16,115],"be":[17,36,68,116],"directly":[18,117],"used":[19],"in":[20,47,83,94,120,124,143,157,170,181,196,227,247,289],"support":[21,39,125,290],"life":[23,274],"science":[24,275],"research":[25,30,51,233,276,287],"projects.":[26,129,234,293],"In":[27,199],"modern":[28],"digital\u2010based":[29],"and":[31,42,63,168,193,206,231,253,270,286],"academic":[32,285],"libraries,":[33],"librarians":[34,78,226],"should":[35],"able":[37],"data":[40,240,272],"discovery":[41,65,128,139,177],"organization":[43],"digital":[45,229],"entities":[46],"order":[48],"foster":[50],"projects":[52],"effectively;":[53],"thus":[54],"aims":[57],"speculate":[59],"that":[60,238],"mining":[62],"knowledge":[64,138],"tools":[66,75,140],"could":[67],"great":[70],"assistance":[71],"librarians.":[73],"Such":[74],"simply":[76],"enable":[77],"overcome":[80],"increasing":[81],"complexity":[82],"number":[85],"as":[86,88,135,137],"well":[87,136],"contents":[89],"literature,":[92],"especially":[93],"emerging":[96],"interdisciplinary":[97],"fields":[98],"science.":[100],"This":[101],"seeks":[103],"present":[105],"an":[106,156,243],"example":[107,263],"evidences":[110],"literature":[114],"integrated":[118],"into":[119,273],"silico":[121,158,182],"disease":[122],"models":[123],"drug":[127,151,176],"Design/methodology/approach":[130],"application":[132,283],"text\u2010mining":[134],"explained":[142],"form":[145],"a":[147,261],"knowledge\u2010based":[148,271],"workflow":[149,184],"for":[150,163,191,264],"target":[152],"candidate":[153],"identification.":[154],"Moreover,":[155],"experimentation":[159,183],"framework":[160],"proposed":[162,258],"enhancement":[165],"efficiency":[167],"productivity":[169],"early":[172],"steps":[173],"workflow.":[178],"Findings":[179],"has":[185],"been":[186],"successfully":[187],"applied":[188],"searching":[190],"hit":[192],"lead":[194],"compounds":[195],"World\u2010wide":[198],"Silico":[200],"Docking":[201],"On":[202],"Malaria":[203],"(WISDOM)":[204],"project":[205],"finding":[208],"novel":[209],"inhibitor":[210],"candidates.":[211],"Practical":[212],"implications":[213],"Direct":[214],"extraction":[215],"biological":[217],"will":[221,241],"ease":[222],"task":[224],"managing":[228],"objects":[230],"supporting":[232],"It":[235],"expected":[237],"textual":[239],"play":[242],"increasingly":[244],"important":[245],"role":[246],"evidence\u2010based":[248],"approaches":[249],"taken":[250],"by":[251,284],"biomedical":[252],"translational":[254],"researchers.":[255],"Originality/value":[256],"approach":[259],"provides":[260],"practical":[262],"direct":[266],"integration":[267],"text\u2010":[269],"projects,":[277],"with":[278],"emphasis":[280],"on":[281],"their":[282],"libraries":[288]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
