{"id":"https://openalex.org/W2050453845","doi":"https://doi.org/10.1093/bioinformatics/btl084","title":"Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)","display_name":"Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)","publication_year":2006,"publication_date":"2006-03-09","ids":{"openalex":"https://openalex.org/W2050453845","doi":"https://doi.org/10.1093/bioinformatics/btl084","mag":"2050453845","pmid":"https://pubmed.ncbi.nlm.nih.gov/16527834"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl084","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl084","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/6/643/48838528/bioinformatics_22_6_643.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/22/6/643/48838528/bioinformatics_22_6_643.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044841280","display_name":"Udo Hahn","orcid":"https://orcid.org/0000-0002-5052-0245"},"institutions":[{"id":"https://openalex.org/I4210104776","display_name":"Centro Nacional de Biotecnolog\u00eda","ror":"https://ror.org/015w4v032","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210104776"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Udo Hahn","raw_affiliation_strings":["Jena University, National Center for Biotechnology \u00a0 CNB-CSIC, Madrid ( Valencia@cnb.uam.es ), ( Udo.Hahn@uni-jena.de )"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jena University, National Center for Biotechnology \u00a0 CNB-CSIC, Madrid ( Valencia@cnb.uam.es ), ( Udo.Hahn@uni-jena.de )","institution_ids":["https://openalex.org/I4210104776"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015217651","display_name":"Alfonso Valencia","orcid":"https://orcid.org/0000-0002-8937-6789"},"institutions":[{"id":"https://openalex.org/I4210104776","display_name":"Centro Nacional de Biotecnolog\u00eda","ror":"https://ror.org/015w4v032","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210104776"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alfonso Valencia","raw_affiliation_strings":["Jena University, National Center for Biotechnology \u00a0 CNB-CSIC, Madrid ( Valencia@cnb.uam.es ), ( Udo.Hahn@uni-jena.de )"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jena University, National Center for Biotechnology \u00a0 CNB-CSIC, Madrid ( Valencia@cnb.uam.es ), ( Udo.Hahn@uni-jena.de )","institution_ids":["https://openalex.org/I4210104776"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210104776"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.0921838,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"22","issue":"6","first_page":"643","last_page":"644"},"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9840999841690063,"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"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9226999878883362,"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/biomedicine","display_name":"Biomedicine","score":0.8299678564071655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.52755206823349},{"id":"https://openalex.org/keywords/library-science","display_name":"Library science","score":0.4377608299255371},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1644842028617859},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0962083637714386}],"concepts":[{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.8299678564071655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.52755206823349},{"id":"https://openalex.org/C161191863","wikidata":"https://www.wikidata.org/wiki/Q199655","display_name":"Library science","level":1,"score":0.4377608299255371},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1644842028617859},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0962083637714386}],"mesh":[{"descriptor_ui":"D001698","descriptor_name":"Biomedical Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001698","descriptor_name":"Biomedical Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001698","descriptor_name":"Biomedical Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016206","descriptor_name":"Databases, Bibliographic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016206","descriptor_name":"Databases, Bibliographic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016206","descriptor_name":"Databases, Bibliographic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl084","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl084","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/6/643/48838528/bioinformatics_22_6_643.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:16527834","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16527834","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":"Editorial"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl084","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl084","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/6/643/48838528/bioinformatics_22_6_643.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":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2050453845.pdf","grobid_xml":"https://content.openalex.org/works/W2050453845.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1994313017","https://openalex.org/W2121940249","https://openalex.org/W2124617249","https://openalex.org/W2126276057","https://openalex.org/W2126469373","https://openalex.org/W2151598682","https://openalex.org/W2157317150","https://openalex.org/W6678097469","https://openalex.org/W6808054400"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2017899917","https://openalex.org/W2080571363","https://openalex.org/W2481322495","https://openalex.org/W2898682754","https://openalex.org/W2889841093","https://openalex.org/W4246603716","https://openalex.org/W2151082141","https://openalex.org/W2365236913","https://openalex.org/W3194374240"],"abstract_inverted_index":{"Researchers":[0],"working":[1],"in":[2,7,40,89,150,206,338,365,407,413,497,515,537,551,566,608,615,660,695,706,770,815,840,843,928,940,973,983,1002,1049,1185,1268,1280,1311,1351,1410,1430,1444,1470],"the":[3,8,18,35,82,138,147,166,176,214,269,297,344,366,394,399,446,465,475,499,510,516,529,538,555,601,621,704,707,735,759,780,786,792,816,836,950,954,963,974,995,1003,1006,1019,1088,1121,1128,1145,1176,1196,1215,1224,1264,1281,1316,1328,1336,1352,1360,1368,1416,1459,1466],"life":[4,817],"sciences":[5,818],"domain":[6,79,886],"past":[9],"years":[10,517],"have":[11,56,102,524,570,715,757,1479],"witnessed":[12],"an":[13,353,747,1102],"enormous":[14],"growth":[15],"of":[16,29,34,51,85,106,115,191,271,299,343,346,355,403,426,469,477,490,501,512,528,554,558,579,610,623,656,666,678,693,738,761,764,802,809,830,869,936,952,997,1005,1025,1032,1047,1059,1090,1095,1140,1153,1172,1199,1204,1218,1227,1266,1286,1318,1323,1330,1338,1354,1384,1391,1396,1418,1447,1451,1461,1468,1483],"literature\u2014for":[17],"whole":[19],"field":[20],"as":[21,23,242,429,431,436,456,472,474,890,892,1189,1363],"well":[22,430,457,473,891],"for":[24,178,254,317,382,503,534,653,724,970,981,1074,1456,1464],"their":[25,591,873,971,1066,1428],"highly":[26,77,108],"specialized":[27],"areas":[28,208],"expertise.":[30],"Only":[31],"small":[32],"portions":[33],"biomedical":[36,86,96,350,504,539,543,630,900,1228],"knowledge":[37,54,87,447,471,631,667,901],"are":[38,98,143,173,377,433,576,604,617,745,1160,1178,1275,1327,1349,1436],"accessible":[39],"a":[41,128,135,153,170,197,245,255,318,349,391,441,567,571,673,696,762,800,820,934,1151,1208,1231,1243,1355,1381,1480],"structured":[42],"way,":[43],"i.e.":[44],"through":[45,904],"formatted":[46],"databases.":[47,662],"These":[48],"few":[49],"pieces":[50,287],"textually":[52],"encoded":[53],"that":[55,201,384,614,720,749,957,1233,1348,1358],"gone":[57],"into":[58,70],"databases":[59,71,97,329],"are,":[60],"by":[61,76,122,184,213,779,852,1077,1211,1292,1333,1399,1441],"default,":[62],"manually":[63,68],"extracted":[64],"from":[65,140,152,162,210,226,348,390,562,641,741,847,1087,1144,1181,1214,1290,1305,1408],"documents":[66,151,229,642],"and":[67,111,250,253,263,312,321,326,330,332,467,480,487,506,575,587,597,600,767,790,812,825,858,878,884,931,945,966,989,1009,1039,1052,1056,1065,1083,1127,1134,1150,1246,1251,1255,1259,1270,1302,1308,1335,1404,1427,1463],"inserted":[69],"after":[72,985],"careful":[73],"curation":[74],"efforts":[75],"skilled":[78],"experts.":[80],"Still,":[81],"vast":[83],"majority":[84],"captured":[88,671],"texts":[90],"is":[91,120,293,352,361,545,636,651,872,1098,1118,1234,1261,1370],"not":[92],"at":[93,221,296,923],"disposal":[94],"when":[95,1477],"queried.":[99],"Life":[100],"scientists":[101,960],"realized":[103],"this":[104,141,462,664,691,710,742,941],"loss":[105],"possibly":[107],"relevant":[109,224,235,277,285],"information":[110,123,225,286,290,313,694,911,1130,1141],"devised":[112],"various":[113],"forms":[114,425],"support.":[116],"The":[117,341,358,520,753,796,828,1012,1092,1115,1137,1158,1240,1273,1313,1413,1432],"weakest":[118],"one":[119],"provided":[121,1131],"retrieval":[124,1249],"(IR)":[125],"systems":[126,280,406,714,937],"[for":[127,819,933],"life-science-centred":[129,256,821],"survey;":[130],"cf.":[131,248,258,316,823],"Hersh":[132],"(2002)].":[133],"Given":[134],"user-formulated":[136],"query":[137,142,167],"terms":[139,148,565,609,1108,1435],"appropriately":[144],"matched":[145],"with":[146,386,620,1101,1166,1230,1277,1380,1393,1438],"occurring":[149],"large":[154,674,1481],"collection":[155],"(e.g.":[156,189,328,594,607,643],"the,":[157],"currently,":[158,397],"14":[159],"million":[160,1155],"abstracts":[161,996],"Medline).":[163],"Documents":[164],"matching":[165,1182],"(up":[168],"to":[169,175,284,452,464,518,548,582,589,639,689,703,734,805,897,925,1034,1120,1195,1236,1263,1372],"specified":[171],"degree)":[172],"returned":[174],"user":[177],"closer":[179],"inspection":[180],"and,":[181,699],"possibly,":[182],"ranked":[183],"some":[185,527],"relevance-based":[186],"sorting":[187],"criterion":[188],"closeness":[190],"match).":[192],"Information":[193,404],"extraction":[194,314],"(IE)":[195],"provides":[196],"more":[198],"powerful":[199],"alternative":[200],"has":[202,668,776,798],"mainly":[203,363],"been":[204,669,777],"developed":[205,723],"other":[207,1186],"different":[209,1387],"molecular":[211,929],"biology":[212,616,930],"natural":[215,227],"language":[216,228,303],"processing":[217,304],"community.":[218],"IE":[219,279,383],"aims":[220],"directly":[222],"extracting":[223,1319],"[usually":[230],"original":[231],"text":[232,437,453,491,535,712,813,907,915,1029],"snippets,":[233],"sentences,":[234],"phrases":[236],"or":[237,584,612,888,908,913,1376],"even":[238],"quasi-logical":[239],"propositions,":[240],"such":[241,1188],"predicate\u2013argument":[243],"structures\u2014for":[244],"general":[246],"survey,":[247,319,822],"Gaizauskas":[249],"Wilks":[251],"(1998)":[252],"view,":[257],"Blaschke":[259,420],"et":[260,265,415,421],"al.":[261,266,416,422],"(2002)":[262],"Hoffmann":[264],"(2005)].":[267,423,947,1011],"Unlike":[268],"output":[270],"IR":[272,339,359,428],"systems,":[273],"which":[274,1326,1471],"only":[275],"list":[276],"documents,":[278],"provide":[281],"immediate":[282],"access":[283],"via":[288],"pre-specified":[289],"templates.":[291],"This":[292,484,649,1449],"achieved,":[294],"however,":[295,523],"price":[298],"supplying":[300],"rather":[301],"sophisticated":[302],"methodologies":[305,335,877,918],"[e.g.":[306],"taggers,":[307],"chunkers,":[308],"light":[309],"semantic":[310,879],"interpreters":[311],"rules;":[315],"Hahn":[320],"Wermter":[322],"(2006)],":[323],"domain-specific":[324],"developments":[325,514],"resources":[327],"ontologies)":[331],"machine":[333],"learning":[334],"usually":[336,450],"lack":[337],"systems.":[340],"evaluation":[342,380],"degree":[345],"achievements":[347],"perspective":[351,449],"issue":[354],"active":[356],"research.":[357],"stream":[360],"currently":[362,938],"investigated":[364],"TREC":[367],"(Text":[368],"Retrieval":[369],"Conference)":[370],"Genomics":[371],"track":[372],"(Author":[373,410],"Webpage),":[374],"whereas":[375],"there":[376],"several":[378],"challenge":[379,521,1149],"platforms":[381],"deal":[385,549],"often":[387,434,577,618],"complementary":[388],"problems":[389,533,756,927],"biological":[392,564,661,1200,1324],"perspective,":[393],"most":[395,530,1192],"important,":[396],"being":[398,919],"BioCreAtIvE":[400],"(Critical":[401],"Assessment":[402],"Extraction":[405,1285],"Biology)":[408],"contest":[409],"Webpage)":[411],"[surveyed":[412],"Hirschman":[414],"(2005);":[417],"see":[418,943],"also":[419,637],"Both":[424],"activities,":[427],"IE,":[432],"labelled":[435],"mining":[438,454,492,713,811,814],"but":[439],"miss":[440],"major":[442],"extra":[443],"requirement,":[444],"namely":[445,687],"discovery":[448],"attributed":[451],"procedures":[455],"(Hearst,":[458],"1999).":[459],"In":[460,541,1366],"particular,":[461,542],"relates":[463],"identification":[466,1046,1058,1245],"elimination":[468],"redundant":[470],"recognition":[476],"(user-new?,":[478],"expert-new?":[479],"community-new?)":[481],"novel":[482],"information.":[483,1114,1365],"value-adding,":[485],"summarizing":[486],"selective":[488],"aspect":[489],"could":[493],"be":[494,509,1237,1454,1475],"particularly":[495],"helpful":[496],"taming":[498],"flood":[500],"literature":[502],"researchers,":[505],"will":[507],"certainly":[508],"focus":[511,874],"new":[513,1060,1062,1221,1420,1434],"come.":[519],"evaluations,":[522],"already":[525],"revealed":[526],"pressing":[531],"research":[532,755,1016],"analysis":[536],"domain.":[540],"terminology":[544],"extremely":[546],"hard":[547,638],"with,":[550],"part":[552],"because":[553],"poor":[556],"introduction":[557],"standards.":[559],"It":[560],"starts":[561],"identifying":[563,1419],"document":[568,905],"(terms":[569],"complex":[572],"internal":[573],"structure":[574],"composed":[578],"multiple,":[580],"up":[581,1458],"four":[583],"five,":[585],"words),":[586],"leads":[588],"determining":[590],"conceptual":[592],"type":[593,1450],"genes,":[595],"proteins":[596],"cell":[598],"lines)":[599],"way":[602,702],"they":[603,1478],"relationally":[605],"linked":[606],"taxonomies":[611],"partonomies":[613],"related":[619,1119,1282],"organization":[622],"protein":[624,647,1331],"families).":[625],"Further":[626],"on,":[627],"concrete":[628],"factual":[629],"(sometimes":[632],"called":[633],"relation":[634],"mining)":[635],"extract":[640,1373],"\u2018protein":[644],"X":[645],"inhibits":[646],"Y\u2019).":[648],"step":[650],"crucial":[652],"any":[654],"sort":[655],"automated":[657],"functional":[658],"annotation":[659],"Once":[663],"kind":[665],"successfully":[670],"on":[672,875,1106,1170,1223],"scale":[675],"making":[676],"thousands":[677],"these":[679,806,831,998],"propositions":[680],"available,":[681],"another":[682],"severe":[683],"follow-up":[684],"problem":[685,1094,1317,1417],"arises,":[686],"how":[688],"communicate":[690],"mass":[692],"concise,":[697],"comprehensible":[698],"finally,":[700],"useful":[701,1455],"researcher":[705],"laboratory.":[708],"For":[709],"purpose,":[711],"simply":[716],"borrowed":[717],"visualization":[718],"techniques":[719],"were":[721,979,1142],"originally":[722],"numerical":[725],"data":[726,810],"mining.":[727,916],"However,":[728],"symbolic":[729],"abstraction":[730],"mechanisms":[731],"leading,":[732],"e.g.":[733,903],"automatic":[736],"generation":[737],"pathway":[739],"diagrams":[740],"huge":[743],"dataset":[744],"still":[746,1179],"area":[748],"requires":[750],"further":[751],"developments.":[752],"above-mentioned":[754],"motivated":[758,1257],"creation":[760],"Network":[763],"Excellence\u2014\u2018Semantic":[765],"Interoperability":[766],"Data":[768],"Mining":[769,839],"Biomedicine\u2019":[771,841],"(Semantic":[772],"Mining,":[773],"Author":[774,864],"Webpage)\u2014which":[775],"funded":[778],"European":[781,793],"Community":[782],"since":[783],"2004":[784],"under":[785,835,1018],"FP6":[787],"Programme":[788],"\u2018Integrating":[789],"Strengthening":[791],"Research":[794,1307],"Area\u2019.":[795],"NoE":[797],"initiated":[799],"series":[801],"conferences":[803],"dedicated":[804],"particular":[807],"challenges":[808],"Ananiadou":[824],"McNaught":[826],"(2006)].":[827],"first":[829],"symposia":[832],"was":[833],"held":[834],"title":[837],"\u2018Semantic":[838],"(SMBM)":[842],"Hinxton":[844,862],"(Cambridgeshire,":[845],"UK)":[846],"April":[848],"10\u201313,":[849],"2005":[850],"organized":[851],"Stefan":[853],"Schulz,":[854],"Freiburg":[855],"University":[856,1089,1216],"Hospital,":[857],"Dietrich":[859],"Rebholz-Schuhmann,":[860],"EBI-EMBL,":[861],"(see":[863],"Webpage).":[865],"A":[866],"specific":[867],"feature":[868],"SMBM":[870],"meetings":[871],"content-oriented":[876],"resources\u2014either":[880],"controlled":[881],"vocabularies,":[882],"terminologies":[883],"formal":[885],"ontologies,":[887],"conceptually":[889],"propositionally":[893],"annotated":[894],"corpora\u2014in":[895],"order":[896],"improve":[898],"text-based":[899],"management,":[902],"classification,":[906],"fact":[909],"retrieval,":[910],"extraction,":[912],"(real)":[914],"Also":[917],"discussed":[920],"should":[921],"look":[922],"applications":[924],"real-world":[926],"biomedicine":[932],"review":[935],"operational":[939],"domain,":[942],"Krallinger":[944],"Valencia":[946,1010],"We":[948],"had":[949],"honour":[951],"chairing":[953],"programme":[955],"committee":[956],"comprised":[958],"21":[959],"who":[961],"evaluated":[962],"28":[964],"submissions":[965],"selected":[967,980,999,1013],"12":[968],"papers":[969,978,993,1014],"presentation":[972],"conference.":[975],"Four":[976],"outstanding":[977],"publication":[982],"Bioinformatics,":[984],"additional":[986,1112,1197],"extensive":[987],"reviews":[988],"revisions.":[990],"Seven":[991],"full":[992],"plus":[994],"presentations":[1000],"appeared":[1001],"proceedings":[1004],"conference":[1007],"[Hahn":[1008],"cover":[1015],"performed":[1017],"following":[1020],"headings:":[1021],"(1)":[1022],"entity":[1023],"identification\u2014identification":[1024],"gene":[1026,1053,1147,1339,1377],"names,":[1027],"(2)":[1028],"classification":[1030,1265],"classification\u2014assignment":[1031],"sentences":[1033,1143,1267],"known":[1035],"Gene":[1036],"Ontology":[1037],"(GO)":[1038],"Medical":[1040],"Subject":[1041],"Headings":[1042],"(MeSH)":[1043],"classes,":[1044],"(3)":[1045],"relations":[1048,1429],"text\u2014extracting":[1050],"phosphorylation":[1051,1334],"control":[1054,1337],"networks;":[1055],"(4)":[1057],"concepts\u2014proposing":[1061],"GO":[1063,1271,1392,1421,1425,1472],"categories":[1064,1229,1469],"corresponding":[1067],"associated":[1068],"genes.":[1069,1173],"Automatic":[1070,1202,1389],"Term":[1071],"List":[1072],"Generation":[1073],"Entity":[1075],"Tagging":[1076],"Ted":[1078],"Sandler,":[1079],"Andrew":[1080],"I.":[1081],"Schein":[1082],"Lyle":[1084],"H.":[1085],"Ungar":[1086],"Pennsylvania.":[1091],"basic":[1093,1138],"term":[1096],"characterization":[1097],"tackled":[1099],"here":[1100],"unsupervised":[1103],"approach":[1104,1117],"based":[1105,1169],"clustering":[1107,1116,1123],"(gene":[1109],"names)":[1110],"using":[1111,1423],"context":[1113,1129],"distributional":[1122],"technique":[1124],"published":[1125],"previously":[1126],"include":[1132],"neighbouring":[1133],"syntactic":[1135],"relations.":[1136],"sources":[1139],"Biocreative":[1146],"tagging":[1148],"set":[1152],"two":[1154,1320],"Medline":[1156,1291],"abstracts.":[1157],"results":[1159,1177,1222,1274],"significantly":[1161],"better":[1162],"than":[1163],"those":[1164,1183,1278,1439],"obtained":[1165,1184,1279],"standard":[1167],"taggers":[1168],"dictionaries":[1171],"Interestingly":[1174],"enough,":[1175],"far":[1180],"domains":[1187],"newswire":[1190],"information,":[1191,1258],"probably":[1193],"owing":[1194],"complexity":[1198],"nomenclature.":[1201],"Assignment":[1203],"Biomedical":[1205],"Categories:":[1206],"Toward":[1207],"Generic":[1209],"Approach":[1210],"Patrick":[1212],"Ruch":[1213],"Hospitals":[1217],"Geneva.":[1219],"Describes":[1220],"automatical":[1225],"assignment":[1226],"system":[1232,1241,1344,1369],"designed":[1235],"largely":[1238],"data-independent.":[1239],"includes":[1242],"pattern-based":[1244],"vector":[1247],"space":[1248],"engine,":[1250],"uses":[1252,1345,1359],"both":[1253,1310],"stems":[1254],"linguistically":[1256],"it":[1260],"applied":[1262],"MeSH":[1269],"classes.":[1272],"compared":[1276,1437],"BioCreative":[1283],"task.":[1284],"Regulatory":[1287],"Gene/Protein":[1288],"Networks":[1289],"Jasmin":[1293],"Saric,":[1294],"Lars":[1295],"Juhl":[1296],"Jensen,":[1297],"Rossitza":[1298],"Ouzounova,":[1299],"Isabel":[1300],"Rojas":[1301],"Peer":[1303],"Bork,":[1304],"EML":[1306],"EMBL":[1309],"Heidelberg.":[1312],"authors":[1314,1414],"address":[1315],"key":[1321],"types":[1322],"relations,":[1325,1379],"regulators":[1329],"function":[1332],"expression.":[1340],"Their":[1341],"rule-based":[1342],"String-IE":[1343],"organism-specific":[1346],"lexicons":[1347],"incorporated":[1350],"training":[1353],"part-of-speech":[1356],"tagger":[1357],"GENIA":[1361],"corpus":[1362],"background":[1364],"practice,":[1367],"able":[1371],"3319":[1374],"phosphorylations":[1375],"expression":[1378],"sustained":[1382],"level":[1383],"accuracy":[1385],"across":[1386],"organisms.":[1388],"Extension":[1390],"Flexible":[1394],"Identification":[1395],"Candidate":[1397],"Terms":[1398],"Jin-Bok":[1400],"Lee,":[1401],"Jung-jae":[1402],"Kim":[1403],"Jong":[1405],"C.":[1406],"Park":[1407],"KAIST":[1409],"Daejeon,":[1411],"Korea.":[1412],"tackle":[1415],"concepts":[1422,1426,1473],"existing":[1424],"text.":[1431],"proposed":[1433],"created":[1440],"human":[1442],"experts":[1443],"subsequent":[1445],"releases":[1446],"GO.":[1448],"approaches":[1452],"can":[1453,1474],"speeding":[1457],"process":[1460],"annotation,":[1462],"increasing":[1465],"number":[1467,1482],"divided":[1476],"genes":[1484],"assigned.":[1485]},"counts_by_year":[{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2016-06-24T00:00:00"}
