{"id":"https://openalex.org/W2056567523","doi":"https://doi.org/10.1142/s0219720010005014","title":"A RE-EVALUATION OF BIOMEDICAL NAMED ENTITY\u2013TERM RELATIONS","display_name":"A RE-EVALUATION OF BIOMEDICAL NAMED ENTITY\u2013TERM RELATIONS","publication_year":2010,"publication_date":"2010-07-15","ids":{"openalex":"https://openalex.org/W2056567523","doi":"https://doi.org/10.1142/s0219720010005014","mag":"2056567523","pmid":"https://pubmed.ncbi.nlm.nih.gov/20981895"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720010005014","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010005014","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5007825608","display_name":"Tomoko Ohta","orcid":"https://orcid.org/0000-0002-9418-8352"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"TOMOKO OHTA","raw_affiliation_strings":["Department of Computer Science, University of Tokyo, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066925770","display_name":"Sampo Pyysalo","orcid":"https://orcid.org/0000-0002-6279-5000"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"SAMPO PYYSALO","raw_affiliation_strings":["Department of Computer Science, University of Tokyo, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063923711","display_name":"Jin-Dong Kim","orcid":"https://orcid.org/0000-0001-9660-6303"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"JIN-DONG KIM","raw_affiliation_strings":["Department of Computer Science, University of Tokyo, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112241147","display_name":"Jun\u2019ichi Tsujii","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["GB","JP"],"is_corresponding":false,"raw_author_name":"JUN'ICHI TSUJII","raw_affiliation_strings":["Department of Computer Science, University of Tokyo, Tokyo, Japan","National Centre for Text Mining, University of Manchester, Manchester, UK","School of Computer Science, University of Manchester, Manchester, UK"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"National Centre for Text Mining, University of Manchester, Manchester, UK","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"School of Computer Science, University of Manchester, Manchester, UK","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007825608"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":null,"apc_paid":null,"fwci":1.4539,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.80727588,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"08","issue":"05","first_page":"917","last_page":"928"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.98580002784729,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9602000117301941,"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":0.7073993682861328},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.7049121260643005},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.6429663896560669},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.6310351490974426},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6276611089706421},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5938259363174438},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5747705698013306},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5710850954055786},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.5578363537788391},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.532603919506073},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.5168383717536926},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5139772295951843},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4985237121582031},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4773956835269928},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.39266109466552734},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3887467384338379},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2559736371040344},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.2119966447353363},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08302059769630432},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06836158037185669}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7073993682861328},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.7049121260643005},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.6429663896560669},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.6310351490974426},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6276611089706421},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5938259363174438},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5747705698013306},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5710850954055786},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.5578363537788391},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.532603919506073},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.5168383717536926},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5139772295951843},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4985237121582031},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4773956835269928},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.39266109466552734},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3887467384338379},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2559736371040344},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.2119966447353363},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08302059769630432},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06836158037185669},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000592","qualifier_name":"standards","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720010005014","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720010005014","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:20981895","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20981895","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.5}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W32302389","https://openalex.org/W1482328859","https://openalex.org/W1850865022","https://openalex.org/W1963925644","https://openalex.org/W1977748891","https://openalex.org/W2032566933","https://openalex.org/W2056616115","https://openalex.org/W2075655036","https://openalex.org/W2078288474","https://openalex.org/W2099369363","https://openalex.org/W2101727078","https://openalex.org/W2108706252","https://openalex.org/W2149803936","https://openalex.org/W2171283231","https://openalex.org/W2186600981","https://openalex.org/W2407338347"],"related_works":["https://openalex.org/W2064314529","https://openalex.org/W2352298027","https://openalex.org/W4319940250","https://openalex.org/W842810586","https://openalex.org/W2092919065","https://openalex.org/W4236762297","https://openalex.org/W3138801416","https://openalex.org/W2369351710","https://openalex.org/W2572241437","https://openalex.org/W4379379356"],"abstract_inverted_index":{"Text":[0],"mining":[1,22],"can":[2],"support":[3],"the":[4,7,26,29,49,64,72,93],"interpretation":[5],"of":[6,10,28,31,48,51,66,71,95,102],"enormous":[8],"quantity":[9],"textual":[11],"data":[12],"produced":[13],"in":[14,19,25,58,113],"biomedical":[15,20],"field.":[16],"Recent":[17],"developments":[18],"text":[21],"include":[23],"advances":[24],"reliability":[27],"recognition":[30],"named":[32],"entities":[33],"(NEs)":[34],"such":[35],"as":[36,41,43],"specific":[37],"genes":[38],"and":[39,77,116],"proteins,":[40],"well":[42],"movement":[44],"toward":[45,85],"richer":[46],"representations":[47],"associations":[50],"NEs.":[52],"We":[53],"argue":[54],"that":[55],"this":[56,86],"shift":[57],"representation":[59],"should":[60],"be":[61],"accompanied":[62],"by":[63],"adoption":[65],"a":[67,83,97],"more":[68],"detailed":[69],"model":[70],"relations":[73,91],"holding":[74],"between":[75],"NEs":[76],"other":[78],"relevant":[79],"domain":[80,108,117],"terms.":[81],"As":[82],"step":[84],"goal,":[87],"we":[88],"study":[89],"NE-term":[90],"with":[92],"aim":[94],"defining":[96],"detailed,":[98],"broadly":[99],"applicable":[100],"set":[101],"relation":[103],"types":[104],"based":[105],"on":[106],"accepted":[107],"standard":[109],"concepts":[110],"for":[111],"use":[112],"corpus":[114],"annotation":[115],"information":[118],"extraction":[119],"approaches.":[120]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
