{"id":"https://openalex.org/W4391229646","doi":"https://doi.org/10.3233/shti231027","title":"Towards Structuring Clinical Texts: Joint Entity and Relation Extraction from Japanese Case Report Corpus","display_name":"Towards Structuring Clinical Texts: Joint Entity and Relation Extraction from Japanese Case Report Corpus","publication_year":2024,"publication_date":"2024-01-25","ids":{"openalex":"https://openalex.org/W4391229646","doi":"https://doi.org/10.3233/shti231027","pmid":"https://pubmed.ncbi.nlm.nih.gov/38269871"},"language":"en","primary_location":{"id":"doi:10.3233/shti231027","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti231027","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI231027","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI231027","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074533898","display_name":"Daisaku Shibata","orcid":"https://orcid.org/0000-0003-3957-0388"},"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":"Daisaku Shibata","raw_affiliation_strings":["Graduate School of Medicine, The University of Tokyo, Tokyo, Japan"],"raw_orcid":"https://orcid.org/0000-0003-3957-0388","affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023820316","display_name":"Emiko Shinohara","orcid":"https://orcid.org/0000-0002-9899-8678"},"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":"Emiko Shinohara","raw_affiliation_strings":["Graduate School of Medicine, The University of Tokyo, Tokyo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-9899-8678","affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009839802","display_name":"Kiminori Shimamoto","orcid":"https://orcid.org/0000-0003-0838-7505"},"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":"Kiminori Shimamoto","raw_affiliation_strings":["Graduate School of Medicine, The University of Tokyo, Tokyo, Japan"],"raw_orcid":"https://orcid.org/0000-0003-0838-7505","affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021892377","display_name":"Yoshimasa Kawazoe","orcid":"https://orcid.org/0000-0002-7277-0827"},"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":"Yoshimasa Kawazoe","raw_affiliation_strings":["Graduate School of Medicine, The University of Tokyo, Tokyo, Japan"],"raw_orcid":"https://orcid.org/0000-0002-7277-0827","affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021892377"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":null,"apc_paid":null,"fwci":2.8253,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.90073471,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"310","issue":null,"first_page":"559","last_page":"563"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9932000041007996,"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"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9932000041007996,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9894999861717224,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9531000256538391,"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/natural-language-processing","display_name":"Natural language processing","score":0.7955777645111084},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7913880944252014},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.7686723470687866},{"id":"https://openalex.org/keywords/relationship-extraction","display_name":"Relationship extraction","score":0.740863561630249},{"id":"https://openalex.org/keywords/structuring","display_name":"Structuring","score":0.6993929743766785},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6556306481361389},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.6011845469474792},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5884418487548828},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5115112066268921},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.46686220169067383},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.43217548727989197},{"id":"https://openalex.org/keywords/joint","display_name":"Joint (building)","score":0.4276856780052185},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3957652747631073},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.14481830596923828}],"concepts":[{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.7955777645111084},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7913880944252014},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.7686723470687866},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.740863561630249},{"id":"https://openalex.org/C2775945657","wikidata":"https://www.wikidata.org/wiki/Q381442","display_name":"Structuring","level":2,"score":0.6993929743766785},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6556306481361389},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.6011845469474792},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5884418487548828},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5115112066268921},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.46686220169067383},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.43217548727989197},{"id":"https://openalex.org/C18555067","wikidata":"https://www.wikidata.org/wiki/Q8375051","display_name":"Joint (building)","level":2,"score":0.4276856780052185},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3957652747631073},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.14481830596923828},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C170154142","wikidata":"https://www.wikidata.org/wiki/Q150737","display_name":"Architectural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007564","descriptor_name":"Japan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007564","descriptor_name":"Japan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007564","descriptor_name":"Japan","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011211","descriptor_name":"Electric Power Supplies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014956","descriptor_name":"Writing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.3233/shti231027","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti231027","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI231027","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmid:38269871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38269871","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":"Studies in health technology and informatics","raw_type":null}],"best_oa_location":{"id":"doi:10.3233/shti231027","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti231027","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI231027","source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.8500000238418579}],"awards":[{"id":"https://openalex.org/G240039914","display_name":null,"funder_award_id":"JPMJCR22N1","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"},{"id":"https://openalex.org/G6718509927","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391229646.pdf"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W165283731","https://openalex.org/W2168041406","https://openalex.org/W2963341956","https://openalex.org/W3093272371","https://openalex.org/W3213545440","https://openalex.org/W4295008589"],"related_works":["https://openalex.org/W2916255597","https://openalex.org/W3095980030","https://openalex.org/W2352298027","https://openalex.org/W4319940250","https://openalex.org/W842810586","https://openalex.org/W2092919065","https://openalex.org/W4286980122","https://openalex.org/W4236762297","https://openalex.org/W3198510869","https://openalex.org/W4379379356"],"abstract_inverted_index":{"Important":[0],"pieces":[1],"of":[2,36,62,67,106,117,124,132],"information":[3,23],"related":[4],"to":[5,122],"patient":[6],"symptoms":[7],"and":[8,41,64,108,112],"diagnosis":[9],"are":[10,120],"often":[11],"written":[12],"in":[13,16],"free-text":[14],"form":[15],"clinical":[17],"texts.":[18],"To":[19],"utilize":[20],"these":[21,128],"texts,":[22],"extraction":[24,43],"using":[25,45],"natural":[26],"language":[27],"processing":[28],"is":[29],"required.":[30],"This":[31],"study":[32,119],"evaluated":[33],"the":[34,101],"performance":[35],"named":[37],"entity":[38],"recognition":[39],"(NER)":[40],"relation":[42],"(RE)":[44],"machine-learning":[46],"methods.":[47],"The":[48,97,115],"Japanese":[49],"case":[50],"report":[51],"corpus":[52],"was":[53,95],"used":[54],"for":[55],"this":[56,118],"study,":[57],"which":[58],"had":[59],"113":[60],"types":[61,66],"entities":[63],"36":[65],"relations":[68],"that":[69,100],"were":[70,74,110],"manually":[71],"annotated.":[72],"There":[73],"183":[75],"cases":[76],"comprising":[77],"2,194":[78],"sentences":[79],"after":[80],"preprocessing.":[81],"In":[82],"addition,":[83],"a":[84],"machine":[85],"learning":[86],"model":[87],"based":[88],"on":[89],"bidirectional":[90],"encoder":[91],"representations":[92],"from":[93],"transformers":[94],"used.":[96],"results":[98,116,129],"revealed":[99],"maximum":[102],"micro-averaged":[103],"F1":[104],"scores":[105],"NER":[107],"RE":[109],"0.912":[111],"0.759,":[113],"respectively.":[114],"comparable":[121],"those":[123],"previous":[125],"studies.":[126],"Hence,":[127],"could":[130],"be":[131],"substantial":[133],"baseline":[134],"accuracy.":[135]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
