{"id":"https://openalex.org/W2127186124","doi":"https://doi.org/10.1136/amiajnl-2013-001766","title":"Discovering body site and severity modifiers in clinical texts","display_name":"Discovering body site and severity modifiers in clinical texts","publication_year":2013,"publication_date":"2013-10-04","ids":{"openalex":"https://openalex.org/W2127186124","doi":"https://doi.org/10.1136/amiajnl-2013-001766","mag":"2127186124","pmid":"https://pubmed.ncbi.nlm.nih.gov/24091648"},"language":"en","primary_location":{"id":"doi:10.1136/amiajnl-2013-001766","is_oa":true,"landing_page_url":"https://doi.org/10.1136/amiajnl-2013-001766","pdf_url":"https://academic.oup.com/jamia/article-pdf/21/3/448/9517794/21-3-448.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/jamia/article-pdf/21/3/448/9517794/21-3-448.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054031099","display_name":"Dmitriy Dligach","orcid":"https://orcid.org/0000-0002-2585-2707"},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dmitriy Dligach","raw_affiliation_strings":["Department of Informatics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA","institution_ids":["https://openalex.org/I1288882113","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068978543","display_name":"Steven Bethard","orcid":"https://orcid.org/0000-0001-9560-6491"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven Bethard","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA","Department of Computer & Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA","institution_ids":["https://openalex.org/I32389192"]},{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA#TAB#","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102946766","display_name":"Lee A. Becker","orcid":"https://orcid.org/0009-0000-6805-2577"},"institutions":[{"id":"https://openalex.org/I32389192","display_name":"University of Alabama at Birmingham","ror":"https://ror.org/008s83205","country_code":"US","type":"education","lineage":["https://openalex.org/I32389192"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lee Becker","raw_affiliation_strings":["Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA","Department of Computer & Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA","institution_ids":["https://openalex.org/I32389192"]},{"raw_affiliation_string":"Department of Computer & Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA#TAB#","institution_ids":["https://openalex.org/I32389192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039901099","display_name":"Timothy A. Miller","orcid":"https://orcid.org/0000-0003-4513-403X"},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy Miller","raw_affiliation_strings":["Department of Informatics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA","institution_ids":["https://openalex.org/I1288882113","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087865794","display_name":"Guergana Savova","orcid":"https://orcid.org/0000-0002-5887-200X"},"institutions":[{"id":"https://openalex.org/I1288882113","display_name":"Boston Children's Hospital","ror":"https://ror.org/00dvg7y05","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1288882113"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guergana K Savova","raw_affiliation_strings":["Department of Informatics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA","institution_ids":["https://openalex.org/I1288882113","https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5054031099"],"corresponding_institution_ids":["https://openalex.org/I1288882113","https://openalex.org/I136199984"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":{"value":3967,"currency":"USD","value_usd":3967},"fwci":8.3997,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.97407477,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"21","issue":"3","first_page":"448","last_page":"454"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.47850000858306885,"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":0.47850000858306885,"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":0.39890000224113464,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.030500000342726707,"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/computer-science","display_name":"Computer science","score":0.5160279273986816},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36043694615364075},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.35669851303100586}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5160279273986816},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36043694615364075},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.35669851303100586}],"mesh":[{"descriptor_ui":"D000715","descriptor_name":"Anatomy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000715","descriptor_name":"Anatomy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000715","descriptor_name":"Anatomy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012720","descriptor_name":"Severity of Illness Index","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012720","descriptor_name":"Severity of Illness Index","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012720","descriptor_name":"Severity of Illness Index","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1136/amiajnl-2013-001766","is_oa":true,"landing_page_url":"https://doi.org/10.1136/amiajnl-2013-001766","pdf_url":"https://academic.oup.com/jamia/article-pdf/21/3/448/9517794/21-3-448.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:24091648","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24091648","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 the American Medical Informatics Association : JAMIA","raw_type":null},{"id":"pmh:oai:dash.harvard.edu:1/12152983","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:12152983","pdf_url":null,"source":{"id":"https://openalex.org/S4306401540","display_name":"Digital Access to Scholarship at Harvard (DASH) (Harvard University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I136199984","host_organization_name":"Harvard University","host_organization_lineage":["https://openalex.org/I136199984"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2972860","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3994852","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1136/amiajnl-2013-001766","is_oa":true,"landing_page_url":"https://doi.org/10.1136/amiajnl-2013-001766","pdf_url":"https://academic.oup.com/jamia/article-pdf/21/3/448/9517794/21-3-448.pdf","source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2127186124.pdf","grobid_xml":"https://content.openalex.org/works/W2127186124.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W30314283","https://openalex.org/W45867036","https://openalex.org/W78632571","https://openalex.org/W79139011","https://openalex.org/W184493884","https://openalex.org/W1540550673","https://openalex.org/W1575184037","https://openalex.org/W1579838312","https://openalex.org/W1604792744","https://openalex.org/W1632114991","https://openalex.org/W1637593105","https://openalex.org/W1981082061","https://openalex.org/W2030408698","https://openalex.org/W2038152972","https://openalex.org/W2053238041","https://openalex.org/W2076424959","https://openalex.org/W2091582906","https://openalex.org/W2094937180","https://openalex.org/W2104381725","https://openalex.org/W2104655020","https://openalex.org/W2115259143","https://openalex.org/W2116786260","https://openalex.org/W2127713198","https://openalex.org/W2127978399","https://openalex.org/W2129367118","https://openalex.org/W2129629757","https://openalex.org/W2134498732","https://openalex.org/W2138627627","https://openalex.org/W2146089916","https://openalex.org/W2158847908","https://openalex.org/W2158922990","https://openalex.org/W2161494021","https://openalex.org/W2166297582","https://openalex.org/W2168041406","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W3204019825"],"abstract_inverted_index":{"OBJECTIVE:":[0],"To":[1],"research":[2],"computational":[3,219],"methods":[4,160,220],"for":[5,135,147,221],"discovering":[6,21,136,148,222],"body":[7,22,80,137,223],"site":[8,23,81,138,224],"and":[9,24,53,82,123,144,166,181,206,225,245],"severity":[10,25,83,149,226],"modifiers":[11,26,139,150,227],"in":[12,32,203,228],"clinical":[13,229,242],"texts.":[14,230],"METHODS:":[15],"We":[16,41,71,85,97,217],"cast":[17],"the":[18,33,48,55,58,61,88,112,125,170,192,204,209,241],"task":[19],"of":[20,35,50,60,94,114,127,132,142,153,172,198,208,240],"as":[27,238],"a":[28,36,66,92],"relation":[29,51],"extraction":[30],"problem":[31],"context":[34],"supervised":[37],"machine":[38,69],"learning":[39],"framework.":[40],"utilize":[42],"rich":[43],"linguistic":[44],"features":[45,178,188],"to":[46,65,91,110,191,211],"represent":[47],"pairs":[49],"arguments":[52],"delegate":[54],"decision":[56],"about":[57],"nature":[59],"relationship":[62],"between":[63],"them":[64],"support":[67],"vector":[68],"model.":[70],"evaluate":[72],"our":[73,133,145],"models":[74],"using":[75],"two":[76],"corpora":[77],"that":[78,158],"annotate":[79],"modifiers.":[84],"also":[86,189],"compare":[87],"model":[89],"performance":[90,131,171],"number":[93],"rule-based":[95],"baselines.":[96],"conduct":[98],"cross-domain":[99],"portability":[100],"experiments.":[101],"In":[102],"addition,":[103],"we":[104,119],"carry":[105],"out":[106],"feature":[107,116],"ablation":[108],"experiments":[109],"determine":[111],"contribution":[113],"various":[115],"groups.":[117],"Finally,":[118],"perform":[120,161],"error":[121],"analysis":[122],"report":[124],"sources":[126,197],"errors.":[128],"RESULTS:":[129],"The":[130,175,195],"method":[134,146],"achieves":[140,151],"F1":[141,152],"0.740-0.908":[143],"0.905-0.929.":[154],"DISCUSSION:":[155],"Results":[156],"indicate":[157],"both":[159,164],"well":[162],"on":[163],"in-domain":[165],"out-domain":[167],"data,":[168],"approaching":[169],"human":[173],"annotators.":[174],"most":[176],"salient":[177],"are":[179,200],"token":[180],"named":[182],"entity":[183],"features,":[184],"although":[185],"syntactic":[186],"dependency":[187],"contribute":[190],"overall":[193],"performance.":[194],"dominant":[196],"errors":[199],"infrequent":[201],"patterns":[202],"data":[205],"inability":[207],"system":[210,233],"discern":[212],"deeper":[213],"semantic":[214],"structures.":[215],"CONCLUSIONS:":[216],"investigated":[218],"Our":[231],"best":[232],"is":[234],"released":[235],"open":[236],"source":[237],"part":[239],"Text":[243],"Analysis":[244],"Knowledge":[246],"Extraction":[247],"System":[248],"(cTAKES).":[249]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
