{"id":"https://openalex.org/W3165453197","doi":"https://doi.org/10.3233/shti210160","title":"Entity Extraction for Clinical Notes, a Comparison Between MetaMap and Amazon Comprehend Medical","display_name":"Entity Extraction for Clinical Notes, a Comparison Between MetaMap and Amazon Comprehend Medical","publication_year":2021,"publication_date":"2021-05-27","ids":{"openalex":"https://openalex.org/W3165453197","doi":"https://doi.org/10.3233/shti210160","mag":"3165453197","pmid":"https://pubmed.ncbi.nlm.nih.gov/34042745"},"language":"en","primary_location":{"id":"doi:10.3233/shti210160","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti210160","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210160","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":"book-chapter","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210160","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011716722","display_name":"Fatemeh Shah-Mohammadi","orcid":"https://orcid.org/0000-0002-9034-7803"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fatemeh Shah-Mohammadi","raw_affiliation_strings":["Icahn School of Medicine at Mount Sinai, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"Icahn School of Medicine at Mount Sinai, New York, NY, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080703401","display_name":"Wanting Cui","orcid":"https://orcid.org/0000-0001-7341-363X"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wanting Cui","raw_affiliation_strings":["Icahn School of Medicine at Mount Sinai, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"Icahn School of Medicine at Mount Sinai, New York, NY, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086304704","display_name":"Joseph Finkelstein","orcid":"https://orcid.org/0000-0002-8084-7441"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Finkelstein","raw_affiliation_strings":["Icahn School of Medicine at Mount Sinai, New York, NY, USA"],"affiliations":[{"raw_affiliation_string":"Icahn School of Medicine at Mount Sinai, New York, NY, USA","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5011716722"],"corresponding_institution_ids":["https://openalex.org/I98704320"],"apc_list":null,"apc_paid":null,"fwci":1.5346,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.81087992,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"281","issue":null,"first_page":"258","last_page":"262"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9768000245094299,"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":0.9768000245094299,"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":0.9473999738693237,"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":0.9442999958992004,"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/recall","display_name":"Recall","score":0.6859089732170105},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.673808217048645},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6250680685043335},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5906671285629272},{"id":"https://openalex.org/keywords/data-extraction","display_name":"Data extraction","score":0.5722603797912598},{"id":"https://openalex.org/keywords/amazon-rainforest","display_name":"Amazon rainforest","score":0.5653060078620911},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.5296979546546936},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.48002973198890686},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.4669996500015259},{"id":"https://openalex.org/keywords/medical-information","display_name":"Medical information","score":0.41593778133392334},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36562567949295044},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33511748909950256},{"id":"https://openalex.org/keywords/medline","display_name":"MEDLINE","score":0.26730281114578247},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.08306464552879333},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.061881035566329956}],"concepts":[{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.6859089732170105},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.673808217048645},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6250680685043335},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5906671285629272},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.5722603797912598},{"id":"https://openalex.org/C535291247","wikidata":"https://www.wikidata.org/wiki/Q177567","display_name":"Amazon rainforest","level":2,"score":0.5653060078620911},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.5296979546546936},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.48002973198890686},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.4669996500015259},{"id":"https://openalex.org/C3019150057","wikidata":"https://www.wikidata.org/wiki/Q92779279","display_name":"Medical information","level":2,"score":0.41593778133392334},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36562567949295044},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33511748909950256},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.26730281114578247},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.08306464552879333},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.061881035566329956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C180747234","wikidata":"https://www.wikidata.org/wiki/Q23373","display_name":"Cognitive psychology","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","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},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.3233/shti210160","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti210160","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210160","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:34042745","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34042745","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/shti210160","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti210160","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210160","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3165453197.pdf","grobid_xml":"https://content.openalex.org/works/W3165453197.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W302317711","https://openalex.org/W1019512417","https://openalex.org/W1550258693","https://openalex.org/W1578843544","https://openalex.org/W2071277394","https://openalex.org/W2120539430","https://openalex.org/W2122402213","https://openalex.org/W2165456953","https://openalex.org/W2891469329","https://openalex.org/W2903309163","https://openalex.org/W2904157398","https://openalex.org/W2968988576","https://openalex.org/W3007523830","https://openalex.org/W6600260692"],"related_works":["https://openalex.org/W3022229171","https://openalex.org/W2004087619","https://openalex.org/W4280620143","https://openalex.org/W2469016277","https://openalex.org/W1982302668","https://openalex.org/W2362196274","https://openalex.org/W2557094866","https://openalex.org/W2757101400","https://openalex.org/W2240384024","https://openalex.org/W2468545057"],"abstract_inverted_index":{"Extracting":[0],"meaningful":[1],"information":[2,22,51],"from":[3],"clinical":[4,46],"notes":[5,16],"is":[6,37,73],"challenging":[7],"due":[8],"to":[9,32,48,56,74,102],"their":[10,25],"semi-":[11],"or":[12],"unstructured":[13],"format.":[14],"Clinical":[15],"such":[17],"as":[18,42,44],"discharge":[19],"summaries":[20],"contain":[21],"about":[23],"diseases,":[24],"risk":[26],"factors,":[27],"and":[28,52,90,97,120],"treatment":[29],"approaches":[30],"associated":[31],"them.":[33],"As":[34],"such,":[35],"it":[36],"critical":[38],"for":[39,45],"healthcare":[40],"quality":[41],"well":[43],"research":[47],"extract":[49],"those":[50],"make":[53],"them":[54],"accessible":[55],"other":[57],"computerized":[58],"applications":[59],"that":[60,112],"rely":[61],"on":[62],"coded":[63],"data.":[64],"In":[65],"this":[66,71],"context,":[67],"the":[68,76,104,107],"goal":[69],"of":[70,82,106],"paper":[72],"compare":[75],"automatic":[77],"medical":[78],"entity":[79,85],"extraction":[80,86],"capacity":[81],"two":[83],"available":[84],"tools:":[87],"MetaMap":[88],"(MM)":[89],"Amazon":[91],"Comprehend":[92],"Medical":[93],"(ACM).":[94],"Recall,":[95],"precision":[96],"F-score":[98,122],"have":[99],"been":[100],"used":[101],"evaluate":[103],"performance":[105],"tools.":[108],"The":[109],"results":[110],"show":[111],"ACM":[113],"achieves":[114],"higher":[115],"average":[116,118,121],"recall,":[117],"precision,":[119],"in":[123],"comparison":[124],"with":[125],"MM.":[126]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}