{"id":"https://openalex.org/W3173561451","doi":"https://doi.org/10.1093/jamia/ocab090","title":"Biomedical and clinical English model packages for the Stanza Python NLP library","display_name":"Biomedical and clinical English model packages for the Stanza Python NLP library","publication_year":2021,"publication_date":"2021-05-04","ids":{"openalex":"https://openalex.org/W3173561451","doi":"https://doi.org/10.1093/jamia/ocab090","mag":"3173561451","pmid":"https://pubmed.ncbi.nlm.nih.gov/34157094"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocab090","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocab090","pdf_url":"https://academic.oup.com/jamia/article-pdf/28/9/1892/39731803/ocab090.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","license_id":"https://openalex.org/licenses/cc-by-nc","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/28/9/1892/39731803/ocab090.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100349345","display_name":"Yuhao Zhang","orcid":"https://orcid.org/0000-0002-2014-4373"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuhao Zhang","raw_affiliation_strings":["Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","Computer Science Department, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Computer Science Department, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100349345","display_name":"Yuhao Zhang","orcid":"https://orcid.org/0000-0002-2014-4373"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuhao Zhang","raw_affiliation_strings":["Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","Computer Science Department, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Computer Science Department, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuhui Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuhui Zhang","raw_affiliation_strings":["Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","Computer Science Department, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Computer Science Department, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuhui Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuhui Zhang","raw_affiliation_strings":["Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","Computer Science Department, Stanford University, Stanford, California, USA","Computer Science and Linguistics Departments, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Informatics Training Program, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Computer Science Department, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Computer Science and Linguistics Departments, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041658523","display_name":"Peng Qi","orcid":"https://orcid.org/0000-0001-9378-3355"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Qi","raw_affiliation_strings":["Computer Science Department, Stanford University, Stanford, California, USA","Department of Radiology, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Department, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Radiology, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046006076","display_name":"Christopher D. Manning","orcid":"https://orcid.org/0000-0001-6155-649X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher D Manning","raw_affiliation_strings":["Computer Science and Linguistics Departments, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Linguistics Departments, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087710258","display_name":"Curtis P. Langlotz","orcid":"https://orcid.org/0000-0002-8972-8051"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Curtis P Langlotz","raw_affiliation_strings":["Department of Radiology, Stanford University, Stanford, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Radiology, Stanford University, Stanford, California, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100349345"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":{"value":3967,"currency":"USD","value_usd":3967},"apc_paid":{"value":3967,"currency":"USD","value_usd":3967},"fwci":5.1749,"has_fulltext":true,"cited_by_count":114,"citation_normalized_percentile":{"value":0.95810197,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"28","issue":"9","first_page":"1892","last_page":"1899"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":0.3361999988555908,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":0.3361999988555908,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.2393999993801117,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.07750000059604645,"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/stanza","display_name":"Stanza","score":0.821662187576294},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.820949912071228},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6725717782974243},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5792214274406433},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5515972971916199},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2240091860294342},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.159372478723526},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.07051801681518555}],"concepts":[{"id":"https://openalex.org/C2776751804","wikidata":"https://www.wikidata.org/wiki/Q1756348","display_name":"Stanza","level":3,"score":0.821662187576294},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.820949912071228},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6725717782974243},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5792214274406433},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5515972971916199},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2240091860294342},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.159372478723526},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.07051801681518555},{"id":"https://openalex.org/C164913051","wikidata":"https://www.wikidata.org/wiki/Q482","display_name":"Poetry","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/jamia/ocab090","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocab090","pdf_url":"https://academic.oup.com/jamia/article-pdf/28/9/1892/39731803/ocab090.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","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:34157094","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34157094","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:pubmedcentral.nih.gov:8363782","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8363782","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Am Med Inform Assoc","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/jamia/ocab090","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocab090","pdf_url":"https://academic.oup.com/jamia/article-pdf/28/9/1892/39731803/ocab090.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","license_id":"https://openalex.org/licenses/cc-by-nc","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":[{"id":"https://metadata.un.org/sdg/4","score":0.5099999904632568,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3173561451.pdf","grobid_xml":"https://content.openalex.org/works/W3173561451.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1602694398","https://openalex.org/W1679133234","https://openalex.org/W1869282115","https://openalex.org/W1976316416","https://openalex.org/W2055032581","https://openalex.org/W2071879021","https://openalex.org/W2087227067","https://openalex.org/W2100627415","https://openalex.org/W2108475224","https://openalex.org/W2120754707","https://openalex.org/W2122402213","https://openalex.org/W2146089916","https://openalex.org/W2149369282","https://openalex.org/W2157814042","https://openalex.org/W2159583324","https://openalex.org/W2163107094","https://openalex.org/W2168041406","https://openalex.org/W2169099542","https://openalex.org/W2346452181","https://openalex.org/W2396881363","https://openalex.org/W2769851464","https://openalex.org/W2887672952","https://openalex.org/W2911489562","https://openalex.org/W2944400536","https://openalex.org/W2963339489","https://openalex.org/W2998068467","https://openalex.org/W3104713542"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4404603537","https://openalex.org/W4317935840","https://openalex.org/W2811421009","https://openalex.org/W4233308327","https://openalex.org/W2996075205","https://openalex.org/W1956940236","https://openalex.org/W3204019825"],"abstract_inverted_index":{"OBJECTIVE:":[0],"The":[1,84],"study":[2],"sought":[3],"to":[4,96,226],"develop":[5],"and":[6,18,24,33,36,93,104,111,126,135,160,168,188,210,232],"evaluate":[7],"neural":[8,91],"natural":[9],"language":[10],"processing":[11],"(NLP)":[12],"packages":[13,213,220],"for":[14,50,108,215,236],"the":[15,43,66,132,139,156,165,173,177,195,216,227,230],"syntactic":[16,146],"analysis":[17],"named":[19,105],"entity":[20,106],"recognition":[21,107],"of":[22,61,76,229,238],"biomedical":[23,35,110,209],"clinical":[25,37,112,211],"English":[26,38],"text.":[27,113],"MATERIALS":[28],"AND":[29],"METHODS:":[30],"We":[31,114,207,250],"implement":[32],"train":[34],"NLP":[39,52,121,212],"pipelines":[40,86],"by":[41],"extending":[42],"widely":[44],"used":[45],"Stanza":[46,217],"library":[47],"originally":[48],"designed":[49],"general":[51],"tasks.":[53],"Our":[54],"models":[55,129,159,162,247],"are":[56,87,94,169,189,233],"trained":[57],"with":[58,72,80,155,172,194],"a":[59,73],"mix":[60],"public":[62],"datasets":[63],"such":[64,123,130],"as":[65,69,71,124,131],"CRAFT":[67,141,178],"treebank":[68],"well":[70],"private":[74],"corpus":[75],"radiology":[77],"reports":[78],"annotated":[79],"5":[81],"radiology-domain":[82],"entities.":[83],"resulting":[85],"fully":[88],"based":[89],"on":[90,164,170,192],"networks,":[92],"able":[95],"perform":[97],"tokenization,":[98],"part-of-speech":[99],"tagging,":[100],"lemmatization,":[101],"dependency":[102],"parsing,":[103],"both":[109],"compare":[115],"our":[116,148,183,246],"systems":[117,137,149,184],"against":[118],"popular":[119],"open-source":[120],"libraries":[122],"CoreNLP":[125,161],"scispaCy,":[127,187],"state-of-the-art":[128,196],"BioBERT":[133],"models,":[134],"winning":[136,174],"from":[138,176,198],"BioNLP":[140],"shared":[142,179],"task.":[143,180],"RESULTS:":[144],"For":[145,181],"analysis,":[147],"achieve":[150],"much":[151,202],"better":[152,190],"performance":[153,197,222],"compared":[154],"released":[157],"scispaCy":[158],"retrained":[163],"same":[166],"treebanks,":[167],"par":[171,193],"system":[175],"NER,":[182],"substantially":[185],"outperform":[186],"or":[191],"BioBERT,":[199],"while":[200],"being":[201],"more":[203],"computationally":[204],"efficient.":[205],"CONCLUSIONS:":[206],"introduce":[208],"built":[214],"library.":[218],"These":[219],"offer":[221],"that":[223],"is":[224],"similar":[225],"state":[228],"art,":[231],"also":[234,251],"optimized":[235],"ease":[237],"use.":[239],"To":[240],"facilitate":[241],"research,":[242],"we":[243],"make":[244],"all":[245],"publicly":[248],"available.":[249],"provide":[252],"an":[253],"online":[254],"demonstration":[255],"(http://stanza.run/bio).":[256]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":34},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":9},{"year":2019,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
