{"id":"https://openalex.org/W4283733789","doi":"https://doi.org/10.3233/shti220747","title":"Mapping SNOMED CT Codes to Semi-Structured Texts via an NLP Pipeline","display_name":"Mapping SNOMED CT Codes to Semi-Structured Texts via an NLP Pipeline","publication_year":2022,"publication_date":"2022-06-29","ids":{"openalex":"https://openalex.org/W4283733789","doi":"https://doi.org/10.3233/shti220747","pmid":"https://pubmed.ncbi.nlm.nih.gov/35773893"},"language":"en","primary_location":{"id":"doi:10.3233/shti220747","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti220747","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI220747","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/SHTI220747","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081765215","display_name":"Sebastian B. Kunz","orcid":null},"institutions":[{"id":"https://openalex.org/I130692619","display_name":"Bern University of Applied Sciences","ror":"https://ror.org/02bnkt322","country_code":"CH","type":"education","lineage":["https://openalex.org/I130692619"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sebastian Kunz","raw_affiliation_strings":["Bern University of Applied Sciences, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bern University of Applied Sciences, Switzerland","institution_ids":["https://openalex.org/I130692619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042271868","display_name":"Cyril R. Zgraggen","orcid":null},"institutions":[{"id":"https://openalex.org/I130692619","display_name":"Bern University of Applied Sciences","ror":"https://ror.org/02bnkt322","country_code":"CH","type":"education","lineage":["https://openalex.org/I130692619"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Cyril Zgraggen","raw_affiliation_strings":["Bern University of Applied Sciences, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bern University of Applied Sciences, Switzerland","institution_ids":["https://openalex.org/I130692619"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102842494","display_name":"Murat Sariyar","orcid":"https://orcid.org/0000-0003-3432-2860"},"institutions":[{"id":"https://openalex.org/I130692619","display_name":"Bern University of Applied Sciences","ror":"https://ror.org/02bnkt322","country_code":"CH","type":"education","lineage":["https://openalex.org/I130692619"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Murat Sariyar","raw_affiliation_strings":["Bern University of Applied Sciences, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bern University of Applied Sciences, Switzerland","institution_ids":["https://openalex.org/I130692619"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5102842494"],"corresponding_institution_ids":["https://openalex.org/I130692619"],"apc_list":null,"apc_paid":null,"fwci":0.4994,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.57628724,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"295","issue":null,"first_page":"390","last_page":"393"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9873999953269958,"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":0.9873999953269958,"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":0.9751999974250793,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9652000069618225,"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/snomed-ct","display_name":"SNOMED CT","score":0.9382392764091492},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8217266201972961},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.7014688849449158},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6489405632019043},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6037278771400452},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5766537189483643},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5510849356651306},{"id":"https://openalex.org/keywords/german","display_name":"German","score":0.487738698720932},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4773312211036682},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4613921642303467},{"id":"https://openalex.org/keywords/open-biomedical-ontologies","display_name":"Open Biomedical Ontologies","score":0.4592862129211426},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4287002384662628},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4143720269203186},{"id":"https://openalex.org/keywords/terminology","display_name":"Terminology","score":0.24678942561149597},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.16995826363563538},{"id":"https://openalex.org/keywords/ontology-alignment","display_name":"Ontology alignment","score":0.12525448203086853},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11968716979026794},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.11707723140716553},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.10839301347732544}],"concepts":[{"id":"https://openalex.org/C206497026","wikidata":"https://www.wikidata.org/wiki/Q1753883","display_name":"SNOMED CT","level":3,"score":0.9382392764091492},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8217266201972961},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.7014688849449158},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6489405632019043},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6037278771400452},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5766537189483643},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5510849356651306},{"id":"https://openalex.org/C154775046","wikidata":"https://www.wikidata.org/wiki/Q188","display_name":"German","level":2,"score":0.487738698720932},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4773312211036682},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4613921642303467},{"id":"https://openalex.org/C137982476","wikidata":"https://www.wikidata.org/wiki/Q7072326","display_name":"Open Biomedical Ontologies","level":5,"score":0.4592862129211426},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4287002384662628},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4143720269203186},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.24678942561149597},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.16995826363563538},{"id":"https://openalex.org/C98893333","wikidata":"https://www.wikidata.org/wiki/Q4339878","display_name":"Ontology alignment","level":4,"score":0.12525448203086853},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11968716979026794},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.11707723140716553},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.10839301347732544},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D039061","descriptor_name":"Systematized Nomenclature of Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039061","descriptor_name":"Systematized Nomenclature of Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D039061","descriptor_name":"Systematized Nomenclature of Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.3233/shti220747","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti220747","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI220747","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:35773893","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35773893","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},{"id":"pmh:oai:arbor.bfh.ch:18475","is_oa":true,"landing_page_url":"https://arbor.bfh.ch/18475/","pdf_url":null,"source":{"id":"https://openalex.org/S4406922806","display_name":"ARBOR - Bern University of Applied Sciences Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Kunz, Sebastian; Zgraggen, Cyril; Sariyar, Murat (2022). Mapping SNOMED CT Codes to Semi-Structured Texts via an NLP Pipeline Studies in Health Technology and Informatics, 295, pp. 390-393. IOS Press 10.3233/SHTI220747 &lt;http://dx.doi.org/10.3233/SHTI220747&gt;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.3233/shti220747","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti220747","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI220747","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":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283733789.pdf","grobid_xml":"https://content.openalex.org/works/W4283733789.grobid-xml"},"referenced_works_count":5,"referenced_works":["https://openalex.org/W1656666520","https://openalex.org/W2911489562","https://openalex.org/W2977940954","https://openalex.org/W3122634526","https://openalex.org/W3158665049"],"related_works":["https://openalex.org/W3031263788","https://openalex.org/W3011412984","https://openalex.org/W3214642209","https://openalex.org/W4308949089","https://openalex.org/W2624106077","https://openalex.org/W2020540721","https://openalex.org/W2578916128","https://openalex.org/W2773616286","https://openalex.org/W4295189479","https://openalex.org/W2916894319"],"abstract_inverted_index":{"In":[0],"the":[1,29,57,65,74,78,85,95,101,110,114,117,142],"project":[2],"presented":[3],"here,":[4],"we":[5,93],"used":[6],"NLP":[7,36,97,111],"tools":[8],"for":[9,40,56,104,150],"annotating":[10],"German":[11],"medical":[12,69],"trainings":[13,70],"documents":[14,33],"with":[15,34,77],"SNOMED":[16,80],"CT":[17,81],"codes.":[18],"Following":[19],"research":[20],"question":[21],"was":[22,62],"addressed:":[23],"Is":[24],"it":[25],"possible":[26],"to":[27,63],"automate":[28],"annotation":[30],"of":[31,50,60],"training":[32],"an":[35,53],"pipeline":[37,112],"especially":[38],"designed":[39],"this":[41],"task":[42],"but":[43],"requiring":[44],"translation":[45,143],"into":[46],"English?":[47],"The":[48],"goal":[49],"our":[51,106,125],"stakeholder,":[52],"institution":[54],"responsible":[55],"continuing":[58],"education":[59],"physicians,":[61],"facilitate":[64],"switch":[66],"between":[67],"different":[68],"programs":[71],"by":[72],"coding":[73],"same":[75,79],"requirement":[76],"code,":[82],"even":[83],"if":[84],"wording":[86],"is":[87,129],"different.":[88],"We":[89,119],"first":[90],"describe":[91],"how":[92],"chose":[94],"concrete":[96,102],"tools,":[98],"after":[99],"which":[100],"steps":[103],"implementing":[105],"prototype":[107],"are":[108],"outlined:":[109],"construction,":[113],"implementation,":[115],"and":[116,133,155],"validation.":[118],"infer":[120],"three":[121],"important":[122],"lessons":[123],"from":[124],"results:":[126],"(i)":[127],"self-supervision":[128],"no":[130],"free":[131],"lunch":[132],"should":[134],"be":[135,147],"based":[136],"on":[137],"a":[138,151],"sophisticated":[139],"task,":[140],"(ii)":[141],"via":[144],"DeepL":[145],"can":[146,159],"too":[148],"context-dependent":[149],"peculiar":[152],"use":[153],"case,":[154],"(iii)":[156],"ontology":[157],"extraction":[158],"increase":[160],"efficiency":[161],"as":[162,164],"well":[163],"accuracy.":[165]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
