{"id":"https://openalex.org/W3208878858","doi":"https://doi.org/10.3233/shti210589","title":"A NLP Pipeline for the Automatic Extraction of Microorganisms Names from Microbiological Notes","display_name":"A NLP Pipeline for the Automatic Extraction of Microorganisms Names from Microbiological Notes","publication_year":2021,"publication_date":"2021-10-27","ids":{"openalex":"https://openalex.org/W3208878858","doi":"https://doi.org/10.3233/shti210589","mag":"3208878858","pmid":"https://pubmed.ncbi.nlm.nih.gov/34734867"},"language":"en","primary_location":{"id":"doi:10.3233/shti210589","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti210589","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210589","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/SHTI210589","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054326254","display_name":"Sara Mora","orcid":"https://orcid.org/0000-0002-0613-3248"},"institutions":[{"id":"https://openalex.org/I83816512","display_name":"University of Genoa","ror":"https://ror.org/0107c5v14","country_code":"IT","type":"education","lineage":["https://openalex.org/I83816512"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Sara Mora","raw_affiliation_strings":["Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Italy","institution_ids":["https://openalex.org/I83816512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083643315","display_name":"Jacopo Attene","orcid":"https://orcid.org/0000-0002-1009-4827"},"institutions":[{"id":"https://openalex.org/I83816512","display_name":"University of Genoa","ror":"https://ror.org/0107c5v14","country_code":"IT","type":"education","lineage":["https://openalex.org/I83816512"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Jacopo Attene","raw_affiliation_strings":["Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Italy","institution_ids":["https://openalex.org/I83816512"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049470110","display_name":"Roberta Gazzarata","orcid":"https://orcid.org/0000-0002-7778-7601"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Roberta Gazzarata","raw_affiliation_strings":["Healthropy, Corso Italia 15/6, 17100 Savona, Italy"],"affiliations":[{"raw_affiliation_string":"Healthropy, Corso Italia 15/6, 17100 Savona, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074984739","display_name":"Giustino Parruti","orcid":"https://orcid.org/0000-0003-3483-8170"},"institutions":[{"id":"https://openalex.org/I4210147037","display_name":"Azienda USL di Pescara","ror":"https://ror.org/048ym4d69","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210147037"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giustino Parruti","raw_affiliation_strings":["Department of Infectious Diseases, AUSL Pescara, Pescara, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, AUSL Pescara, Pescara, Italy","institution_ids":["https://openalex.org/I4210147037"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052329168","display_name":"Mauro Giacomini","orcid":"https://orcid.org/0000-0001-5646-2034"},"institutions":[{"id":"https://openalex.org/I83816512","display_name":"University of Genoa","ror":"https://ror.org/0107c5v14","country_code":"IT","type":"education","lineage":["https://openalex.org/I83816512"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mauro Giacomini","raw_affiliation_strings":["Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS), University of Genoa, Italy","institution_ids":["https://openalex.org/I83816512"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5054326254"],"corresponding_institution_ids":["https://openalex.org/I83816512"],"apc_list":null,"apc_paid":null,"fwci":1.5346,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.83221654,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"285","issue":null,"first_page":"153","last_page":"158"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9979000091552734,"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":0.9979000091552734,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9311000108718872,"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/pipeline","display_name":"Pipeline (software)","score":0.7516024112701416},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6091597676277161},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5823328495025635},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5581014156341553},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.5185382962226868},{"id":"https://openalex.org/keywords/health-care","display_name":"Health care","score":0.4650484323501587},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.4487093389034271},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.06716278195381165}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7516024112701416},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6091597676277161},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5823328495025635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5581014156341553},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.5185382962226868},{"id":"https://openalex.org/C160735492","wikidata":"https://www.wikidata.org/wiki/Q31207","display_name":"Health care","level":2,"score":0.4650484323501587},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.4487093389034271},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.06716278195381165},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"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/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","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}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D003695","descriptor_name":"Delivery of Health Care","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003695","descriptor_name":"Delivery of Health Care","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003695","descriptor_name":"Delivery of Health Care","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009626","descriptor_name":"Terminology as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.3233/shti210589","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti210589","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210589","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:34734867","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34734867","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:iris.unige.it:11567/1083028","is_oa":true,"landing_page_url":"https://hdl.handle.net/11567/1083028","pdf_url":null,"source":{"id":"https://openalex.org/S4377196291","display_name":"CINECA IRIS Institutial Research Information System (University of Genoa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I83816512","host_organization_name":"University of Genoa","host_organization_lineage":["https://openalex.org/I83816512"],"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":"","raw_type":"info:eu-repo/semantics/bookPart"}],"best_oa_location":{"id":"doi:10.3233/shti210589","is_oa":true,"landing_page_url":"https://doi.org/10.3233/shti210589","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/SHTI210589","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":[{"id":"https://metadata.un.org/sdg/4","score":0.5799999833106995,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3208878858.pdf","grobid_xml":"https://content.openalex.org/works/W3208878858.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W156770688","https://openalex.org/W2767642786","https://openalex.org/W2912338293","https://openalex.org/W2951296967","https://openalex.org/W2953320089","https://openalex.org/W2956133827","https://openalex.org/W3047431235"],"related_works":["https://openalex.org/W3107474891","https://openalex.org/W2368651715","https://openalex.org/W2020540721","https://openalex.org/W2747680751","https://openalex.org/W2577861415","https://openalex.org/W1590308178","https://openalex.org/W3120899676","https://openalex.org/W159132833","https://openalex.org/W1496799114","https://openalex.org/W1510733122"],"abstract_inverted_index":{"According":[0],"to":[1,48,76,121],"the":[2,11,36,44,49,56,61,65,85,89,95,108,113,122,126],"\"Istituto":[3],"Superiore":[4],"di":[5],"Sanita'\"":[6],"(ISS),":[7],"hospital":[8],"infections":[9],"are":[10,58],"most":[12],"frequent":[13],"and":[14,29,38,111],"serious":[15],"complication":[16],"of":[17,35,43,51,64,72,88,91,100],"health":[18,24,40],"care.":[19],"This":[20],"constitutes":[21],"a":[22,52,78],"real":[23],"emergency":[25],"which":[26],"requires":[27],"incisive":[28],"joint":[30],"action":[31],"at":[32],"all":[33,112],"levels":[34],"local":[37],"national":[39],"organization.":[41],"Most":[42],"valuable":[45],"information":[46],"related":[47],"presence":[50],"specific":[53],"microorganism":[54],"in":[55,94],"blood":[57],"written":[59],"into":[60],"notes":[62,103],"field":[63],"laboratory":[66],"exams":[67],"results.":[68],"The":[69],"main":[70],"objective":[71],"this":[73],"work":[74],"is":[75],"build":[77],"Natural":[79],"Language":[80],"Processing":[81],"(NLP)":[82],"pipeline":[83],"for":[84],"automatic":[86],"extraction":[87],"names":[90,115],"microorganisms":[92,114],"present":[93],"clinical":[96],"texts.":[97],"A":[98],"sample":[99],"499":[101],"microbiological":[102],"have":[104,116],"been":[105,117],"analysed":[106],"with":[107],"developed":[109],"system":[110],"extracted":[118],"correctly,":[119],"according":[120],"labels":[123],"given":[124],"by":[125],"expert.":[127]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
