{"id":"https://openalex.org/W4403455956","doi":"https://doi.org/10.1093/bioinformatics/btae613","title":"Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition","display_name":"Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition","publication_year":2024,"publication_date":"2024-10-15","ids":{"openalex":"https://openalex.org/W4403455956","doi":"https://doi.org/10.1093/bioinformatics/btae613","pmid":"https://pubmed.ncbi.nlm.nih.gov/39412443"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae613","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae613","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae613","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064688874","display_name":"Esmaeil Nouran\u0131","orcid":"https://orcid.org/0000-0003-1933-2550"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I51301133","display_name":"Azarbaijan Shahid Madani University","ror":"https://ror.org/05pg2cw06","country_code":"IR","type":"education","lineage":["https://openalex.org/I51301133"]}],"countries":["DK","IR"],"is_corresponding":false,"raw_author_name":"Esmaeil Nourani","raw_affiliation_strings":["Faculty of Information Technology and Computer Engineering, Azarbaijan Shahid Madani University , Tabriz,","Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-1933-2550","affiliations":[{"raw_affiliation_string":"Faculty of Information Technology and Computer Engineering, Azarbaijan Shahid Madani University , Tabriz,","institution_ids":["https://openalex.org/I51301133"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054476841","display_name":"Mikaela Koutrouli","orcid":"https://orcid.org/0000-0002-8953-3561"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Mikaela Koutrouli","raw_affiliation_strings":["Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark"],"raw_orcid":"https://orcid.org/0000-0002-8953-3561","affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019411388","display_name":"Yijia Xie","orcid":"https://orcid.org/0000-0002-7654-6662"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Yijia Xie","raw_affiliation_strings":["Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066570583","display_name":"Danai Vagiaki","orcid":"https://orcid.org/0000-0002-1674-5141"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Danai Vagiaki","raw_affiliation_strings":["Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066925770","display_name":"Sampo Pyysalo","orcid":"https://orcid.org/0000-0002-6279-5000"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Sampo Pyysalo","raw_affiliation_strings":["TurkuNLP Group, Department of Computing, Faculty of Technology, University of Turku , Turku 20014,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TurkuNLP Group, Department of Computing, Faculty of Technology, University of Turku , Turku 20014,","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026049213","display_name":"Katerina Nastou","orcid":"https://orcid.org/0000-0003-3611-5726"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Katerina Nastou","raw_affiliation_strings":["Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-3611-5726","affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011862057","display_name":"S\u00f8ren Brunak","orcid":"https://orcid.org/0000-0003-0316-5866"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"S\u00f8ren Brunak","raw_affiliation_strings":["Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-0316-5866","affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005772961","display_name":"Lars Juhl Jensen","orcid":"https://orcid.org/0000-0001-7885-715X"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Lars Juhl Jensen","raw_affiliation_strings":["Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-7885-715X","affiliations":[{"raw_affiliation_string":"Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen 2200, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I124055696"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3963,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.63056993,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"40","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.4729999899864197,"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":0.4729999899864197,"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":0.2085999995470047,"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":0.09910000115633011,"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/ontology","display_name":"Ontology","score":0.7503652572631836},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6336666345596313},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4643927216529846},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3853333294391632},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3726659417152405},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.36239588260650635},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.0600590705871582}],"concepts":[{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7503652572631836},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6336666345596313},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4643927216529846},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3853333294391632},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3726659417152405},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.36239588260650635},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0600590705871582},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008019","descriptor_name":"Life Style","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008019","descriptor_name":"Life Style","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008019","descriptor_name":"Life Style","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008019","descriptor_name":"Life Style","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008019","descriptor_name":"Life Style","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008019","descriptor_name":"Life Style","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","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":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064229","descriptor_name":"Biological Ontologies","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btae613","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae613","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39412443","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39412443","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11543612","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11543612","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11543612/pdf/btae613.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/375eb666-c7e5-4d87-ac78-0ff80afa7f8c","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/375eb666-c7e5-4d87-ac78-0ff80afa7f8c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Nourani , E , Koutrouli , M , Xie , Y , Vagiaki , D , Pyysalo , S , Nastou , K , Brunak , S & Jensen , L J 2024 , ' Lifestyle factors in the biomedical literature : an ontology and comprehensive resources for named entity recognition ' , Bioinformatics , vol. 40 , no. 11 , btae613 . https://doi.org/10.1093/bioinformatics/btae613","raw_type":"article"},{"id":"pmh:oai:www.utupub.fi:10024/186128","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/186128","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae613","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae613","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3307575839","display_name":null,"funder_award_id":"NFF17OC0027594","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G4282887365","display_name":null,"funder_award_id":"NNF14CC0001","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G5327834047","display_name":null,"funder_award_id":"NNF20SA0035590","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G6662978750","display_name":null,"funder_award_id":"NNF14CC0001","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8441515038","display_name":"Deep learning-based text mining for interpretation of omics data","funder_award_id":"101023676","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1552847225","https://openalex.org/W2071879021","https://openalex.org/W2097877306","https://openalex.org/W2122496897","https://openalex.org/W2123152121","https://openalex.org/W2138648054","https://openalex.org/W2146086501","https://openalex.org/W2788766073","https://openalex.org/W2903298154","https://openalex.org/W2921415194","https://openalex.org/W2923532199","https://openalex.org/W2986767149","https://openalex.org/W3014750679","https://openalex.org/W3082330004","https://openalex.org/W3104015140","https://openalex.org/W3112526052","https://openalex.org/W3186054896","https://openalex.org/W4379878431","https://openalex.org/W4380371036","https://openalex.org/W4387328184","https://openalex.org/W4388615775","https://openalex.org/W4389105137","https://openalex.org/W4389674515","https://openalex.org/W4402253472","https://openalex.org/W4402533779","https://openalex.org/W4402535087","https://openalex.org/W6770372785"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2003333417","https://openalex.org/W2378862226","https://openalex.org/W118236634","https://openalex.org/W2355326633","https://openalex.org/W2804669904","https://openalex.org/W2149777447","https://openalex.org/W2347456287","https://openalex.org/W2121651557","https://openalex.org/W2782969047"],"abstract_inverted_index":{"MOTIVATION:":[0],"Despite":[1],"lifestyle":[2,82],"factors":[3],"(LSFs)":[4],"being":[5],"increasingly":[6],"acknowledged":[7],"in":[8,14,24,30,48,171,187],"shaping":[9],"individual":[10],"health":[11],"trajectories,":[12],"particularly":[13],"chronic":[15],"diseases,":[16],"they":[17],"have":[18],"still":[19],"not":[20],"been":[21],"systematically":[22],"described":[23],"the":[25,127,134,142,148,172,179,184,202,222],"biomedical":[26,173],"literature.":[27,174],"This":[28,207],"is":[29,52,225],"part":[31],"because":[32],"no":[33],"named":[34],"entity":[35],"recognition":[36,95],"(NER)":[37],"system":[38,93,144],"exists,":[39],"which":[40,86],"can":[41],"comprehensively":[42],"detect":[43],"all":[44],"types":[45],"of":[46,60,70,98,115,129,139,153,169],"LSFs":[47,108,186],"text.":[49],"The":[50],"task":[51],"challenging":[53],"due":[54],"to":[55,89,121,211,221],"their":[56],"inherent":[57],"diversity,":[58],"lack":[59,69],"a":[61,71,80,91,103,123,217],"comprehensive":[62],"LSF":[63,170],"classification":[64],"for":[65,73,94,107,111,141,147],"dictionary-based":[66,92,143],"NER,":[67],"and":[68,96,113,118,145,159,183,189,216],"corpus":[72,106,135],"deep":[74],"learning-based":[75],"NER.":[76],"RESULTS:":[77],"We":[78],"present":[79],"novel":[81],"factor":[83],"ontology":[84],"(LSFO),":[85],"we":[87,101],"used":[88],"develop":[90],"normalization":[97],"LSFs.":[99],"Additionally,":[100],"introduce":[102],"manually":[104],"annotated":[105,180],"(LSF200)":[109],"suitable":[110],"training":[112],"evaluation":[114],"NER":[116,131,194],"systems,":[117,195],"use":[119],"it":[120],"train":[122],"transformer-based":[124,149],"system.":[125,150],"Evaluating":[126],"performance":[128],"both":[130,193],"systems":[132,155],"on":[133,156],"revealed":[136],"an":[137],"F-score":[138],"64%":[140],"76%":[146],"Large-scale":[151],"application":[152],"these":[154],"PubMed":[157,188],"abstracts":[158],"PMC":[160],"Open":[161],"Access":[162],"articles":[163,191],"identified":[164],"over":[165],"300":[166],"million":[167],"mentions":[168],"AVAILABILITY":[175],"AND":[176],"IMPLEMENTATION:":[177],"LSFO,":[178],"LSF200":[181],"corpus,":[182],"detected":[185],"PMC-OA":[190],"using":[192],"are":[196],"available":[197,227],"under":[198],"open":[199],"licenses":[200],"via":[201],"following":[203],"GitHub":[204,214],"repository:":[205],"https://github.com/EsmaeilNourani/LSFO-expansion.":[206],"repository":[208],"contains":[209],"links":[210],"two":[212],"associated":[213],"repositories":[215],"Zenodo":[218],"project":[219],"related":[220],"study.":[223],"LSFO":[224],"also":[226],"at":[228],"BioPortal:":[229],"https://bioportal.bioontology.org/ontologies/LSFO.":[230]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-29T08:53:18.405633","created_date":"2025-10-10T00:00:00"}
