{"id":"https://openalex.org/W2019493309","doi":"https://doi.org/10.1186/1471-2105-10-28","title":"Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy","display_name":"Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy","publication_year":2009,"publication_date":"2009-01-21","ids":{"openalex":"https://openalex.org/W2019493309","doi":"https://doi.org/10.1186/1471-2105-10-28","mag":"2019493309","pmid":"https://pubmed.ncbi.nlm.nih.gov/19159460"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-28","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-28","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-28","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004567684","display_name":"Dimitra Alexopoulou","orcid":"https://orcid.org/0000-0002-3715-1756"},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Dimitra Alexopoulou","raw_affiliation_strings":["Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany. dimitra.alexopoulou@boitec.tu-dresden.de","Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany. dimitra.alexopoulou@boitec.tu-dresden.de","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104010009","display_name":"Bill Andreopoulos","orcid":null},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bill Andreopoulos","raw_affiliation_strings":["Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018344062","display_name":"Heiko Dietze","orcid":"https://orcid.org/0000-0003-0234-1688"},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Heiko Dietze","raw_affiliation_strings":["Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062561147","display_name":"Andreas Doms","orcid":null},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Andreas Doms","raw_affiliation_strings":["Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044946197","display_name":"Fabien Gandon","orcid":"https://orcid.org/0000-0003-0543-1232"},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Fabien Gandon","raw_affiliation_strings":["INRIA Sophia Antipolis, 2004 Route des Lucioles, 06902, Sophia Antipolis, France","INRIA\u2014Sophia Antipolis, Sophia Antipolis, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Sophia Antipolis, 2004 Route des Lucioles, 06902, Sophia Antipolis, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"INRIA\u2014Sophia Antipolis, Sophia Antipolis, France","institution_ids":["https://openalex.org/I1326498283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034893893","display_name":"J\u00f6rg Hakenberg","orcid":"https://orcid.org/0000-0001-8781-7766"},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Hakenberg","raw_affiliation_strings":["Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049147763","display_name":"Khaled Khelif","orcid":null},"institutions":[{"id":"https://openalex.org/I1326498283","display_name":"Institut national de recherche en sciences et technologies du num\u00e9rique","ror":"https://ror.org/02kvxyf05","country_code":"FR","type":"government","lineage":["https://openalex.org/I1326498283"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Khaled Khelif","raw_affiliation_strings":["INRIA Sophia Antipolis, 2004 Route des Lucioles, 06902, Sophia Antipolis, France","INRIA\u2014Sophia Antipolis, Sophia Antipolis, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"INRIA Sophia Antipolis, 2004 Route des Lucioles, 06902, Sophia Antipolis, France","institution_ids":["https://openalex.org/I1326498283"]},{"raw_affiliation_string":"INRIA\u2014Sophia Antipolis, Sophia Antipolis, France","institution_ids":["https://openalex.org/I1326498283"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016411406","display_name":"Michael Schroeder","orcid":"https://orcid.org/0000-0003-2848-6949"},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Schroeder","raw_affiliation_strings":["Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083599531","display_name":"Thomas W\u00e4chter","orcid":null},"institutions":[{"id":"https://openalex.org/I78650965","display_name":"Technische Universit\u00e4t Dresden","ror":"https://ror.org/042aqky30","country_code":"DE","type":"education","lineage":["https://openalex.org/I78650965"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas W\u00e4chter","raw_affiliation_strings":["Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biotechnology Center (BIOTEC), Technische Universit\u00e4t Dresden, 01062, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]},{"raw_affiliation_string":"Biotechnology Center (BIOTEC) Technische Universit\u00e4t Dresden, Dresden, Germany","institution_ids":["https://openalex.org/I78650965"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5004567684"],"corresponding_institution_ids":["https://openalex.org/I78650965"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.6425,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.82677133,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"10","issue":"1","first_page":"28","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9864000082015991,"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":0.9864000082015991,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0024999999441206455,"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":0.002400000113993883,"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/computer-science","display_name":"Computer science","score":0.8443810939788818},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.7972898483276367},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.7028802633285522},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.6553581953048706},{"id":"https://openalex.org/keywords/ontology-based-data-integration","display_name":"Ontology-based data integration","score":0.4517882466316223},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.44894811511039734},{"id":"https://openalex.org/keywords/upper-ontology","display_name":"Upper ontology","score":0.4359101951122284},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.39318931102752686},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19847789406776428},{"id":"https://openalex.org/keywords/semantic-web","display_name":"Semantic Web","score":0.1921614110469818}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8443810939788818},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7972898483276367},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.7028802633285522},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.6553581953048706},{"id":"https://openalex.org/C22550185","wikidata":"https://www.wikidata.org/wiki/Q7095047","display_name":"Ontology-based data integration","level":3,"score":0.4517882466316223},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.44894811511039734},{"id":"https://openalex.org/C78726541","wikidata":"https://www.wikidata.org/wiki/Q3882785","display_name":"Upper ontology","level":3,"score":0.4359101951122284},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.39318931102752686},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19847789406776428},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.1921614110469818},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","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/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008490","descriptor_name":"Medical Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008490","descriptor_name":"Medical Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008490","descriptor_name":"Medical Informatics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017432","descriptor_name":"Unified Medical Language System","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046650","descriptor_name":"Medical Subject Headings","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-10-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-28","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-28","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19159460","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19159460","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:scholarworks.sjsu.edu:computer_sci_pub-1006","is_oa":false,"landing_page_url":"https://scholarworks.sjsu.edu/computer_sci_pub/7","pdf_url":null,"source":{"id":"https://openalex.org/S4377196389","display_name":"San Jos\u00e9 State University ScholarWorks (San Jose State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I51504820","host_organization_name":"San Jose State University","host_organization_lineage":["https://openalex.org/I51504820"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications, Computer Science","raw_type":"text"},{"id":"pmh:oai:HAL:inria-00378553v1","is_oa":true,"landing_page_url":"https://inria.hal.science/inria-00378553","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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":"BMC Bioinformatics, 2009, 10, &#x27E8;10.1186/1471-2105-10-28&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:doaj.org/article:1150d28ef6e94c28bfa2f004fe0c7a0b","is_oa":false,"landing_page_url":"https://doaj.org/article/1150d28ef6e94c28bfa2f004fe0c7a0b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 28 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2663782","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2663782","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-28","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-28","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-28","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2019493309.pdf","grobid_xml":"https://content.openalex.org/works/W2019493309.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W116705248","https://openalex.org/W126722120","https://openalex.org/W170684085","https://openalex.org/W1512170015","https://openalex.org/W1532254950","https://openalex.org/W1546317785","https://openalex.org/W1552651695","https://openalex.org/W1555354714","https://openalex.org/W1592870675","https://openalex.org/W1647729745","https://openalex.org/W1756650108","https://openalex.org/W1840759059","https://openalex.org/W1869958975","https://openalex.org/W1885010341","https://openalex.org/W1907380269","https://openalex.org/W1959755538","https://openalex.org/W1969664420","https://openalex.org/W1984293430","https://openalex.org/W1994352268","https://openalex.org/W2000951787","https://openalex.org/W2038721957","https://openalex.org/W2047620598","https://openalex.org/W2054518234","https://openalex.org/W2056105869","https://openalex.org/W2085032889","https://openalex.org/W2085306687","https://openalex.org/W2087739686","https://openalex.org/W2096175520","https://openalex.org/W2097058215","https://openalex.org/W2098162425","https://openalex.org/W2101171038","https://openalex.org/W2101210369","https://openalex.org/W2103017472","https://openalex.org/W2108491719","https://openalex.org/W2116040937","https://openalex.org/W2116972916","https://openalex.org/W2117805756","https://openalex.org/W2121343862","https://openalex.org/W2127480960","https://openalex.org/W2127563440","https://openalex.org/W2130337399","https://openalex.org/W2132784310","https://openalex.org/W2132819807","https://openalex.org/W2134769633","https://openalex.org/W2156540941","https://openalex.org/W2159583324","https://openalex.org/W2159882563","https://openalex.org/W2160842254","https://openalex.org/W2168091548","https://openalex.org/W2171647789","https://openalex.org/W2175779775","https://openalex.org/W2531563875","https://openalex.org/W2599152927","https://openalex.org/W3020747745","https://openalex.org/W4235505822","https://openalex.org/W4248219478"],"related_works":["https://openalex.org/W2066689607","https://openalex.org/W1794266373","https://openalex.org/W1506177826","https://openalex.org/W2159818280","https://openalex.org/W2114954739","https://openalex.org/W2889792096","https://openalex.org/W2363188691","https://openalex.org/W2357775360","https://openalex.org/W4251889114","https://openalex.org/W2804669904"],"abstract_inverted_index":{"BACKGROUND:":[0],"Ontology":[1,182,226],"term":[2],"labels":[3],"can":[4,304],"be":[5],"ambiguous":[6,177],"and":[7,85,183],"have":[8],"multiple":[9,98],"senses.":[10,118],"While":[11],"this":[12],"is":[13,20,236,259],"no":[14,272],"problem":[15],"for":[16,68,127,175,261,319],"human":[17],"annotators,":[18],"it":[19],"a":[21,124,141,167,238,243,275,292,306],"challenge":[22],"to":[23,34,78,114,310],"automated":[24],"methods,":[25],"which":[26,82,155,280],"identify":[27],"ontology":[28,55,96,135],"terms":[29,110,129,178],"in":[30,111,326],"text.":[31],"Classical":[32],"approaches":[33,77,164,186],"word":[35,79],"sense":[36,80],"disambiguation":[37,69,323],"use":[38,52,83],"co-occurring":[39,109,128],"words":[40],"or":[41,57],"terms.":[42,62],"However,":[43],"most":[44],"treat":[45],"ontologies":[46,84,303],"as":[47,211,234],"simple":[48],"terminologies,":[49],"without":[50],"making":[51],"of":[53,66,100,108,116,172,213,322],"the":[54,58,95,101,105,112,134,156,180,214,297,320],"structure":[56],"semantic":[59],"similarity":[60],"between":[61],"Another":[63],"useful":[64],"source":[65],"information":[67],"are":[70,281,324],"metadata.":[71,144],"Here,":[72],"we":[73,165],"systematically":[74],"compare":[75],"three":[76,315],"disambiguation,":[81,262],"metadata,":[86],"respectively.":[87],"RESULTS:":[88],"The":[89,119,137,196,218,247,314],"'Closest":[90,248],"Sense'":[91,249],"method":[92,122],"assumes":[93],"that":[94,300],"defines":[97,123],"senses":[99],"term.":[102],"It":[103,145],"computes":[104],"shortest":[106],"path":[107],"document":[113],"one":[115],"these":[117,163],"'Term":[120,219],"Cooc'":[121,220],"log-odds":[125],"ratio":[126],"including":[130],"co-occurrences":[131],"inferred":[132],"from":[133,179],"structure.":[136],"'MetaData'":[138,197],"approach":[139,198,221,250],"trains":[140],"classifier":[142],"on":[143,194,205,224,230,252],"does":[146],"not":[147,237],"require":[148],"any":[149],"ontology,":[150,279],"but":[151,241,263,274],"requires":[152,264,271],"training":[153,170,215,267],"data,":[154],"other":[157],"methods":[158],"do":[159],"not.":[160],"To":[161],"evaluate":[162],"defined":[166],"manually":[168],"curated":[169],"corpus":[171],"2600":[173],"documents":[174],"seven":[176],"Gene":[181,225],"MeSH.":[184],"All":[185],"over":[187],"all":[188],"conditions":[189],"achieve":[190],"80%":[191,254],"success":[192,255,290],"rate":[193],"average.":[195],"performed":[199],"best":[200],"with":[201],"96%,":[202],"when":[203],"trained":[204],"high-quality":[206],"data.":[207,268],"Its":[208],"performance":[209],"deteriorates":[210],"quality":[212,266],"data":[216],"decreases.":[217],"performs":[222],"better":[223],"(92%":[227],"success)":[228,233],"than":[229],"MeSH":[231,235],"(73%":[232],"strict":[239],"is-a/part-of,":[240],"rather":[242],"loose":[244],"is-related-to":[245],"hierarchy.":[246],"achieves":[251,287],"average":[253],"rate.":[256],"CONCLUSION:":[257],"Metadata":[258],"valuable":[260],"high":[265],"Closest":[269],"Sense":[270],"training,":[273],"large,":[276],"consistently":[277,293],"modelled":[278,294],"two":[282],"opposing":[283],"conditions.":[284],"Term":[285],"Cooc":[286],"greater":[288],"90%":[289],"given":[291],"ontology.":[295],"Overall,":[296],"results":[298],"show":[299],"well":[301],"structured":[302],"play":[305],"very":[307],"important":[308],"role":[309],"improve":[311],"disambiguation.":[312],"AVAILABILITY:":[313],"benchmark":[316],"datasets":[317],"created":[318],"purpose":[321],"available":[325],"Additional":[327],"file":[328],"1.":[329]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":6},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
