{"id":"https://openalex.org/W4220735656","doi":"https://doi.org/10.1016/j.jbi.2022.104059","title":"PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology","display_name":"PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology","publication_year":2022,"publication_date":"2022-03-26","ids":{"openalex":"https://openalex.org/W4220735656","doi":"https://doi.org/10.1016/j.jbi.2022.104059","pmid":"https://pubmed.ncbi.nlm.nih.gov/35351638"},"language":"en","primary_location":{"id":"doi:10.1016/j.jbi.2022.104059","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.jbi.2022.104059","pdf_url":null,"source":{"id":"https://openalex.org/S11622463","display_name":"Journal of Biomedical Informatics","issn_l":"1532-0464","issn":["1532-0464","1532-0480"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1016/j.jbi.2022.104059","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016741865","display_name":"Shankai Yan","orcid":"https://orcid.org/0000-0003-0369-4979"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shankai Yan","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100619435","display_name":"Ling Luo","orcid":"https://orcid.org/0000-0002-5141-0259"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ling Luo","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016587469","display_name":"Po\u2010Ting Lai","orcid":"https://orcid.org/0000-0003-2025-318X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Po-Ting Lai","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044587037","display_name":"Daniel Veltri","orcid":"https://orcid.org/0000-0002-6101-6693"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Veltri","raw_affiliation_strings":["Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017008767","display_name":"Andrew J. Oler","orcid":"https://orcid.org/0000-0002-6310-0434"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew J. Oler","raw_affiliation_strings":["Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000331278","display_name":"Sandhya Xirasagar","orcid":null},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sandhya Xirasagar","raw_affiliation_strings":["Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030284017","display_name":"Rajarshi Ghosh","orcid":"https://orcid.org/0000-0001-7368-8940"},"institutions":[{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajarshi Ghosh","raw_affiliation_strings":["Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA"],"affiliations":[{"raw_affiliation_string":"Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081895942","display_name":"Morgan Similuk","orcid":"https://orcid.org/0000-0002-0403-2689"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210134534","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210134534"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Morgan Similuk","raw_affiliation_strings":["Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA"],"affiliations":[{"raw_affiliation_string":"Centralized Sequencing Program, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA","institution_ids":["https://openalex.org/I4210134534","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033225381","display_name":"Peter N. Robinson","orcid":"https://orcid.org/0000-0002-0736-9199"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter N. Robinson","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA"],"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083081872","display_name":"Zhiyong Lu","orcid":"https://orcid.org/0000-0001-9998-916X"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhiyong Lu","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA. Electronic address: Zhiyong.Lu@nih.gov","National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA. Electronic address: Zhiyong.Lu@nih.gov","institution_ids":[]},{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5083081872"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":2980,"currency":"USD","value_usd":2980},"apc_paid":{"value":2980,"currency":"USD","value_usd":2980},"fwci":0.5207,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60526031,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"129","issue":null,"first_page":"104059","last_page":"104059"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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/T10028","display_name":"Topic Modeling","score":0.9952999949455261,"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":0.9937999844551086,"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":0.8041781783103943},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.7936763763427734},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6494216322898865},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.6490037441253662},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5560085773468018},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.5079720616340637},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5078006386756897},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.4948107600212097},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4514748156070709},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.44721555709838867},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.42981240153312683},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.426017701625824},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4210091531276703},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4193820357322693},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.39128533005714417},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36297607421875}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8041781783103943},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.7936763763427734},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6494216322898865},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.6490037441253662},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5560085773468018},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.5079720616340637},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5078006386756897},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.4948107600212097},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4514748156070709},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.44721555709838867},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.42981240153312683},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.426017701625824},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4210091531276703},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4193820357322693},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39128533005714417},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36297607421875},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1016/j.jbi.2022.104059","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.jbi.2022.104059","pdf_url":null,"source":{"id":"https://openalex.org/S11622463","display_name":"Journal of Biomedical Informatics","issn_l":"1532-0464","issn":["1532-0464","1532-0480"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Informatics","raw_type":"journal-article"},{"id":"pmid:35351638","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35351638","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of biomedical informatics","raw_type":null},{"id":"pmh:oai:mouseion.jax.org:stfb2022-1079","is_oa":false,"landing_page_url":"https://mouseion.jax.org/stfb2022/76","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2022","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:11040548","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11040548","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Biomed Inform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/j.jbi.2022.104059","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.jbi.2022.104059","pdf_url":null,"source":{"id":"https://openalex.org/S11622463","display_name":"Journal of Biomedical Informatics","issn_l":"1532-0464","issn":["1532-0464","1532-0480"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Biomedical Informatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5299999713897705,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1481389199","https://openalex.org/W2025349319","https://openalex.org/W2057900969","https://openalex.org/W2080770151","https://openalex.org/W2105290783","https://openalex.org/W2119613819","https://openalex.org/W2122402213","https://openalex.org/W2137724373","https://openalex.org/W2138621090","https://openalex.org/W2146241755","https://openalex.org/W2159583324","https://openalex.org/W2162323699","https://openalex.org/W2318368071","https://openalex.org/W2557385283","https://openalex.org/W2558643140","https://openalex.org/W2767470330","https://openalex.org/W2778310824","https://openalex.org/W2901332105","https://openalex.org/W2901527454","https://openalex.org/W2921612399","https://openalex.org/W2928818852","https://openalex.org/W2946102094","https://openalex.org/W2951146425","https://openalex.org/W2963373823","https://openalex.org/W2971258845","https://openalex.org/W3087028093","https://openalex.org/W3104015140","https://openalex.org/W4212919921","https://openalex.org/W6664979998","https://openalex.org/W6747741389","https://openalex.org/W6761288102"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W1557094818","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516"],"abstract_inverted_index":{"The":[0,40,60,113,187],"study":[1],"aims":[2],"at":[3],"developing":[4],"a":[5,53,83,89],"neural":[6],"network":[7],"model":[8,73,77,119,170,197],"to":[9,36,42,56,164],"improve":[10,121],"the":[11,23,29,33,64,71,79,94,105,110,122,125,138,144,153,158,172,176,179,183,191,195,201,209],"performance":[12,106,123],"of":[13,109,124,152,203],"Human":[14],"Phenotype":[15],"Ontology":[16],"(HPO)":[17],"concept":[18,205],"recognition":[19,206],"tools.":[20],"We":[21,92],"used":[22],"terms,":[24],"definitions,":[25],"and":[26,50,82,103,132,178,194],"comments":[27],"about":[28],"phenotypic":[30],"concepts":[31],"in":[32,134,162,167,175,182],"HPO":[34,100,204],"database":[35],"train":[37],"our":[38,118],"model.":[39],"document":[41],"be":[43],"analyzed":[44],"is":[45],"first":[46],"split":[47],"into":[48,70],"sentences":[49,184],"annotated":[51],"with":[52,63,143,208],"base":[54,145,159,210],"method":[55],"generate":[57],"candidate":[58,65],"concepts.":[59],"sentences,":[61],"along":[62],"concepts,":[66],"are":[67],"then":[68],"fed":[69],"pre-trained":[72,80],"for":[74,185],"re-ranking.":[75,186],"Our":[76,169],"comprises":[78],"BlueBERT":[81],"feature":[84],"selection":[85],"module,":[86],"followed":[87],"by":[88,97,157],"contrastive":[90],"loss.":[91],"re-ranked":[93],"results":[95,115,188],"generated":[96],"three":[98],"robust":[99],"annotation":[101],"tools":[102],"compared":[104,142,207],"against":[107],"most":[108],"existing":[111,126],"approaches.":[112],"experimental":[114],"show":[116],"that":[117,190],"can":[120,198],"methods.":[127,146],"Significantly,":[128],"it":[129],"boosted":[130],"3.0%":[131],"5.6%":[133],"F1":[135],"score":[136],"on":[137],"two":[139],"evaluated":[140],"datasets":[141],"It":[147],"removed":[148],"more":[149],"than":[150],"80%":[151],"false":[154],"positives":[155],"predicted":[156],"methods,":[160],"resulting":[161],"up":[163],"18%":[165],"improvement":[166],"precision.":[168],"utilizes":[171],"descriptive":[173],"data":[174],"ontology":[177],"contextual":[180],"information":[181,193],"indicate":[189],"additional":[192],"re-ranking":[196],"significantly":[199],"enhance":[200],"precision":[202],"method.":[211]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
