{"id":"https://openalex.org/W3017463390","doi":"https://doi.org/10.1371/journal.pcbi.1007617","title":"BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale","display_name":"BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale","publication_year":2020,"publication_date":"2020-04-23","ids":{"openalex":"https://openalex.org/W3017463390","doi":"https://doi.org/10.1371/journal.pcbi.1007617","mag":"3017463390","pmid":"https://pubmed.ncbi.nlm.nih.gov/32324731"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007617","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007617","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007617&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007617&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042874172","display_name":"Qingyu Chen","orcid":"https://orcid.org/0000-0002-6036-1516"},"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":"Qingyu Chen","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004629166","display_name":"Kyubum Lee","orcid":"https://orcid.org/0000-0003-2015-3939"},"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":"Kyubum Lee","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016741865","display_name":"Shankai Yan","orcid":"https://orcid.org/0000-0003-0369-4979"},"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":"Shankai Yan","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100460452","display_name":"Sun Kim","orcid":"https://orcid.org/0000-0003-3072-6649"},"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":"Sun Kim","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058918482","display_name":"Chih-Hsuan Wei","orcid":"https://orcid.org/0000-0001-5094-7321"},"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":"Chih-Hsuan Wei","raw_affiliation_strings":["National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"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, Maryland, United States of America"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, Maryland, United States of America","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5083081872"],"corresponding_institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210109390"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.9213,"has_fulltext":true,"cited_by_count":65,"citation_normalized_percentile":{"value":0.9478925,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"16","issue":"4","first_page":"e1007617","last_page":"e1007617"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9976999759674072,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9939000010490417,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7031899094581604},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6577739715576172},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5983616709709167},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5164337754249573},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.49122685194015503},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4848116934299469},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.337302029132843},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.22743096947669983}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7031899094581604},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6577739715576172},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5983616709709167},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5164337754249573},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.49122685194015503},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4848116934299469},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.337302029132843},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.22743096947669983},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","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":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D039781","descriptor_name":"PubMed","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":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057286","descriptor_name":"Electronic Health Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007617","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007617","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007617&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:32324731","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32324731","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:arXiv.org:1912.10846","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1912.10846","pdf_url":"https://arxiv.org/pdf/1912.10846","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:doaj.org/article:672492f8e3f84727b53d4b19eac823a1","is_oa":true,"landing_page_url":"https://doaj.org/article/672492f8e3f84727b53d4b19eac823a1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 4, p e1007617 (2020)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/12184326","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:7237030","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7237030","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007617","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007617","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007617&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.44999998807907104}],"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":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3017463390.pdf","grobid_xml":"https://content.openalex.org/works/W3017463390.grobid-xml"},"referenced_works_count":77,"referenced_works":["https://openalex.org/W202767273","https://openalex.org/W1597195725","https://openalex.org/W1610821757","https://openalex.org/W1611787727","https://openalex.org/W1644749979","https://openalex.org/W1958077162","https://openalex.org/W1964670939","https://openalex.org/W2010457001","https://openalex.org/W2011365423","https://openalex.org/W2022484638","https://openalex.org/W2099307202","https://openalex.org/W2101680936","https://openalex.org/W2109651326","https://openalex.org/W2118582067","https://openalex.org/W2125117006","https://openalex.org/W2148488766","https://openalex.org/W2153579005","https://openalex.org/W2159583324","https://openalex.org/W2163480486","https://openalex.org/W2170189740","https://openalex.org/W2250539671","https://openalex.org/W2252211741","https://openalex.org/W2284851926","https://openalex.org/W2414378847","https://openalex.org/W2493916176","https://openalex.org/W2514071032","https://openalex.org/W2515248967","https://openalex.org/W2517259736","https://openalex.org/W2564387948","https://openalex.org/W2617241599","https://openalex.org/W2752636837","https://openalex.org/W2753199411","https://openalex.org/W2757849489","https://openalex.org/W2765742249","https://openalex.org/W2765765241","https://openalex.org/W2767891136","https://openalex.org/W2780932362","https://openalex.org/W2786757148","https://openalex.org/W2787031888","https://openalex.org/W2787243831","https://openalex.org/W2794764220","https://openalex.org/W2796398651","https://openalex.org/W2883618792","https://openalex.org/W2886946814","https://openalex.org/W2887377515","https://openalex.org/W2891469329","https://openalex.org/W2896016608","https://openalex.org/W2900569176","https://openalex.org/W2904741621","https://openalex.org/W2906258332","https://openalex.org/W2913962323","https://openalex.org/W2914171828","https://openalex.org/W2916047525","https://openalex.org/W2924331208","https://openalex.org/W2939903565","https://openalex.org/W2940542551","https://openalex.org/W2941748305","https://openalex.org/W2944400536","https://openalex.org/W2946690328","https://openalex.org/W2952631022","https://openalex.org/W2962739339","https://openalex.org/W2962969117","https://openalex.org/W2962986031","https://openalex.org/W2963271116","https://openalex.org/W2963563735","https://openalex.org/W2963611386","https://openalex.org/W2963923670","https://openalex.org/W2971291422","https://openalex.org/W2973105206","https://openalex.org/W2997522493","https://openalex.org/W3020931369","https://openalex.org/W3040301513","https://openalex.org/W3104059174","https://openalex.org/W4206006351","https://openalex.org/W4236122429","https://openalex.org/W4294170691","https://openalex.org/W4294367149"],"related_works":["https://openalex.org/W2887358545","https://openalex.org/W2914463643","https://openalex.org/W4241083716","https://openalex.org/W2096951189","https://openalex.org/W3185751515","https://openalex.org/W4255692567","https://openalex.org/W3179963059","https://openalex.org/W2108706252","https://openalex.org/W2961085424","https://openalex.org/W97427318"],"abstract_inverted_index":{"A":[0],"massive":[1],"number":[2],"of":[3,19,23,45,48,60,152,170],"biological":[4,24,30],"entities,":[5],"such":[6,32],"as":[7,33],"genes":[8],"and":[9,37,75,81,108,123,150,168,184,187,194,216,258,284,291],"mutations,":[10],"are":[11,70,87,294],"mentioned":[12,146],"in":[13,147,255,280],"the":[14,20,43,58,79,91,148,153,156,166,229,263],"biomedical":[15,97,144,159,285],"literature.":[16],"The":[17,236],"capturing":[18],"semantic":[21],"relatedness":[22],"entities":[25],"is":[26,151],"vital":[27],"to":[28,56,73,89,162,232],"many":[29],"applications,":[31],"protein-protein":[34],"interaction":[35,192,196],"prediction":[36,193],"literature-based":[38],"discovery.":[39],"Concept":[40],"embeddings-which":[41],"involve":[42],"learning":[44,52,85,133,274],"vector":[46],"representations":[47],"concepts":[49,77,145,180],"using":[50,199,269],"machine":[51,84,116,132],"models-have":[53],"been":[54],"employed":[55,114],"capture":[57],"semantics":[59],"concepts.":[61,260],"To":[62,164],"develop":[63],"concept":[64,98,121,126,160,253],"embeddings,":[65,127],"named-entity":[66],"recognition":[67,122],"(NER)":[68],"tools":[69,119],"first":[71],"used":[72,88],"identify":[74],"normalize":[76],"from":[78,102,204,211,220],"literature,":[80],"then":[82],"different":[83,131],"models":[86,134,275],"train":[90],"embeddings.":[92],"Despite":[93],"multiple":[94],"attempts,":[95],"existing":[96,252],"embeddings":[99,161,254,290],"generally":[100],"suffer":[101],"suboptimal":[103],"NER":[104,118],"tools,":[105],"small-scale":[106],"evaluation,":[107],"limited":[109],"availability.":[110],"In":[111],"response,":[112],"we":[113,172],"high-performance":[115],"learning-based":[117],"for":[120],"trained":[124],"our":[125,233],"BioConceptVec,":[128,171],"via":[129],"four":[130],"on":[135,182],"~30":[136],"million":[137,202,209,218],"PubMed":[138],"abstracts.":[139],"BioConceptVec":[140,242,270,289],"covers":[141],"over":[142,200],"400,000":[143],"literature":[149],"largest":[154],"among":[155],"publicly":[157,295],"available":[158,296],"date.":[163],"evaluate":[165],"validity":[167],"utility":[169],"respectively":[173],"performed":[174],"two":[175,188],"intrinsic":[176,213,237],"evaluations":[177,190],"(identifying":[178],"related":[179,259],"based":[181],"drug-gene":[183],"gene-gene":[185],"interactions)":[186],"extrinsic":[189,222,264],"(protein-protein":[191],"drug-drug":[195],"extraction),":[197],"collectively":[198],"25":[201],"instances":[203,210,219],"nine":[205],"independent":[206],"datasets":[207,293],"(17":[208],"six":[212],"evaluation":[214,223,238,265],"tasks":[215],"8":[217],"three":[221],"tasks),":[224],"which":[225],"is,":[226],"by":[227,245],"far,":[228],"most":[230],"comprehensive":[231],"best":[234],"knowledge.":[235],"results":[239,266],"demonstrate":[240,267],"that":[241,268],"consistently":[243],"has,":[244],"a":[246],"large":[247],"margin,":[248],"better":[249],"performance":[250,279],"than":[251],"identifying":[256],"similar":[257],"More":[261],"importantly,":[262],"with":[271],"advanced":[272],"deep":[273],"can":[276],"significantly":[277],"improve":[278],"downstream":[281],"bioinformatics":[282],"studies":[283],"text-mining":[286],"applications.":[287],"Our":[288],"benchmarking":[292],"at":[297],"https://github.com/ncbi-nlp/BioConceptVec.":[298]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":5},{"year":2018,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
