{"id":"https://openalex.org/W4309745330","doi":"https://doi.org/10.1186/s12859-022-05051-9","title":"BioByGANS: biomedical named entity recognition by fusing contextual and syntactic features through graph attention network in node classification framework","display_name":"BioByGANS: biomedical named entity recognition by fusing contextual and syntactic features through graph attention network in node classification framework","publication_year":2022,"publication_date":"2022-11-22","ids":{"openalex":"https://openalex.org/W4309745330","doi":"https://doi.org/10.1186/s12859-022-05051-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/36418937"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-05051-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05051-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05051-9","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/s12859-022-05051-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052284551","display_name":"Xiangwen Zheng","orcid":"https://orcid.org/0000-0001-7940-0514"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiangwen Zheng","raw_affiliation_strings":["Academy of Military Medical Sciences, Beijing, 100039, China"],"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences, Beijing, 100039, China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112123850","display_name":"Haijian Du","orcid":null},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haijian Du","raw_affiliation_strings":["Academy of Military Medical Sciences, Beijing, 100039, China"],"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences, Beijing, 100039, China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101884175","display_name":"Xiaowei Luo","orcid":"https://orcid.org/0009-0005-9682-3136"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaowei Luo","raw_affiliation_strings":["Academy of Military Medical Sciences, Beijing, 100039, China"],"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences, Beijing, 100039, China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101683944","display_name":"Fan Tong","orcid":"https://orcid.org/0000-0002-4588-8520"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Tong","raw_affiliation_strings":["Academy of Military Medical Sciences, Beijing, 100039, China"],"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences, Beijing, 100039, China","institution_ids":["https://openalex.org/I2802541053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074371475","display_name":"Wei Song","orcid":"https://orcid.org/0000-0002-0828-7486"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wei Song","raw_affiliation_strings":["Beijing MedPeer Information Technology Co., Ltd, Beijing, 102300, China"],"affiliations":[{"raw_affiliation_string":"Beijing MedPeer Information Technology Co., Ltd, Beijing, 102300, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102751782","display_name":"Dongsheng Zhao","orcid":"https://orcid.org/0000-0003-2616-8891"},"institutions":[{"id":"https://openalex.org/I2802541053","display_name":"Academy of Military Medical Sciences","ror":"https://ror.org/02bv3c993","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802541053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongsheng Zhao","raw_affiliation_strings":["Academy of Military Medical Sciences, Beijing, 100039, China. dszhao@bmi.ac.cn","Academy of Military Medical Sciences, Beijing, 100039, China"],"affiliations":[{"raw_affiliation_string":"Academy of Military Medical Sciences, Beijing, 100039, China. dszhao@bmi.ac.cn","institution_ids":[]},{"raw_affiliation_string":"Academy of Military Medical Sciences, Beijing, 100039, China","institution_ids":["https://openalex.org/I2802541053"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5052284551"],"corresponding_institution_ids":["https://openalex.org/I2802541053"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.3459,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.90199108,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"23","issue":"1","first_page":"501","last_page":"501"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9995999932289124,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9987999796867371,"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":0.9937000274658203,"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/softmax-function","display_name":"Softmax function","score":0.8843458890914917},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8194893598556519},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.6232714056968689},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6175984144210815},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5541884303092957},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.509601354598999},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.47764718532562256},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4756184220314026},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.4597570598125458},{"id":"https://openalex.org/keywords/sequence-labeling","display_name":"Sequence labeling","score":0.4424901604652405},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.4213230013847351},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.3844417333602905},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.34821754693984985},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.2706626355648041},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.24920985102653503},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.23588290810585022}],"concepts":[{"id":"https://openalex.org/C188441871","wikidata":"https://www.wikidata.org/wiki/Q7554146","display_name":"Softmax function","level":3,"score":0.8843458890914917},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8194893598556519},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.6232714056968689},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6175984144210815},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5541884303092957},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.509601354598999},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.47764718532562256},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4756184220314026},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.4597570598125458},{"id":"https://openalex.org/C35639132","wikidata":"https://www.wikidata.org/wiki/Q7452468","display_name":"Sequence labeling","level":3,"score":0.4424901604652405},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.4213230013847351},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.3844417333602905},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.34821754693984985},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.2706626355648041},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.24920985102653503},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.23588290810585022},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"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":"D012660","descriptor_name":"Semantics","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":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013060","descriptor_name":"Speech","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013060","descriptor_name":"Speech","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013060","descriptor_name":"Speech","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-05051-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05051-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05051-9","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:36418937","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36418937","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:doaj.org/article:bd5230aee24c4045ac1c666d2f8c6675","is_oa":true,"landing_page_url":"https://doaj.org/article/bd5230aee24c4045ac1c666d2f8c6675","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-19 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9682683","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9682683","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":"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/s12859-022-05051-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-05051-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-05051-9","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":[{"score":0.6800000071525574,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309745330.pdf","grobid_xml":"https://content.openalex.org/works/W4309745330.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1592053870","https://openalex.org/W1610821757","https://openalex.org/W1980867644","https://openalex.org/W2008639146","https://openalex.org/W2020073413","https://openalex.org/W2047782770","https://openalex.org/W2050006154","https://openalex.org/W2064675550","https://openalex.org/W2068602529","https://openalex.org/W2071879021","https://openalex.org/W2100627415","https://openalex.org/W2123442489","https://openalex.org/W2145870108","https://openalex.org/W2149369282","https://openalex.org/W2154142897","https://openalex.org/W2162461580","https://openalex.org/W2167992389","https://openalex.org/W2168990503","https://openalex.org/W2169099542","https://openalex.org/W2169491861","https://openalex.org/W2171374484","https://openalex.org/W2250539671","https://openalex.org/W2296283641","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2562426122","https://openalex.org/W2769387903","https://openalex.org/W2771737522","https://openalex.org/W2800535933","https://openalex.org/W2890830728","https://openalex.org/W2907492528","https://openalex.org/W2911489562","https://openalex.org/W2914754444","https://openalex.org/W2919115771","https://openalex.org/W2925613093","https://openalex.org/W2944400536","https://openalex.org/W2962739339","https://openalex.org/W2963339489","https://openalex.org/W2964242047","https://openalex.org/W3037333170","https://openalex.org/W3082330004","https://openalex.org/W3105491236","https://openalex.org/W3107083523","https://openalex.org/W3114761096","https://openalex.org/W3157876196","https://openalex.org/W3166508187","https://openalex.org/W3173473737","https://openalex.org/W3186054896","https://openalex.org/W4206380771","https://openalex.org/W4210257598","https://openalex.org/W4244103815","https://openalex.org/W4245267204","https://openalex.org/W6673674451","https://openalex.org/W6679436768","https://openalex.org/W6787641335"],"related_works":["https://openalex.org/W2186562580","https://openalex.org/W3198729192","https://openalex.org/W189110383","https://openalex.org/W2530283981","https://openalex.org/W4300474194","https://openalex.org/W2792659145","https://openalex.org/W3094868181","https://openalex.org/W2901060953","https://openalex.org/W2027233318","https://openalex.org/W2899463504"],"abstract_inverted_index":{"The":[0],"experimental":[1],"results":[2],"on":[3],"8":[4],"biomedical":[5],"benchmark":[6],"datasets":[7],"demonstrate":[8],"the":[9,18,31],"effectiveness":[10],"of":[11],"our":[12],"model,":[13],"and":[14,26],"indicate":[15],"that":[16],"formulating":[17],"BioNER":[19],"task":[20],"into":[21,30],"a":[22],"node":[23],"classification":[24],"problem":[25],"combining":[27],"syntactic":[28],"features":[29],"graph":[32],"attention":[33],"networks":[34],"can":[35],"significantly":[36],"improve":[37],"model":[38],"performance.":[39]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
