{"id":"https://openalex.org/W4311573037","doi":"https://doi.org/10.1186/s12859-022-04993-4","title":"Extract antibody and antigen names from biomedical literature","display_name":"Extract antibody and antigen names from biomedical literature","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4311573037","doi":"https://doi.org/10.1186/s12859-022-04993-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/36474140"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04993-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04993-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04993-4","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/s12859-022-04993-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019522730","display_name":"Thuy Trang Dinh","orcid":null},"institutions":[{"id":"https://openalex.org/I23582244","display_name":"Ho Chi Minh City University of Science","ror":"https://ror.org/05jfbgm49","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I23582244"]},{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Thuy Trang Dinh","raw_affiliation_strings":["Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","Vietnam National University, Ho Chi Minh City, Vietnam"],"affiliations":[{"raw_affiliation_string":"Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I23582244"]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037715286","display_name":"Trang Phuong Vo-Chanh","orcid":null},"institutions":[{"id":"https://openalex.org/I23582244","display_name":"Ho Chi Minh City University of Science","ror":"https://ror.org/05jfbgm49","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I23582244"]},{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Trang Phuong Vo-Chanh","raw_affiliation_strings":["Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","Vietnam National University, Ho Chi Minh City, Vietnam"],"affiliations":[{"raw_affiliation_string":"Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I23582244"]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101875400","display_name":"Chau Nguyen","orcid":"https://orcid.org/0000-0003-0068-0387"},"institutions":[{"id":"https://openalex.org/I23582244","display_name":"Ho Chi Minh City University of Science","ror":"https://ror.org/05jfbgm49","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I23582244"]},{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Chau Nguyen","raw_affiliation_strings":["Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","Vietnam National University, Ho Chi Minh City, Vietnam"],"affiliations":[{"raw_affiliation_string":"Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I23582244"]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005823542","display_name":"Viet Quoc Huynh","orcid":null},"institutions":[{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]},{"id":"https://openalex.org/I23582244","display_name":"Ho Chi Minh City University of Science","ror":"https://ror.org/05jfbgm49","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I23582244"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Viet Quoc Huynh","raw_affiliation_strings":["Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","Vietnam National University, Ho Chi Minh City, Vietnam"],"affiliations":[{"raw_affiliation_string":"Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I23582244"]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018747497","display_name":"Nam Vo","orcid":"https://orcid.org/0000-0003-2196-1946"},"institutions":[{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]},{"id":"https://openalex.org/I23582244","display_name":"Ho Chi Minh City University of Science","ror":"https://ror.org/05jfbgm49","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I23582244"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Nam Vo","raw_affiliation_strings":["Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam","Vietnam National University, Ho Chi Minh City, Vietnam"],"affiliations":[{"raw_affiliation_string":"Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I23582244"]},{"raw_affiliation_string":"Laboratory of Molecular Biotechnology, University of Science, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I23582244"]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100766549","display_name":"Hoang Duc Nguyen","orcid":"https://orcid.org/0000-0003-2437-3568"},"institutions":[{"id":"https://openalex.org/I123565023","display_name":"Vietnam National University Ho Chi Minh City","ror":"https://ror.org/00waaqh38","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Hoang Duc Nguyen","raw_affiliation_strings":["Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam. nguyen_hoang.xuatban@hotmail.com","Vietnam National University, Ho Chi Minh City, Vietnam. nguyen_hoang.xuatban@hotmail.com","Vietnam National University, Ho Chi Minh City, Vietnam"],"affiliations":[{"raw_affiliation_string":"Center for Bioscience and Biotechnology, University of Science, Ho Chi Minh City, Vietnam. nguyen_hoang.xuatban@hotmail.com","institution_ids":[]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam. nguyen_hoang.xuatban@hotmail.com","institution_ids":[]},{"raw_affiliation_string":"Vietnam National University, Ho Chi Minh City, Vietnam","institution_ids":["https://openalex.org/I123565023"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5019522730"],"corresponding_institution_ids":["https://openalex.org/I123565023","https://openalex.org/I23582244"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.3466,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.56591239,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"23","issue":"1","first_page":"524","last_page":"524"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.996999979019165,"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":0.996999979019165,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9940000176429749,"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":0.9896000027656555,"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":0.6712231040000916},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.6548218727111816},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.6445904970169067},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5899975895881653},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.38029855489730835},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37783297896385193},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33518552780151367},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.2097162902355194},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1812157928943634},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.07506418228149414}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6712231040000916},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.6548218727111816},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.6445904970169067},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5899975895881653},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.38029855489730835},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37783297896385193},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33518552780151367},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2097162902355194},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1812157928943634},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.07506418228149414},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-022-04993-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04993-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04993-4","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:36474140","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36474140","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:da2e5a068cb747b4bb37b598f94ee0fd","is_oa":true,"landing_page_url":"https://doaj.org/article/da2e5a068cb747b4bb37b598f94ee0fd","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 1-21 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9727932","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9727932","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/s12859-022-04993-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04993-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04993-4","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":0.7099999785423279,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4311573037.pdf","grobid_xml":"https://content.openalex.org/works/W4311573037.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W47135330","https://openalex.org/W2001927093","https://openalex.org/W2110505462","https://openalex.org/W2164777277","https://openalex.org/W2170189740","https://openalex.org/W2296283641","https://openalex.org/W2610394652","https://openalex.org/W2769387903","https://openalex.org/W2769697870","https://openalex.org/W2779457220","https://openalex.org/W2803614960","https://openalex.org/W2890830728","https://openalex.org/W2911489562","https://openalex.org/W2919115771","https://openalex.org/W2929208326","https://openalex.org/W2948614377","https://openalex.org/W2967886424","https://openalex.org/W2972482444","https://openalex.org/W2997394673","https://openalex.org/W2998141384","https://openalex.org/W3023249475","https://openalex.org/W3036430163","https://openalex.org/W3047082542","https://openalex.org/W3091311542","https://openalex.org/W3105491236","https://openalex.org/W3110882441","https://openalex.org/W3130583616","https://openalex.org/W3198335263"],"related_works":["https://openalex.org/W3199871245","https://openalex.org/W2915436880","https://openalex.org/W2078793151","https://openalex.org/W3017222382","https://openalex.org/W3128216712","https://openalex.org/W3136915866","https://openalex.org/W2886890203","https://openalex.org/W4313535650","https://openalex.org/W2287770975","https://openalex.org/W3215585698"],"abstract_inverted_index":{"Our":[0],"antibody-antigen":[1,39],"NER":[2,32,56],"models":[3],"enable":[4],"users":[5],"to":[6,36],"automatically":[7,37],"extract":[8],"antibody":[9,42],"and":[10,24,44],"antigen":[11],"names":[12],"from":[13],"scientific":[14],"articles":[15],"without":[16],"manually":[17],"scanning":[18],"through":[19],"vast":[20],"amounts":[21],"of":[22,31,52],"data":[23],"information":[25],"in":[26],"the":[27,48],"literature.":[28],"The":[29,54],"output":[30],"can":[33],"be":[34],"used":[35],"populate":[38],"databases,":[40],"support":[41],"validation,":[43],"facilitate":[45],"researchers":[46],"with":[47],"most":[49],"appropriate":[50],"antibodies":[51],"interest.":[53],"packaged":[55],"model":[57],"is":[58],"available":[59],"at":[60],"https://github.com/TrangDinh44/ABAG_BioBERT.git":[61],".":[62]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}