{"id":"https://openalex.org/W4402035795","doi":"https://doi.org/10.1093/database/baae094","title":"Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach","display_name":"Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4402035795","doi":"https://doi.org/10.1093/database/baae094","pmid":"https://pubmed.ncbi.nlm.nih.gov/39213391"},"language":"en","primary_location":{"id":"doi:10.1093/database/baae094","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae094","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/database/baae094","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047519255","display_name":"Alfredo Varela-Vega","orcid":"https://orcid.org/0000-0003-4857-4997"},"institutions":[{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Alfredo Varela-Vega","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, UNAM , Av. Universidad S/N Col. Chamilpa, Cuernavaca, Morelos 62210, M\u00e9xico"],"raw_orcid":"https://orcid.org/0000-0003-4857-4997","affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, UNAM , Av. Universidad S/N Col. Chamilpa, Cuernavaca, Morelos 62210, M\u00e9xico","institution_ids":["https://openalex.org/I884181516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088514901","display_name":"Ali-Berenice Posada-Reyes","orcid":"https://orcid.org/0000-0003-3165-6099"},"institutions":[{"id":"https://openalex.org/I4210093304","display_name":"Universidad de Cuautitl\u00e1n Izcalli","ror":"https://ror.org/00nrr4d03","country_code":"MX","type":"education","lineage":["https://openalex.org/I4210093304"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Ali-Berenice Posada-Reyes","raw_affiliation_strings":["Laboratorio de Microbiolog\u00eda, Inmunolog\u00eda y Salud P\u00fablica, Facultad de Estudios Superiores Cuautitl\u00e1n, UNAM , Carretera Cuautitl\u00e1n-Teoloyucan Km. 2.5, Xhala, Cuautitl\u00e1n Izcalli, Estado de M\u00e9xico 54714, M\u00e9xico"],"raw_orcid":"https://orcid.org/0000-0003-3165-6099","affiliations":[{"raw_affiliation_string":"Laboratorio de Microbiolog\u00eda, Inmunolog\u00eda y Salud P\u00fablica, Facultad de Estudios Superiores Cuautitl\u00e1n, UNAM , Carretera Cuautitl\u00e1n-Teoloyucan Km. 2.5, Xhala, Cuautitl\u00e1n Izcalli, Estado de M\u00e9xico 54714, M\u00e9xico","institution_ids":["https://openalex.org/I4210093304"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086154618","display_name":"Carlos-Francisco M\u00e9ndez-Cruz","orcid":"https://orcid.org/0000-0002-2549-1614"},"institutions":[{"id":"https://openalex.org/I884181516","display_name":"Universidad Aut\u00f3noma del Estado de Morelos","ror":"https://ror.org/03rzb4f20","country_code":"MX","type":"education","lineage":["https://openalex.org/I884181516"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"Carlos-Francisco M\u00e9ndez-Cruz","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, UNAM , Av. Universidad S/N Col. Chamilpa, Cuernavaca, Morelos 62210, M\u00e9xico"],"raw_orcid":"https://orcid.org/0000-0002-2549-1614","affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas, UNAM , Av. Universidad S/N Col. Chamilpa, Cuernavaca, Morelos 62210, M\u00e9xico","institution_ids":["https://openalex.org/I884181516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5086154618"],"corresponding_institution_ids":["https://openalex.org/I884181516"],"apc_list":{"value":1415,"currency":"GBP","value_usd":1735},"apc_paid":{"value":1415,"currency":"GBP","value_usd":1735},"fwci":0.8137,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.70457782,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"2024","issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9968000054359436,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9968000054359436,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9957000017166138,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9664999842643738,"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":0.6409299969673157},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.5684700608253479},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5324239730834961},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.44602033495903015},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.41707438230514526},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3764494061470032},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34680914878845215},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3208770155906677},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23841512203216553},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.16509166359901428},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.12361946702003479},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10132068395614624}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6409299969673157},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.5684700608253479},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5324239730834961},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.44602033495903015},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.41707438230514526},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3764494061470032},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34680914878845215},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3208770155906677},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23841512203216553},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.16509166359901428},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.12361946702003479},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10132068395614624}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D066289","descriptor_name":"Data Curation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/database/baae094","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae094","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},{"id":"pmid:39213391","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39213391","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":"Database : the journal of biological databases and curation","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11363960","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11363960","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Database (Oxford)","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/database/baae094","is_oa":true,"landing_page_url":"https://doi.org/10.1093/database/baae094","pdf_url":null,"source":{"id":"https://openalex.org/S4210201630","display_name":"Database","issn_l":"1758-0463","issn":["1758-0463"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311647","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/P4310311647"],"host_organization_lineage_names":["University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Database","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1339342173","display_name":null,"funder_award_id":"IN219523","funder_id":"https://openalex.org/F4320335100","funder_display_name":"Direcci\u00f3n General de Asuntos del Personal Acad\u00e9mico, Universidad Nacional Aut\u00f3noma de M\u00e9xico"}],"funders":[{"id":"https://openalex.org/F4320335100","display_name":"Direcci\u00f3n General de Asuntos del Personal Acad\u00e9mico, Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1484811165","https://openalex.org/W1587741467","https://openalex.org/W1785999156","https://openalex.org/W1992837017","https://openalex.org/W1993342843","https://openalex.org/W2001394772","https://openalex.org/W2068436541","https://openalex.org/W2074162075","https://openalex.org/W2085809930","https://openalex.org/W2096951189","https://openalex.org/W2099264294","https://openalex.org/W2105440823","https://openalex.org/W2111757225","https://openalex.org/W2114363816","https://openalex.org/W2122343132","https://openalex.org/W2123442489","https://openalex.org/W2129522786","https://openalex.org/W2131590438","https://openalex.org/W2759211898","https://openalex.org/W2761468778","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2965373594","https://openalex.org/W2971258845","https://openalex.org/W3021976483","https://openalex.org/W3024890774","https://openalex.org/W3028004046","https://openalex.org/W3034238904","https://openalex.org/W3102602010","https://openalex.org/W3104415840","https://openalex.org/W3104578551","https://openalex.org/W3126232929","https://openalex.org/W3140854437","https://openalex.org/W3176196997","https://openalex.org/W4205460703","https://openalex.org/W4211053952","https://openalex.org/W4213009331","https://openalex.org/W4213153652","https://openalex.org/W4220967417","https://openalex.org/W4221153690","https://openalex.org/W4225664334","https://openalex.org/W4226028990","https://openalex.org/W4226191767","https://openalex.org/W4280626237","https://openalex.org/W4281263550","https://openalex.org/W4285185772","https://openalex.org/W4302333993","https://openalex.org/W4307135222","https://openalex.org/W4319323476","https://openalex.org/W4365150760","https://openalex.org/W4366213854","https://openalex.org/W4378745597","https://openalex.org/W4385245566","https://openalex.org/W4388140134","https://openalex.org/W6678224444","https://openalex.org/W6739901393","https://openalex.org/W6744712484","https://openalex.org/W6755207826","https://openalex.org/W6764537895","https://openalex.org/W6766673545","https://openalex.org/W6776277508","https://openalex.org/W6777935872","https://openalex.org/W6783806699","https://openalex.org/W6784328601","https://openalex.org/W6785528558","https://openalex.org/W6787329981","https://openalex.org/W6787703507","https://openalex.org/W6809711173","https://openalex.org/W6810929352","https://openalex.org/W6845797411","https://openalex.org/W6849437824","https://openalex.org/W6852177738","https://openalex.org/W6853016923"],"related_works":["https://openalex.org/W2050457088","https://openalex.org/W2354441856","https://openalex.org/W4327971719","https://openalex.org/W307290524","https://openalex.org/W2802106743","https://openalex.org/W2366985903","https://openalex.org/W2377397314","https://openalex.org/W2991103221","https://openalex.org/W2947475210","https://openalex.org/W2357913628"],"abstract_inverted_index":{"Transcriptional":[0],"regulatory":[1,10,160,209],"networks":[2,20],"(TRNs)":[3],"give":[4],"a":[5,27,107,116,144,165,176,180,217,267,280],"global":[6],"view":[7],"of":[8,12,41,45,52,63,105,127,136,162,183,185,196,219,237,255,275,287,290,294],"the":[9,36,53,60,72,103,149,201,208,229,238,253,258,262,285],"mechanisms":[11],"bacteria":[13,163,291],"to":[14,16,38,75,95,123,132,157,168,206,215,233,245,265,270,283],"respond":[15],"environmental":[17],"signals.":[18],"These":[19],"are":[21,56],"published":[22],"in":[23,179,249],"biological":[24,295],"databases":[25],"as":[26,164],"valuable":[28],"resource":[29],"for":[30,115,152],"experimental":[31],"and":[32,50,83,138,240,292],"bioinformatics":[33],"researchers.":[34],"Despite":[35],"efforts":[37],"publish":[39],"TRNs":[40,55,170,289],"diverse":[42],"bacteria,":[43],"many":[44,51],"them":[46],"still":[47],"lack":[48,135],"one":[49],"existing":[54],"incomplete.":[57],"In":[58],"addition,":[59],"manual":[61],"extraction":[62],"information":[64,129],"from":[65,99,171],"biomedical":[66,100,128],"literature":[67,140],"(\"literature":[68],"curation\")":[69],"has":[70],"been":[71,93],"traditional":[73],"way":[74],"extract":[76,96,169,216,235,246,271],"these":[77],"networks,":[78],"despite":[79],"this":[80,134,272],"being":[81],"demanding":[82],"time-consuming.":[84],"Recently,":[85],"language":[86],"models":[87],"based":[88,147],"on":[89,148],"pretrained":[90,109],"transformers":[91],"have":[92],"used":[94],"relevant":[97],"knowledge":[98,137],"literature.":[101,172],"Moreover,":[102],"benefit":[104],"fine-tuning":[106],"large":[108],"model":[110,197,202],"with":[111],"new":[112,125,145],"limited":[113],"data":[114],"specific":[117,273],"task":[118],"(\"transfer":[119],"learning\")":[120],"opens":[121],"roads":[122],"address":[124,284],"problems":[126],"extraction.":[130],"Here,":[131],"alleviate":[133],"assist":[139],"curation,":[141],"we":[142],"present":[143,259],"approach":[146,174,212,230,269,278],"Bidirectional":[150],"Transformer":[151],"Language":[153],"Understanding":[154],"(BERT)":[155],"architecture":[156],"classify":[158],"transcriptional":[159],"interactions":[161,247],"first":[166,263],"step":[167],"The":[173,194,211,225],"achieved":[175],"significant":[177],"performance":[178],"test":[181],"dataset":[182],"sentences":[184],"Escherichia":[186],"coli":[187],"(F1-Score:":[188],"0.8685,":[189],"Matthew's":[190],"correlation":[191],"coefficient:":[192],"0.8163).":[193],"examination":[195],"predictions":[198],"revealed":[199],"that":[200,228,241],"learned":[203],"different":[204],"ways":[205],"express":[207],"interaction.":[210,276],"was":[213,231,243],"evaluated":[214],"TRN":[218],"Salmonella":[220],"using":[221],"264":[222],"complete":[223],"articles.":[224],"evaluation":[226],"showed":[227],"able":[232,244],"accurately":[234],"82%":[236],"network":[239],"it":[242],"absent":[248],"curation":[250],"data.":[251],"To":[252],"best":[254],"our":[256],"knowledge,":[257],"study":[260],"is":[261,279],"effort":[264],"obtain":[266],"BERT-based":[268],"kind":[274],"This":[277],"starting":[281],"point":[282],"limitations":[286],"reconstructing":[288],"diseases":[293],"interest.":[296],"Database":[297],"URL:":[298],"https://github.com/laigen-unam/BERT-trn-extraction.":[299]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
