{"id":"https://openalex.org/W4283215538","doi":"https://doi.org/10.1186/s12859-022-04768-x","title":"Using BERT to identify drug-target interactions from whole PubMed","display_name":"Using BERT to identify drug-target interactions from whole PubMed","publication_year":2022,"publication_date":"2022-06-21","ids":{"openalex":"https://openalex.org/W4283215538","doi":"https://doi.org/10.1186/s12859-022-04768-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/35729494"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04768-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04768-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04768-x","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/s12859-022-04768-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026730333","display_name":"Jehad Aldahdooh","orcid":"https://orcid.org/0000-0002-9947-4067"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jehad Aldahdooh","raw_affiliation_strings":["Doctoral Programme in Computer Science, University of Helsinki, Helsinki, Finland","Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Doctoral Programme in Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025335008","display_name":"Markus V\u00e4h\u00e4\u2010Koskela","orcid":"https://orcid.org/0000-0001-7764-7820"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I4210107997","display_name":"Finland University","ror":"https://ror.org/014rks409","country_code":"FI","type":"education","lineage":["https://openalex.org/I4210107997"]},{"id":"https://openalex.org/I4210133586","display_name":"Institute for Molecular Medicine Finland","ror":"https://ror.org/030sbze61","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4210133586"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Markus V\u00e4h\u00e4-Koskela","raw_affiliation_strings":["Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4210107997","https://openalex.org/I4210133586"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083397767","display_name":"Jing Tang","orcid":"https://orcid.org/0000-0001-7480-7710"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Jing Tang","raw_affiliation_strings":["Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. jing.tang@helsinki.fi","Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. jing.tang@helsinki.fi","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084617577","display_name":"Ziaurrehman Tanoli","orcid":"https://orcid.org/0000-0003-2435-9862"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I4210122519","display_name":"Biocenter Finland","ror":"https://ror.org/03aay6c48","country_code":"FI","type":"facility","lineage":["https://openalex.org/I4210122519"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Ziaurrehman Tanoli","raw_affiliation_strings":["BioICAWtech, Helsinki, Finland. zia.rehman@helsinki.fi","Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. zia.rehman@helsinki.fi","BioICAWtech, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioICAWtech, Helsinki, Finland. zia.rehman@helsinki.fi","institution_ids":["https://openalex.org/I4210122519"]},{"raw_affiliation_string":"Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland. zia.rehman@helsinki.fi","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"BioICAWtech, Helsinki, Finland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5083397767","https://openalex.org/A5084617577"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4210122519"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2190,"currency":"EUR","value_usd":2361},"fwci":2.7841,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.9161982,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"23","issue":"1","first_page":"245","last_page":"245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.9970999956130981,"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":0.9940999746322632,"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/repurposing","display_name":"Repurposing","score":0.7506616115570068},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.7358092069625854},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7063627243041992},{"id":"https://openalex.org/keywords/drugbank","display_name":"DrugBank","score":0.6649302840232849},{"id":"https://openalex.org/keywords/approved-drug","display_name":"Approved drug","score":0.5793660283088684},{"id":"https://openalex.org/keywords/chembl","display_name":"chEMBL","score":0.5766860842704773},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.507497251033783},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4919571578502655},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.43187853693962097},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.3594230115413666},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35593122243881226},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3306512236595154},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3035394549369812},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16929852962493896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15021398663520813},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.11100035905838013}],"concepts":[{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.7506616115570068},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.7358092069625854},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7063627243041992},{"id":"https://openalex.org/C155261790","wikidata":"https://www.wikidata.org/wiki/Q1122544","display_name":"DrugBank","level":3,"score":0.6649302840232849},{"id":"https://openalex.org/C2777494893","wikidata":"https://www.wikidata.org/wiki/Q4781752","display_name":"Approved drug","level":3,"score":0.5793660283088684},{"id":"https://openalex.org/C63222358","wikidata":"https://www.wikidata.org/wiki/Q6120337","display_name":"chEMBL","level":3,"score":0.5766860842704773},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.507497251033783},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4919571578502655},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.43187853693962097},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.3594230115413666},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35593122243881226},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3306512236595154},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3035394549369812},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16929852962493896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15021398663520813},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.11100035905838013},{"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/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-022-04768-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04768-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04768-x","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:35729494","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35729494","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:pubmedcentral.nih.gov:9214985","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9214985","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:98b3aa6968ba4cd8a924da4cd87352a2","is_oa":false,"landing_page_url":"https://doaj.org/article/98b3aa6968ba4cd8a924da4cd87352a2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-13 (2022)","raw_type":"article"},{"id":"pmh:oai:helda.helsinki.fi:10138/346168","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/346168","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04768-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04768-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04768-x","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":[],"awards":[{"id":"https://openalex.org/G1427963301","display_name":null,"funder_award_id":"317680","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G468277736","display_name":null,"funder_award_id":"824087","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G495187929","display_name":null,"funder_award_id":"EU\u2010H2020","funder_id":"https://openalex.org/F4320332999","funder_display_name":"Horizon 2020 Framework Programme"},{"id":"https://openalex.org/G5933564417","display_name":null,"funder_award_id":"824087","funder_id":"https://openalex.org/F4320319638","funder_display_name":"EOSC-Life"},{"id":"https://openalex.org/G7453577612","display_name":null,"funder_award_id":"No. 317680","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7502487667","display_name":null,"funder_award_id":"EU H2020","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320319638","display_name":"EOSC-Life","ror":null},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283215538.pdf","grobid_xml":"https://content.openalex.org/works/W4283215538.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1905245397","https://openalex.org/W1964670939","https://openalex.org/W1968682237","https://openalex.org/W1974475138","https://openalex.org/W1980129409","https://openalex.org/W2046379971","https://openalex.org/W2074370114","https://openalex.org/W2122590558","https://openalex.org/W2152265294","https://openalex.org/W2171757104","https://openalex.org/W2204695023","https://openalex.org/W2250539671","https://openalex.org/W2279949369","https://openalex.org/W2533611849","https://openalex.org/W2537679995","https://openalex.org/W2558366645","https://openalex.org/W2558461040","https://openalex.org/W2558999090","https://openalex.org/W2777884179","https://openalex.org/W2801930304","https://openalex.org/W2890507936","https://openalex.org/W2903953910","https://openalex.org/W2911489562","https://openalex.org/W2912942083","https://openalex.org/W2913445039","https://openalex.org/W2916534270","https://openalex.org/W2935632020","https://openalex.org/W2962739339","https://openalex.org/W2963026768","https://openalex.org/W2970771982","https://openalex.org/W2971258845","https://openalex.org/W2979826702","https://openalex.org/W2980708516","https://openalex.org/W2985843002","https://openalex.org/W3000043291","https://openalex.org/W3006508031","https://openalex.org/W3015453090","https://openalex.org/W3037553555","https://openalex.org/W3039465695","https://openalex.org/W3094217983","https://openalex.org/W3123655913","https://openalex.org/W3164680581","https://openalex.org/W3195937938","https://openalex.org/W3198396834","https://openalex.org/W4210466552","https://openalex.org/W6694985117"],"related_works":["https://openalex.org/W2155958387","https://openalex.org/W2029912875","https://openalex.org/W4387572939","https://openalex.org/W3114988578","https://openalex.org/W2431109715","https://openalex.org/W2946902764","https://openalex.org/W2894906875","https://openalex.org/W2793261026","https://openalex.org/W3162953117","https://openalex.org/W4319318083"],"abstract_inverted_index":{"BACKGROUND:":[0],"Drug-target":[1],"interactions":[2],"(DTIs)":[3],"are":[4,15,130],"critical":[5],"for":[6,66,146,156,167],"drug":[7,12,125,218],"repurposing":[8],"and":[9,14,26,51,60,126,181,207,221],"elucidation":[10],"of":[11,31,39,73,98,159],"mechanisms,":[13],"manually":[16],"curated":[17,32],"by":[18],"large":[19],"databases,":[20],"such":[21,49,88],"as":[22],"ChEMBL,":[23],"BindingDB,":[24],"DrugBank":[25],"DrugTargetCommons.":[27],"However,":[28],"the":[29,41,53,71,96,112,157,182],"number":[30],"articles":[33,42,50,122,148,192],"likely":[34],"constitutes":[35],"only":[36],"a":[37,57,63,200,214],"fraction":[38],"all":[40],"that":[43],"contain":[44],"experimentally":[45],"determined":[46],"DTIs.":[47,74,195],"Finding":[48],"extracting":[52],"experimental":[54],"information":[55],"is":[56,62,162,179],"challenging":[58],"task,":[59],"there":[61],"pressing":[64],"need":[65],"systematic":[67],"approaches":[68],"to":[69,86,101,107,110,188,212,217],"assist":[70],"curation":[72],"To":[75],"this":[76,177],"end,":[77],"we":[78,104,141],"applied":[79],"Bidirectional":[80],"Encoder":[81],"Representations":[82],"from":[83],"Transformers":[84],"(BERT)":[85],"identify":[87,189],"articles.":[89],"Because":[90],"DTI":[91,136,205],"data":[92],"intimately":[93],"depends":[94],"on":[95],"type":[97],"assays":[99],"used":[100,187],"generate":[102],"it,":[103],"also":[105],"aimed":[106],"incorporate":[108],"functions":[109],"predict":[111],"assay":[113,160],"format.":[114],"RESULTS:":[115],"Our":[116],"novel":[117],"method":[118,198],"identified":[119],"0.6":[120],"million":[121],"(along":[123],"with":[124],"protein":[127],"information)":[128],"which":[129,164],"not":[131],"previously":[132,190],"included":[133],"in":[134,169,176,203],"public":[135],"databases.":[137],"Using":[138],"10-fold":[139],"cross-validation,":[140],"obtained":[142],"~":[143],"99%":[144],"accuracy":[145],"identifying":[147],"containing":[149,193],"quantitative":[150,194],"drug-target":[151],"profiles.":[152],"The":[153,173],"F1":[154],"micro":[155],"prediction":[158],"format":[161],"88%,":[163],"leaves":[165],"room":[166],"improvement":[168],"future":[170],"studies.":[171],"CONCLUSION:":[172],"BERT":[174],"model":[175],"study":[178],"robust":[180],"proposed":[183],"pipeline":[184],"can":[185],"be":[186,213],"overlooked":[191],"Overall,":[196],"our":[197],"provides":[199],"significant":[201],"advancement":[202],"machine-assisted":[204],"extraction":[206],"curation.":[208],"We":[209],"expect":[210],"it":[211],"useful":[215],"addition":[216],"mechanism":[219],"discovery":[220],"repurposing.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2022-06-22T00:00:00"}
