{"id":"https://openalex.org/W4407140906","doi":"https://doi.org/10.1186/s13321-025-00962-0","title":"Improving drug repositioning with negative data labeling using large language models","display_name":"Improving drug repositioning with negative data labeling using large language models","publication_year":2025,"publication_date":"2025-02-04","ids":{"openalex":"https://openalex.org/W4407140906","doi":"https://doi.org/10.1186/s13321-025-00962-0","pmid":"https://pubmed.ncbi.nlm.nih.gov/39905466"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00962-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00962-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-00962-0.pdf","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-00962-0.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049180015","display_name":"Milan Picard","orcid":"https://orcid.org/0000-0002-2466-2012"},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Milan Picard","raw_affiliation_strings":["Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada"],"affiliations":[{"raw_affiliation_string":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001570122","display_name":"Micka\u00ebl Leclercq","orcid":"https://orcid.org/0000-0001-6205-888X"},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Mickael Leclercq","raw_affiliation_strings":["Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada"],"affiliations":[{"raw_affiliation_string":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006446024","display_name":"Antoine Bodein","orcid":"https://orcid.org/0000-0002-9843-504X"},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Antoine Bodein","raw_affiliation_strings":["Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada"],"affiliations":[{"raw_affiliation_string":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011459941","display_name":"Marie\u2010Pier Scott\u2010Boyer","orcid":"https://orcid.org/0000-0003-2626-4584"},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Marie Pier Scott-Boyer","raw_affiliation_strings":["Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada"],"affiliations":[{"raw_affiliation_string":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063027027","display_name":"Olivier P\u00e9rin","orcid":"https://orcid.org/0000-0002-2590-7974"},"institutions":[{"id":"https://openalex.org/I14285755","display_name":"L'Or\u00e9al (France)","ror":"https://ror.org/00nb3j622","country_code":"FR","type":"company","lineage":["https://openalex.org/I14285755"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Olivier Perin","raw_affiliation_strings":["Digital Transformation and Innovation Department, L'Or\u00e9al Advanced Research, Aulnay-Sous-Bois, France","Digital Transformation and Innovation Department, L\u2032Or\u00e9al Advanced Research, Aulnay-Sous-Bois, France"],"affiliations":[{"raw_affiliation_string":"Digital Transformation and Innovation Department, L'Or\u00e9al Advanced Research, Aulnay-Sous-Bois, France","institution_ids":["https://openalex.org/I14285755"]},{"raw_affiliation_string":"Digital Transformation and Innovation Department, L\u2032Or\u00e9al Advanced Research, Aulnay-Sous-Bois, France","institution_ids":["https://openalex.org/I14285755"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071487081","display_name":"Arnaud Droit","orcid":"https://orcid.org/0000-0001-7922-790X"},"institutions":[{"id":"https://openalex.org/I43406934","display_name":"Universit\u00e9 Laval","ror":"https://ror.org/04sjchr03","country_code":"CA","type":"education","lineage":["https://openalex.org/I43406934"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Arnaud Droit","raw_affiliation_strings":["Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada. arnaud.droit@crchuq.ulaval.ca","Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada"],"affiliations":[{"raw_affiliation_string":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada. arnaud.droit@crchuq.ulaval.ca","institution_ids":["https://openalex.org/I43406934"]},{"raw_affiliation_string":"Molecular Medicine Department, CHU de Qu\u00e9bec Research Center, Universit\u00e9 Laval, Qu\u00e9bec, QC, Canada","institution_ids":["https://openalex.org/I43406934"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5049180015"],"corresponding_institution_ids":["https://openalex.org/I43406934"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":12.2722,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.98477704,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"16","last_page":"16"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9988999962806702,"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":0.9988999962806702,"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":0.9835000038146973,"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/T10028","display_name":"Topic Modeling","score":0.9793999791145325,"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":0.6844683885574341},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.5880787372589111},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4297829568386078},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38478708267211914},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3749198913574219},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3651290237903595},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16147059202194214},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.16100823879241943}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6844683885574341},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.5880787372589111},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4297829568386078},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38478708267211914},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3749198913574219},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3651290237903595},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16147059202194214},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.16100823879241943}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-00962-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00962-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-00962-0.pdf","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:39905466","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39905466","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":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11796214","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11796214","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11796214/pdf/13321_2025_Article_962.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:f2b48bfe9f3942cea9a71a3a59c23c1a","is_oa":true,"landing_page_url":"https://doaj.org/article/f2b48bfe9f3942cea9a71a3a59c23c1a","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":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-12 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00962-0","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00962-0","pdf_url":"https://link.springer.com/content/pdf/10.1186/s13321-025-00962-0.pdf","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4407140906.pdf","grobid_xml":"https://content.openalex.org/works/W4407140906.grobid-xml"},"referenced_works_count":96,"referenced_works":["https://openalex.org/W1496135731","https://openalex.org/W2001955769","https://openalex.org/W2010457001","https://openalex.org/W2028133290","https://openalex.org/W2045303797","https://openalex.org/W2045895507","https://openalex.org/W2049804312","https://openalex.org/W2080845101","https://openalex.org/W2092025391","https://openalex.org/W2097360283","https://openalex.org/W2099308584","https://openalex.org/W2106248311","https://openalex.org/W2112475888","https://openalex.org/W2136579005","https://openalex.org/W2144540144","https://openalex.org/W2145578524","https://openalex.org/W2149215961","https://openalex.org/W2149379006","https://openalex.org/W2417851811","https://openalex.org/W2417990257","https://openalex.org/W2481479138","https://openalex.org/W2531470489","https://openalex.org/W2537623931","https://openalex.org/W2597385103","https://openalex.org/W2612436700","https://openalex.org/W2739787656","https://openalex.org/W2744720080","https://openalex.org/W2765222180","https://openalex.org/W2765777509","https://openalex.org/W2767891136","https://openalex.org/W2770261575","https://openalex.org/W2774091970","https://openalex.org/W2783291377","https://openalex.org/W2791703906","https://openalex.org/W2799845593","https://openalex.org/W2800410357","https://openalex.org/W2800595743","https://openalex.org/W2801804034","https://openalex.org/W2803664483","https://openalex.org/W2807726778","https://openalex.org/W2894962939","https://openalex.org/W2899867782","https://openalex.org/W2914461815","https://openalex.org/W2946099214","https://openalex.org/W2997159096","https://openalex.org/W2997939586","https://openalex.org/W3000600836","https://openalex.org/W3004658896","https://openalex.org/W3009356789","https://openalex.org/W3030241638","https://openalex.org/W3042289107","https://openalex.org/W3045080056","https://openalex.org/W3048641598","https://openalex.org/W3058926349","https://openalex.org/W3088088961","https://openalex.org/W3093194543","https://openalex.org/W3094762523","https://openalex.org/W3095876941","https://openalex.org/W3115919135","https://openalex.org/W3117622225","https://openalex.org/W3121054017","https://openalex.org/W3139171397","https://openalex.org/W3153588864","https://openalex.org/W3177209274","https://openalex.org/W3196073854","https://openalex.org/W3200266393","https://openalex.org/W3211622570","https://openalex.org/W3217663596","https://openalex.org/W4200489832","https://openalex.org/W4200604629","https://openalex.org/W4206547282","https://openalex.org/W4206596291","https://openalex.org/W4214529013","https://openalex.org/W4226006793","https://openalex.org/W4246768811","https://openalex.org/W4249972823","https://openalex.org/W4280492560","https://openalex.org/W4294541781","https://openalex.org/W4306651466","https://openalex.org/W4307496915","https://openalex.org/W4309266899","https://openalex.org/W4309310688","https://openalex.org/W4311599515","https://openalex.org/W4313414681","https://openalex.org/W4319598746","https://openalex.org/W4367281317","https://openalex.org/W4376874231","https://openalex.org/W4385605480","https://openalex.org/W4386514047","https://openalex.org/W4390774264","https://openalex.org/W4391135056","https://openalex.org/W4391611056","https://openalex.org/W4399700702","https://openalex.org/W4400013637","https://openalex.org/W4400457299","https://openalex.org/W4401691221"],"related_works":["https://openalex.org/W4281673370","https://openalex.org/W4206422705","https://openalex.org/W2886266969","https://openalex.org/W4366527864","https://openalex.org/W4287114073","https://openalex.org/W2903687253","https://openalex.org/W2006667691","https://openalex.org/W2399140686","https://openalex.org/W1980001478","https://openalex.org/W3166711969"],"abstract_inverted_index":{"By":[0],"expanding":[1],"our":[2,14],"negative":[3],"data":[4],"labeling":[5],"approach":[6],"to":[7],"all":[8],"diseases":[9],"within":[10],"the":[11],"ClinicalTrials.gov":[12],"database,":[13],"method":[15],"could":[16],"greatly":[17],"advance":[18],"supervised":[19],"drug":[20],"repositioning,":[21],"offering":[22],"a":[23],"more":[24],"accurate":[25],"and":[26],"data-driven":[27],"path":[28],"for":[29],"discovering":[30],"new":[31],"treatments.":[32]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
