{"id":"https://openalex.org/W4412823429","doi":"https://doi.org/10.1186/s12859-025-06237-7","title":"Literature data-based de novo candidates for drug repurposing","display_name":"Literature data-based de novo candidates for drug repurposing","publication_year":2025,"publication_date":"2025-08-01","ids":{"openalex":"https://openalex.org/W4412823429","doi":"https://doi.org/10.1186/s12859-025-06237-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/40750838"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06237-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06237-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06237-7","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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/s12859-025-06237-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027203231","display_name":"Xianglong Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I3045169105","display_name":"Southern University of Science and Technology","ror":"https://ror.org/049tv2d57","country_code":"CN","type":"education","lineage":["https://openalex.org/I3045169105"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xianglong Liang","raw_affiliation_strings":["Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen, China"],"affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen, China","institution_ids":["https://openalex.org/I3045169105"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020416270","display_name":"Jiang Xin","orcid":"https://orcid.org/0000-0003-3727-1288"},"institutions":[{"id":"https://openalex.org/I4210165198","display_name":"Beijing Advanced Sciences and Innovation Center","ror":"https://ror.org/05qm21180","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165198"]},{"id":"https://openalex.org/I105126617","display_name":"Zhejiang International Studies University","ror":"https://ror.org/01vwvvq12","country_code":"CN","type":"education","lineage":["https://openalex.org/I105126617"]},{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Jiang","raw_affiliation_strings":["Hangzhou International Innovation Institute, Beihang University, Hangzhou, China","Institute of Artificial Intelligence & Beijing Advanced Innovation Center for Future Blockchain and Privacy Computing & LMIB, Beihang University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Hangzhou International Innovation Institute, Beihang University, Hangzhou, China","institution_ids":["https://openalex.org/I105126617","https://openalex.org/I82880672"]},{"raw_affiliation_string":"Institute of Artificial Intelligence & Beijing Advanced Innovation Center for Future Blockchain and Privacy Computing & LMIB, Beihang University, Beijing, China","institution_ids":["https://openalex.org/I4210165198"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087257186","display_name":"Yifang Ma","orcid":"https://orcid.org/0000-0003-0326-7993"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yifang Ma","raw_affiliation_strings":["Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen, China. mayf@sustech.edu.cn","Zhengzhou Aerotropolis of Institute of Artificial Intelligence, Zhengzhou, China. mayf@sustech.edu.cn"],"affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen, China. mayf@sustech.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Zhengzhou Aerotropolis of Institute of Artificial Intelligence, Zhengzhou, China. mayf@sustech.edu.cn","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5027203231"],"corresponding_institution_ids":["https://openalex.org/I3045169105"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.19728186,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"203","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"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":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9918000102043152,"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/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.980400025844574,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.8441463708877563},{"id":"https://openalex.org/keywords/repurposing","display_name":"Repurposing","score":0.6215610504150391},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5496811866760254},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5260669589042664},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5163635015487671},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5153726935386658},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3505175709724426},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.3112565577030182},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2954738736152649},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.26309821009635925},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12621158361434937},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09759524464607239}],"concepts":[{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.8441463708877563},{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.6215610504150391},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5496811866760254},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5260669589042664},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5163635015487671},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5153726935386658},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3505175709724426},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3112565577030182},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2954738736152649},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.26309821009635925},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12621158361434937},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09759524464607239},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06237-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06237-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06237-7","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40750838","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40750838","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:b682937d5eda4b6fb17259fe54c0f67c","is_oa":true,"landing_page_url":"https://doaj.org/article/b682937d5eda4b6fb17259fe54c0f67c","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 26, Iss 1, Pp 1-17 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12317455","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12317455","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06237-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06237-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06237-7","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2981938667","display_name":null,"funder_award_id":"Shenzhen","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G37568934","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5203892415","display_name":null,"funder_award_id":"62006109","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5505629366","display_name":null,"funder_award_id":"No. 62006109","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7174558747","display_name":null,"funder_award_id":"Group","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412823429.pdf","grobid_xml":"https://content.openalex.org/works/W4412823429.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W200828812","https://openalex.org/W1500036797","https://openalex.org/W1984054151","https://openalex.org/W2012746420","https://openalex.org/W2087768671","https://openalex.org/W2100761975","https://openalex.org/W2162011385","https://openalex.org/W2263739890","https://openalex.org/W2399140686","https://openalex.org/W2612436700","https://openalex.org/W2619948933","https://openalex.org/W2789816271","https://openalex.org/W2826750344","https://openalex.org/W2889722506","https://openalex.org/W2898623469","https://openalex.org/W2916879436","https://openalex.org/W2922229918","https://openalex.org/W3009999522","https://openalex.org/W3017154096","https://openalex.org/W3128618129","https://openalex.org/W3134564766","https://openalex.org/W3152623144","https://openalex.org/W3177793743","https://openalex.org/W4220885170","https://openalex.org/W4293199358","https://openalex.org/W6608091888","https://openalex.org/W6672364634"],"related_works":["https://openalex.org/W2899096130","https://openalex.org/W3190782215","https://openalex.org/W2902729297","https://openalex.org/W3110500039","https://openalex.org/W4255531208","https://openalex.org/W4396858017","https://openalex.org/W4400165188","https://openalex.org/W4206422705","https://openalex.org/W4320009247","https://openalex.org/W3186872001"],"abstract_inverted_index":{"Drug":[0,9],"repurposing":[1,10,81,108,140],"offers":[2],"a":[3,117,171,189],"promising":[4,136],"strategy":[5],"for":[6,16,29,35,57,71,80,105,153,182,193,204],"drug":[7,30,36,42,61,78,107,139,145,183,194,205],"discovery.":[8],"involves":[11],"identifying":[12,106],"new":[13],"therapeutic":[14],"indications":[15],"existing,":[17],"marketed":[18],"drugs,":[19],"thereby":[20],"reducing":[21],"the":[22,88,95,100,121,129,143,186,198,219],"risks,":[23],"costs,":[24],"and":[25,160,163,166,179,216],"time":[26],"typically":[27],"required":[28],"development.":[31],"Various":[32],"methods":[33,54],"exist":[34],"repurposing,":[37,154],"including":[38,155],"high-throughput":[39],"screening":[40],"of":[41,128,175,200],"compound":[43],"libraries,":[44],"computation":[45],"in":[46,60],"silico":[47],"approaches,":[48],"literature-based":[49,96],"methods,":[50],"etc.":[51,168],"Currently,":[52],"numerous":[53],"utilize":[55],"literature":[56,68,85],"data":[58,86],"mining":[59],"repositioning;":[62],"however,":[63],"relatively":[64],"few":[65],"approaches":[66],"leverage":[67],"citation":[69],"networks":[70],"this":[72],"purpose.":[73],"We":[74,169],"identified":[75,144],"19,553":[76],"potential":[77,152],"pairs":[79,184],"by":[82,120],"analyzing":[83],"biomedical":[84],"through":[87],"Jaccard":[89,97,130],"coefficient.":[90],"Our":[91],"results":[92],"demonstrated":[93],"that":[94],"coefficient":[98],"was":[99],"most":[101],"effective":[102],"similarity":[103,202],"metric":[104],"opportunities.":[109],"To":[110,196],"refine":[111],"our":[112],"selection":[113],"process,":[114],"we":[115,147,207],"applied":[116],"threshold":[118],"defined":[119],"upper":[122],"$$\\gamma":[123],"$$":[124],"th":[125],"quantile":[126],"value":[127],"coefficient,":[131],"enabling":[132],"us":[133],"to":[134],"prioritize":[135],"de":[137],"novo":[138],"candidates.":[141],"Among":[142],"pairs,":[146,206],"found":[148],"several":[149],"with":[150],"strong":[151],"combinations":[156],"such":[157],"as":[158],"adapalene":[159],"bexarotene,":[161],"guanabenz":[162],"tizanidine,":[164],"alvimopan":[165],"methylnaltrexone,":[167],"created":[170],"validation":[172,220],"set":[173],"consisting":[174],"both":[176],"true":[177,180],"positives":[178],"negatives":[181],"using":[185,218],"repoDB":[187],"dataset,":[188],"widely":[190],"recognized":[191],"resource":[192],"repurposing.":[195],"evaluate":[197],"performance":[199],"various":[201],"metrics":[203],"compared":[208],"their":[209],"effectiveness":[210],"based":[211],"on":[212],"AUC,":[213],"F1":[214],"score,":[215],"AUCPR":[217],"set.":[221]},"counts_by_year":[],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
