DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules

BMC Bioinformatics

Eryk Kropiwnicki¹  Daniel J. B. Clarke¹  Zhuorui Xie¹  Kathleen M. Jagodnik¹  Avi Ma’ayan¹  Alexander Lachmann¹ 

[1] Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, Box 1603, One Gustave L. Levy Place, 10029, New York, NY, USA;

关键词: Drug repurposing;    Text mining;    Machine learning;    Search engine;    Transcriptomics;   

DOI  :  10.1186/s12859-022-04590-5

来源: Springer

【 摘 要 】

BackgroundPubMed contains millions of abstracts that co-mention terms that describe drugs with other biomedical terms such as genes or diseases. Unique opportunities exist for leveraging these co-mentions by integrating them with other drug-drug similarity resources such as the Library of Integrated Network-based Cellular Signatures (LINCS) L1000 signatures to develop novel hypotheses.ResultsDrugShot is a web-based server application and an Appyter that enables users to enter any biomedical search term into a simple input form to receive ranked lists of drugs and other small molecules based on their relevance to the search term. To produce ranked lists of small molecules, DrugShot cross-references returned PubMed identifiers (PMIDs) with DrugRIF or AutoRIF, which are curated resources of drug-PMID associations, to produce an associated small molecule list where each small molecule is ranked according to total co-mentions with the search term from shared PubMed IDs. Additionally, using two types of drug-drug similarity matrices, lists of small molecules are predicted to be associated with the search term. Such predictions are based on literature co-mentions and signature similarity from LINCS L1000 drug-induced gene expression profiles.ConclusionsDrugShot prioritizes drugs and small molecules associated with biomedical search terms. In addition to listing known associations, DrugShot predicts additional drugs and small molecules related to any search term. Hence, DrugShot can be used to prioritize drugs and preclinical compounds for drug repurposing and suggest indications and adverse events for preclinical compounds. DrugShot is freely and openly available at: https://maayanlab.cloud/drugshot and https://appyters.maayanlab.cloud/#/DrugShot.

【 授权许可】

CC BY