Datasets for Integration into UAB UBRITE/PHARMALCHEMY Resource

<p>This represents a semester project completed for INFO603 at the University of Alabama at Birmingham. This is a collection of datasets which were curated, either directly from the original source or from staged UAB-Cheaha copies, for integration into the UAB PharmAlchemy system.</p> <p>Some data were used to complete a personal semester project to test the viability of using cell painting data to determine compound toxicities.</p> <p>All data can be found within the UAB-Cheaha-UBRITE system at the following location: /data/project/ubrite/PharmAlchemy24/RomanFinalDeliverables/ . The attached table of contents describes where to find the datasets and code used to generate them.</p> <p>Coversheets explaining each delivered dataset in more detail can be found within the UAB-Cheaha-UBRITE system at the following location: /data/project/ubrite/PharmAlchemy24/RomanFinalDeliverables/Coversheets/</p> <p>&nbsp;</p> <p>Data was analyzed directly or indirectly from the following sources:</p> <ul> <li>https://clinicaltrials.gov/</li> <li>Drugbank: Knox C, Wilson M, Klinger CM, et al.&nbsp;<em>DrugBank 6.0: the DrugBank Knowledgebase for 2024.</em> Nucleic Acids Res. 2024 Jan 5;52(D1):D1265-D1275. doi: 10.1093/nar/gkad976.</li> <li>Drug Repurposing Hub: Corsello, S., Bittker, J., Liu, Z. et al. The Drug Repurposing Hub: a next-generation drug library and information resource. Nat Med 23, 405&ndash;408 (2017). https://doi.org/10.1038/nm.4306</li> <li>Disease Ontology: Schriml, L. M., Mitraka, E., Munro, J., Tauber, B., Schor, M., Nickle, L., &hellip; Greene, C. (2018). Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic acids research, 47(D1), D955&ndash;D962. doi:10.1093/nar/gky1032</li> <li>Mitotoxicity Data: Predicting the Mitochondrial Toxicity of Small Molecules: Insights from Mechanistic Assays and Cell Painting Data,&nbsp;Marina Garcia de Lomana, Paula Andrea Marin Zapata, and Floriane Montanari&nbsp;Chemical Research in Toxicology 2023 36 (7), 1107-1120&nbsp;DOI: 10.1021/acs.chemrestox.3c00086</li> <li>Cell Painting Data: Haghighi, M., Caicedo, J.C., Cimini, B.A. et al. High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nat Methods 19, 1550&ndash;1557 (2022). https://doi.org/10.1038/s41592-022-01667-0</li> <li>Online Mendelian Inheritance in Man: Online Mendelian Inheritance in Man, OMIM&reg;. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), 2024. World Wide Web URL: https://omim.org/</li> <li>Therapeutic Target Database: Chen X, Ji ZL, Chen YZ. TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. doi: 10.1093/nar/30.1.412. PMID: 11752352; PMCID: PMC99057.</li> </ul> <p>&nbsp;</p>