Datasets for Integration into UAB UBRITE/PHARMALCHEMY Resource

Publication Date

2-7-2024

Abstract

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.

Some data were used to complete a personal semester project to test the viability of using cell painting data to determine compound toxicities.

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.

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/

Data was analyzed directly or indirectly from the following sources:

  • https://clinicaltrials.gov/
  • Drugbank: Knox C, Wilson M, Klinger CM, et al. DrugBank 6.0: the DrugBank Knowledgebase for 2024. Nucleic Acids Res. 2024 Jan 5;52(D1):D1265-D1275. doi: 10.1093/nar/gkad976.
  • 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, 405–408 (2017). https://doi.org/10.1038/nm.4306
  • Disease Ontology: Schriml, L. M., Mitraka, E., Munro, J., Tauber, B., Schor, M., Nickle, L., … Greene, C. (2018). Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic acids research, 47(D1), D955–D962. doi:10.1093/nar/gky1032
  • Mitotoxicity Data: Predicting the Mitochondrial Toxicity of Small Molecules: Insights from Mechanistic Assays and Cell Painting Data, Marina Garcia de Lomana, Paula Andrea Marin Zapata, and Floriane Montanari Chemical Research in Toxicology 2023 36 (7), 1107-1120 DOI: 10.1021/acs.chemrestox.3c00086
  • 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, 1550–1557 (2022). https://doi.org/10.1038/s41592-022-01667-0
  • Online Mendelian Inheritance in Man: Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), 2024. World Wide Web URL: https://omim.org/
  • 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.

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