Getting Started with the IDG KMC Datasets and Tools

Abstract

The Illuminating the Druggable Genome (IDG) consortium is a National Institutes of Health (NIH) Common Fund program designed to enhance our knowledge of under-studied proteins, more specifically, proteins unannotated within the three most commonly drug-targeted protein families: G-protein coupled receptors, ion channels, and protein kinases. Since 2014, the IDG Knowledge Management Center (IDG-KMC) has generated several open-access datasets and resources that jointly serve as a highly translational machine-learning-ready knowledgebase focused on human protein-coding genes and their products. The goal of the IDG-KMC is to develop comprehensive integrated knowledge for the druggable genome to illuminate the uncharacterized or poorly annotated portion of the druggable genome. The tools derived from the IDG-KMC provide either user-friendly visualizations or ways to impute the knowledge about potential targets using machine learning strategies. In the following protocols, we describe how to use each web-based tool to accelerate illumination in under-studied proteins. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Interacting with the Pharos user interface. Basic Protocol 2: Accessing the data in Harmonizome. Basic Protocol 3: The ARCHS4 resource. Basic Protocol 4: Making predictions about gene function with PrismExp. Basic Protocol 5: Using Geneshot to illuminate knowledge about under-studied targets. Basic Protocol 6: Exploring under-studied targets with TIN-X. Basic Protocol 7: Interacting with the DrugCentral user interface. Basic Protocol 8: Estimating Anti-SARS-CoV-2 activities with DrugCentral REDIAL-2020. Basic Protocol 9: Drug Set Enrichment Analysis using Drugmonizome. Basic Protocol 10: The Drugmonizome-ML Appyter. Basic Protocol 11: The Harmonizome-ML Appyter. Basic Protocol 12: GWAS target illumination with TIGA. Basic Protocol 13: Prioritizing kinases for lists of proteins and phosphoproteins with KEA3. Basic Protocol 14: Converting PubMed searches to drug sets with the DrugShot Appyter.