Register Here

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.

Nucleic Acid Research Database issue features IDG digital resources: TCRD and Pharos

TCRD and Pharos 2021: mining the human proteome for disease biology.
Two resources produced from these efforts are: The Target Central Resource Database (TCRD) (http://juniper.health.unm.edu/tcrd/) and Pharos (https://pharos.nih.gov/), a web interface to browse the TCRD. The ultimate goal of these resources is to highlight and facilitate research into currently understudied proteins, by aggregating a multitude of data sources, and ranking targets based on the amount of data available, and presenting data in machine learning ready format. Since the 2017 release, both TCRD and Pharos have produced two major releases, which have incorporated or expanded an additional 25 data sources. Recently incorporated data types include human and viral-human protein-protein interactions, protein-disease and protein-phenotype associations, and drug-induced gene signatures, among others. These aggregated data have enabled us to generate new visualizations and content sections in Pharos, in order to empower users to find new areas of study in the druggable genome.

IDG Digital Tool Fest - Spring 2022

IDG is hosting the first IDG DIGITAL TOOL FEST on Tuesday, November 30th with an exciting line-up of 10-minute demonstrations. The presented tools were developed within the IDG consortium covering mechanisms for exploring Drugs and their gene Targets within the context of information extracted from text-mining, expression data, and signaling pathways. The tools offer users the ability to construct their own specialized queries to access information programmatically.

Register For the Event

Nucleic Acid Research Database issue features IDG digital resource: Drugcentral.org

New additions to DrugCentral.org include a set of pharmacokinetic properties for ∼1000 drugs, and a sex-based separation of side effects, processed from FAERS (FDA Adverse Event Reporting System); as well as a drug repositioning prioritization scheme based on the market availability and intellectual property rights forFDA approved drugs. In the context of the COVID19 pandemic, we also incorporated REDIAL-2020, a machine learning platform that estimates anti-SARS-CoV-2 activities, as well as the 'drugs in news' feature offers a brief enumeration of the most interesting drugs at the present moment. The full database dump and data files are available for download from the DrugCentral web portal.

Nucleic Acid Research Database issue features IDG digital resource: The Dark Kinase Knowledgebase

Here, we describe a data resource, the Dark Kinase Knowledgebase (DKK; https://darkkinome.org), that is specifically focused on providing data and reagents for these understudied kinases to the broader research community. Supported through NIH’s Illuminating the Druggable Genome (IDG) Program, the DKK is focused on data and knowledge generation for 162 poorly studied or ‘dark’ kinases. Types of data provided through the DKK include parallel reaction monitoring (PRM) peptides for quantitative proteomics, protein interactions, NanoBRET reagents, and kinase-specific compounds.

IDG Consortium

Sponsorship by NIH’s Common Fund has established the program called Illuminating Druggable Genome (IDG) Consortium with the aim of highlighting current knowledge of protein targets through integration of informatics tools, and further study the function of specific understudied targets in three main druggable protein families: G-protein coupled receptors, Ion Channels and protein kinases. This consortium consists of a network of Data and Resource Generation Centers (DRGCs), each focusing their research on one of the three protein families, the Knowledge Management Center (KMC) organizing data and integrated informatics tools across various resources to illuminate understudied protein targets, and the Resource Dissemination and Outreach Center (RDOC) facilitating annotation and distribution of resources brought forth to shed light on to targets. In the spring of 2019, three additional groups joined IDG focusing on making Cutting Edge Informatics Tools for Illuminating the Druggable Genome (CEIT).

Pharos.nih.gov

Pharos is the user interface to the Knowledge Management Center (KMC) for the Illuminating the Druggable Genome (IDG) program funded by the National Institutes of Health (NIH) Common Fund. (Grant No. 1U24CA224370-01). The goal of KMC is to develop a comprehensive, integrated knowledge-base for the Druggable Genome (DG) to illuminate the uncharacterized and/or poorly annotated portion of the DG, focusing on four of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs); nuclear receptors (NRs); Ion Channels (ICs); and kinases.

Harmonizome

Thanks to technological advances in genomics, transcriptomics, proteomics, metabolomics, and related fields, projects that generate a large number of measurements of the properties of cells, tissues, model organisms, and patients are becoming commonplace in biomedical research. In addition, curation projects are making great progress mining biomedical literature to extract and aggregate decades worth of research findings into online databases. Such projects are generating a wealth of information that potentially can guide research toward novel biomedical discoveries and advances in healthcare. To facilitate access to and learning from biomedical Big Data, we created the Harmonizome: a collection of information about genes and proteins from 114 datasets provided by 66 online resources.

Target2035:

On June 15th, the Target2035 webinar series will be highlighting "Drugging the dead – selective targeting of pseudokinases". It is a free webinar with four speakers: Patrick Eyers (University of Liverpool, IDG), Ben Major (Washington University in St. Louis, IDG), James Murphy (Walter and Eliza Hall Institute, Melbourne), Michael Lazarus (Mount Sinai School of Medicine). Please register at https://ki-se.zoom.us/webinar/register/WN_-GVR7lZ1QkWbWRwXwQmxJw.

Reactome:

Exciting news from the CEIT awardee group at Reactome. Today, June 7th, they announced the new Reactome IDG Portal: https://idg.reactome.org/ - where users can leverage Reactome's extensive pathway knowledge together with IDG’s Target Central Resource Database for numerous explorations of biochemical reactions, protein expression and biological pathways. Check it out!