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. Registration: click this link

 

Agenda for Tuesday, November 30th, 2021:

Target Track

9:00-10:30 AM PT / 10:00 – 11:30 AM MT / 12:00 - 1:30 PM ET:

  • 9:00-9:10 AM PT / 10:00–10:10 AM MT / 12:00-12:10 PM ET
    Pharos – User interface for the IDG generated TCRD (Target Central Research Database) with collated displays of information on targets, diseases and ligands.
    Presenter: Tim Sheils, NCATS (IDG KMC)

    • Participants will learn how to browse through Pharos, upload and save lists, analyze lists and get predicted ligand interactions.

  • 9:10-9:20 AM PT / 10:10–10:20 AM MT / 12:10-12:20 PM ET
    TIGA – Target Illumination GWAS Analytics, an algorithm, automated workflow, and web application providing rational ranking, filtering and interpretation of inferred gene–trait associations and aggregated GWAS evidence by leveraging existing curation and harmonization efforts from the NHGRI-EBI GWAS Catalog.
    Presenter: Jeremy Yang, UNM (IDG KMC)

    • This demo will feature the TIGA web app as a tool for conveniently finding, prioritizing, and exploring gene-trait associations from aggregated GWAS evidence, in the context of drug target illumination scientific use cases.

  • 9:20-9:30 AM PT / 10:20–10:30 AM MT / 12:20-12:30 PM ET
    Geneshot – Search engine developed to illuminate and promote attention to the under-studied genome producing ranked gene lists contain genes that were previously published in association with the search terms, as well as genes predicted to be associated with the terms based on data integration from multiple sources.
    Presenter: Alexander Lachmann, ISMMS (IDG KMC)

    • Using the Geneshot user interface; Accessing Geneshot programmatically; Making gene function predictions with data from Geneshot.

  • 9:30-9:40 AM PT / 10:30–10:40 AM MT / 12:30-12:40 PM ET
    TIN-X – Target Importance and Novelty eXplorer, an interactive visualization tool for illuminating associations between diseases and potential drug targets
    Presenter: Vincent T. Metzger, UNM (IDG KMC)

    • Using TIN-X to visually explore understudied drug targets; Demonstration of interactive features of the TIN-X User Interface.

  • 9:40-9:50 AM PT / 10:40–10:50 AM MT / 12:40-12:50 PM ET
    Reactome-IDG Portal – Web-based tool for viewing understudied proteins in the context of biological pathways of The Reactome Pathway Diagram View to facilitates the generation of experimentally testable hypotheses to infer potential functions of these proteins.
    Presenter: Robin Haw, OICR (IDG CEIT)

    • Search the web portal with understudied protein identifiers to identify primary and interacting pathways reachable via one-hop pairwise relationships; Visualize understudied proteins location in Reactome’s annotated pathways and interacting pathways and network visualizations; Overlay multiple tissue specific gene or protein expression values from 19 data sources collected in the Target Central Resource Database onto Reactome pathway and network visualizations; Overlay protein/protein pairwise relationships or drug/target interactions onto Reactome pathways and network visualizations.

  • 9:50-10:00 AM PT /10:50-11:00 AM MT / 12:50-1:00 PM ET
    Clinical Kinase Index (CKI) – An, interactive web application with harmonized datasets extracted from several resources that allows researchers and clinicians to prioritize and evaluate the clinical relevance of kinases as cancer drug targets across solid tumors.
    Presenters: Rimpi Khurana, Stephan Schürer, U Miami (IDGRDOC)

    • Demonstration will show the different options to rank prospective kinase targets for each cancer and to identify relevant tumors for a given kinase. CKI also provides visualization of the clinical data, various ways to query and filter results, and interactive visualizations of the gene expression and CKI scores across kinases and cancers. Data can also be downloaded.

  • 10:00-10:10 AM PT / 11:00-11:10 AM MT / 1:00-1:10 PM ET
    Protein Kinase Ontology (ProKinO) – An integrated knowledge graph conceptualizing the wealth of information connecting protein kinase sequence, structure, function, evolution and disease (cancer) in human and machine readable format.
    Presenters: Saber Soleymani, Krystof Kochut, Natarajan Kannan, UGA (IDG CEIT)

    • Demonstrations will focus on ProKinO knowledge graph mining using SPARQL and visualization tools for mining kinase sequence and regulatory features in light of structural models (AlphaFold) and crystal structures. Attendees will learn to formulate new testable hypotheses on understudied dark kinases using evolutionary and functional context of the entire kinome in one place.

  • 10:10-10:30 AM PT / 11:10-11:30 AM MT / 1:10-1:30 PM ET
    Breakout Sessions for individual Q&A

    • Breakout rooms for each highlighted IDG Digital Tool will be open for attendees to self-select.

 

Drugs and Programmatic Queries Track

10:30 AM-12:00 PM PT / 11:30 AM – 1:00 PM MT/ 1:30-3:00 PM ET:

  • 10:30-10:40 AM PT / 11:30-11:40 AM MT / 1:30-1:40 PM ET
    Drugshot – 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.
    Presenter: Eryk Kropiwnicki, ISMMS (IDG KMC)

    • Using the Drugshot user interface; Accessing Drugshot programmatically; Making predictions about the properties of drugs with Drugshot.

  • 10:40-10:50 AM PT / 11:40-11:50 AM MT / 1:40-1:50 PM ET
    DrugCentral – Online drug compendium with annotations of mechanism of action for clinically approved drugs.
    Presenter: Tudor Oprea, UNM (IDG KMC)

    • Participants will learn about the information content currently included in DrugCentral, from mode-of-action drug targets to side effects, chemical information and drug formulations. The use of the L1000 gene profile similarity for drugs and the machine learning prediction of anti-SARS-CoV-2 activities will also be discussed.

  • 10:50-11:00 AM PT / 11:50 AM -12:00 PM MT / 1:50-2:00 PM ET
    Gene and Drug Landing Page Aggregator – A collection of all primary resources and databases that provide gene and drug landing pages into one website allowing for users submit a gene or drug name to utilize the simple search engine.
    Presenter: Maxim Kuleshov, ISMMS (IDG KMC)

    • Case studies of using the resource for finding knowledge about IDG targets.

  • 11:00-11:10 AM PT / 12:00-12:10 PM MT / 2:00-2:10 PM ET
    ARCHS4 – Provides access to gene counts from HiSeq 2000, HiSeq 2500 and NextSeq 500 platforms for human and mouse experiments from GEO and SRA.
    Presenter: Alexander Lachmann, ISMMS (IDG KMC)

    • Using the ARCHS4 user interface; Accessing ARCHS4 programmatically; Making gene function predictions with data from ARCHS4.

  • 11:10-11:20 AM PT / 12:10-12:20 PM MT / 2:10-2:20 PM ET
    Pharos GraphQL API – User interface for the IDG generated TCRD (Target Central Research Database) with GraphQL API methodology allowing for more fine-tuned queries.
    Presenters: Keith Kelleher, NCATS (IDG KMC)

    • Participants will learn how to query the Pharos API using GraphQL.

  • 11:20-11:30 AM PT / 12:20-12:30 PM MT / 2:20-2:30 PM ET
    Appyters – Turns Jupyter Notebooks into fully functional standalone web-based bioinformatics applications.
    Presenter: Daniel Clarke, ISMMS (IDG KMC)

    • Using the IDG related Appyetrs; Running Appyters locally; Developing Appyters.

  • 11:30-11:40 AM PT / 12:30-12:40 PM MT / 2:30-2:40 PM ET
    Case Study with Appyters - To identify perturbations that modulate the expression of single genes – My Gene’s Transcription in Type 2 Diabetes (T2D) Transcriptomics Signatures Appyter / Gene Centric GEO Reverse Search Appyter / Transformed L1000 to RNA-seq Perturbational Signatures Gene Search Appyter
    Presenter: Sherry Xie, ISMMS (IDG KMC)

    • Using these 3 Appyters to form hypotheses about ways to modulate the expression of worthy IDG targets in a disease context.

  • 11:40 AM-12:00 PM PT / 12:40-1:00 PM MT / 2:40-3:00 PM ET
    Breakout Sessions for individual Q&A

    • Breakout rooms for each highlighted IDG Digital Tool will be open for attendees to self-select.

FAQs

What are the IDG Digital Tools covered by this event?

A PDF listing of all 14 IDG Digital Tools covered during this Digital Tool Fest can be found at this link.

What is the IDG consortium?

The NIH sponsored IDG consortium aims to illuminated understudied targets in three protein families; GPCR, kinase, and ion channels, by producing data and resources via the DRGC, collating and managing whole human proteome knowledge via the KMC, expand outreach of IDG outcomes via RDOC, and developing tools for facilitating data representation by CEITs. Please visit DruggableGenome.net for further information.

When do I receive the webinar information for this event?

In the confirmation email for your registration you will find the Zoom link information. To register for this event, click here (** https://hsc-unm.zoom.us/meeting/register/tJEpfuGqqTooG9DC2YjXf5ah72tBXPcOGLaS)

How can I contact the organizer with any questions?

Please contact organizer: idg.rdoc [at] gmail.com