CFDE Information Portal

Friday, Jul 26, 2024

A Tour of the Human Reference Atlas v2.1
Katy Börner
Center Director for the Cyberinfrastructure for Network Science Center (CNS)
Bruce Herr
Technical Director for CNS

Friday, Jun 28, 2024

Illuminating the Druggable Genome (IDG) History and Background
Jeremy Yang, Ph.D
Research Associate Professor, UNM SoM, DoIM, TI Division
Summary
Jeremy Yang, PhD, provides a brief overview of the workshop and the history and background of the IDG DCC. He explains the network of institutions and collaborators involved and introduces the IDG portal and Pharos data portal. He then covers how they categorize targets into four target development levels (TDLs).

Relevant resources that will be discussed:
IDG portal: https://druggablegenome.net/
Pharos: https://pharos.nih.gov/
Illuminating the Druggable Genome (IDG) Importance and Impact
Anna Waller, Ph.D.
Scientist & Project Manager, UNM SoM, Dept of Pathology
Summary
Anna Waller, PhD introduced the importance and impact of the IDG program. She explains the collaborative efforts within the IDG consortium. She then covered the research output, global collaborations, and outreach initiatives that have advanced the understanding of understudied proteins and their potential for clinical therapeutics.
DrugCentral, Exemplar and Featured IDG Knowledge Base
Jayme Holmes
Sr Engineer & Lead Developer, UNM SoM, DoIM, TI Division
Summary
Jayme Holmes, a lead programmer for DrugCentral, introduced the features and growth of DrugCentral including the demonstration of an AI-powered Avatar, designed to assist DrugCentral users.

Relevant resources that will be discussed:
DrugCentral: https://drugcentral.org/
Pharos, the IDG Data Portal
Timothy Sheils
Sr Engineer & Project Manager, NIH NCATS
Summary
Timothy Sheils, a senior engineer at NIH NCATS, introduced the Pharos resource, covering how Pharos aggregated 78 data resources, the Pharos user-interface, filters, and ways to download and interact with the data using APIs.

Relevant resources that will be discussed:
Pharos: https://pharos.nih.gov/

Friday, May 31, 2024

Improved Methods to Query the LINCS L1000 Data
Avi Ma'ayan, PhD
LINCS Data Coordination Center and the CFDE Data Resource Center
Summary
The Library of Integrated Network-Based Cellular Signatures (LINCS) was an NIH Common Fund program that was established to catalog how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and gene expression signatures. The presentation will cover LINCS datasets, tools, and a newly developed method to query the LINCS L1000 data for better prioritization of drugs, small molecules and single gene perturbations.

Relevant resources that will be discussed:
Rummagene: https://rummagene.com/
SigCom LINCS: https://maayanlab.cloud/sigcom-lincs/
Playbook Workflow Builder: https://playbook-workflow-builder.cloud/
Automatic Mining of Human and Mouse Gene Sets from GEO
Giacomo Marino
LINCS Data Coordination Center and the CFDE Data Resource Center
Summary
RummaGEO is a web server application that enables gene expression signature search against thousands of human and mouse RNA-seq studies deposited into GEO. To enable such a search engine, an offline automatic process was established to identify the experimental conditions from uniformly aligned GEO studies available from ARCHS4. Once conditions are identified, differential expression signatures are computed to extract gene sets from these signatures. In total, RummaGEO currently contains 135,264 human and 158,062 mouse gene sets from 23,395 GEO studies. Overall, RummaGEO provides an unprecedented resource for the biomedical research community enabling hypothesis generation for many future studies.

Relevant resources that will be discussed:
RummaGEO: https://rummageo.com/
ARCHS4: https://maayanlab.cloud/archs4/

Friday, Apr 26, 2024

Overview of the Common Fund Data Ecosystem
George Papanicolaou, PhD
NIH, CFDE Program Leader
Christy Kano, PhD
NIH, CFDE Program Officer
Metabolomics Workbench/National Metabolomics Data Repository
Shankar Subramaniam, PhD and Mano Maurya, PhD
Metabolomics Workbench DCC and CFDE Data Resource Center
CFDE and the Biomedical Research Community
Noël Burtt and Kyle Gaulton, PhD
CFDE Knowledge Center

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