Alison Yao, Ph.D. Program Officer, Office of Genomics and Advanced TechnologiesDivision of Microbiology and Infectious DiseasesNational Institute of Allergy and Infectious Diseases National Institutes of Health

July 2014

*

*

BIG DATA

NIH Big Data to KnowledgeInitiative for Research Data

BD2K

*

Other ‘Omic

Imaging Phenotypic

Clinical

Genomic

ExposureCourtesy of NHGRI

Primary dataDerived dataInterpreted data/

knowledge

Experimental metadata

Analytical metadata

*BIG DATA

Courtesy of Richard Scheuermann

*BIG DATA*Lots and lots of data in individual labs

Lab 6

Lab 5

Lab 1Lab 2

Lab 4

Lab 3

Courtesy of Michael F. Huerta

Scientific Data Council(SDC)

Big Data to Knowledge

(BD2K)

Associate Directorfor Data Science

(ADDS)

*NIH is Tackling the ‘Big Data’ Problem

Courtesy of NHGRI

*Big Data to Knowledge (BD2K):

Major trans-NIH initiative addressing an NIH imperative and key roadblock

Aims to be catalytic to biomedical research and synergistic across different scientific communities

Overarching goal: BD2K aims to develop the new approaches, standards, methods, tools, software, and competencies that will enhance the use of biomedical Big Data by supporting research, implementation, and training in data science.

• Advance the science & technology of biomedical big data

Data Computing centers and Software development

• Facilitate the broad use of biomedical research data

Data standards, catalog, and data sharing policies

• Enhance & develop the workforce in biomedical big data

Training

*NIH BD2K Initiative

* Impact of NIH BD2K*Increased data sharing will make data available*Promotion of standards will make data useable*Data will be brought into the research ecosystem

*Discoverable, citable & linked to data, tools & literature

*Data science & tools will enable scientific innovation

BD2K will make the biomedical research enterprise more data centric

TomorrowData

centric

TodayHypothesis

driven

Transforming

Biomedical research

*

*The DDICC will support*Data Discoverability

*Data Access

*Data Citation

*Approaches*Community engagement and Outreach

*Task Forces

*Pilot Projects

*Deliverables: *White paper and examples to help inform development of a fully

functional DDI

* NIAID/DMID Genomics Program

Sequencing Functional Genomics

ProteomicsStructural Genomics

SystemsBiology

Bioinformatics

Genomic Sequencing

CentersFunctional Genomic Research Centers

Clinical Proteomics

CentersStructural Genomics Centers

Systems Biology Centers

Bioinformatics Resource Centers

To address key questions in microbiology and infectious disease

Genomic Research ResourcesGenomic/Omics Data Sets, Databases, Bioinformatics Tools, Biomarkers, 3D Structures, Protein Clones, Predictive Models

*Genome Sequencing Centers

Systems Biology Centers

Structure Genomics Centers

Clinical Proteomics Centers

Bioinformatics Resource Centers(BRCs)

*Bioinformatics Resource Centers(BRCs)

Goal: Provide integrated bioinformatics resources in support of basic and applied infectious diseases research

• Data and metadata management and integration solutions• Computational analysis and visualization tools• Work spaces and web interfaces • Training and outreach activities• Free bioinformatics services• Rapid response to new

and emerging pandemic threats

*Bioinformatics Resource Centers(BRCs)

*

Data Management & Integration

Web interfaces and workspaces

Computational analysis tools

Software Engineering

Social Engineering

Collaboration Bioinformatics Services

Training Workshop

*Data Tools

*

BRCs

DBPs

ICEMR

CEIRS

**Key Features:

*~16,000 bacterial genomes and standardized annotations

*Free bioinformatics services

* Genome annotation service (RAST)

* Comparative genome analysis

* Integrated genomic and omics data, metadata and tools

*Comparative analyses and interactive visualizations

*Personal workspace

*TB Portal

*Genomes Metadata

Phylogenetic Trees Genes & Proteins

*Protein-protein interactions Structures

Pathways

Proteomics, ChIP-Seq data coming January 2014

Transcriptomics (Microarray, RNA-Seq)

*Reference genomes (H37Rv)

Gene/ Protein search

Analysis Tools

tb.patricbrc.org

OmicsData

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Data Generation• Infectious disease

community• CEIRS

Data Processing• Bioinformatics

centers, IRD• CEIRS data

coordinating center

Knowledge Presentation• Open access• Visualization• Analysis

Training Services Collaboration

QueryAnalysis

InsightHypothesis

DMID/OGAT

Maria GiovanniValentina Di FrancescoJulia PuzakEun Mi LeePunam MathurMalu PolanskiVivien DuganChristina Giblin

The Influenza Research Database Team

J. Craig Venter Institute Northrop Grumman Health SolutionsVecna Technologies Los Alamos National LaboratoryUniversity of California Davis

*Acknowledgment