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Health and Biomedical Big Data

for Translational Research

Yu-Chuan (Jack) Li, M.D., Ph.D., FACMI Professor in Biomedical Informatics,

Dean, College of Medical Science and Technology

Taipei Medical University

Taipei Medical University

6000 students, 620 faculty members, 7 colleges

3 teaching hospitals; 3150 total beds

All JCI Accredited, in the Taipei metropolitan area

Closest to the world’s 2nd highest building

– Taipei 101

School of Medical Technology and Biotechnology

Graduate Institute of Neural Regenerative Medicine

Graduate Institute of Biomedical Informatics

Graduate Institute of Cancer Biology and Drug Discovery

Graduate Institute of Translational Medicine

College of Medical Science and

Technology

Total: 300 undergrad and 150 M.S. and

Ph.D. students

Computer Methods and

Programs in Biomedicine

International Journal for

Quality in Health Care

Editor-in-Chief

ISQua / OUP Elsevier

2000 submissions, 340 paper published / year

Defining Big Data

Big Data is a collection of data sets so

large and complex that it becomes

difficult to process using on-hand

database management tools or

traditional data processing applications.

http://en.wikipedia.org/wiki/Big_data

Elements of “Big Data”

The degree of complexity within the

data set

The amount of value that can be

derived from innovative vs. traditional

analysis techniques

The use of longitudinal (time-series)

information supplements the analysis

http://mike2.openmethodology.org/wiki/Big_Data_Definition

Challenges Biomedical BD

Locating/accessing data and software tools

Standardizing data and metadata

Extending policies for sharing BD

Organizing, managing, and processing

Developing new methods for analyzing &

integrating BD

Training researchers who can use BD

effectively

From http://bd2k.nih.gov/about_bd2k.html#sthash.jNfoKrca.dpbs

http://youtu.be/za0xQbI79vo

Sharing Data

Defining Translational Research

T1: translation to humans

T2: translation to patients

T3: translation to practice

T4: translation to population

Big Data Sources for Translational

Bioinformatics Research

T1: genomics, SNPs, expression…

T2: clinical trials, registries, EHR…

T3: EBM, guidelines, protocols…

T4: Insurance claims, OTC drugs

consumptions, social networks…

SNP – Single Nucleotide Polymorphism

EHR – Electronic Health Record

EBM – Evidence-base medicine

OTC – Over the counter

GM Weber; KD Mandl; IS Kohane. JAMA. Published online May 22, 2014. doi:10.1001/jama.2014.4228

TBI for T1

Cancer new drug design and discovery

Target therapy like EGFRi – gefitinib,

afatinib

Druggable genome

Drug-Gene-Interaction database (DGIdb)

TBI for T2

Clinicaltrial.gov

SEER (Surveillance, Epidemiology, and

End Results) from NCI – outcome

research

Association between complex and

Mendelian diseases – Blair et. al. Cell 2013

NHIRDB Taiwan

DzMap (The Disease Map)

CAMA (Cancer Association Map Animation)

44,033 studies found for: cancer

7.3 million cancer patients

Data set

+ Tools

DR Blair et al. Cell. 155(1), 26 Sep 2013, P.70–80

The Disease Map

http://disease-map.net

3 years, 1 billion outpatient visits

A window size of 12 months

CAMA

Link

25

26

Hands-on session

• SEER - demo

• NHIRDB - files

• CAMA - demo

• DzMap - demo

http://seer.cancer.gov/manuals/

2014/appendixc.html

Site-Specific Collaborative Staging

Codes

http://seer.cancer.gov/tools/codi

ngmanuals/

TBI for T3

EBM paradigm

Guideline databases

Decision support systems

Behavioral change for clinicians

TBI for T4

Patient support groups –

patientslikeme.com

Social network – FB, Twitter, Weibo…

Behavioral guidance for large groups of

patients – PCEHR in Australia

Research Paradigm from Data Perspective

What does it mean

Translational research can be achieved

through bio-medical informatics

With the Big Data approach,

translational research can be sped-up,

value-added and more innovative

Collect, share and utilize – bigger is

better – major breakthroughs rely on it

Exercise

Try to find on CAMA -

http://203.71.86.98/web/runq16.html#

Digestive diseases associated with

colon cancer in female across all ages

Download the and unzip the files

What are the diagnoses of patient with

pid of 9f6766287dd1bbb1bbf1ee767bbc738f

What are the drugs given? Cancer_2011_OPD_Data-mapped-new

Cancer_2011_Drug-mapped-new

Answers-Dx

Malignant bronchus and lung neoplasm,

unspecified site

Secondary bone malignant neoplasm

Acute upper respiratory infections of

unspecified site

Death occurring in less than 24 hours

from onset of symptoms, not otherwise

explained

Answers-Rx

SODIUM BICARBONATE

SODIUM CHLORIDE

SODIUM CHLORIDE

DOPAMINE HCL

SODIUM CHLORIDE

CEFTRIAXONE (DISODIUM 3.5 H2O)

Thank you for your attention