Copyright 2010 Digital Enterprise Research Institute. All rights reserved.

Digital Enterprise Research Institute www.deri.ie

Solving Problems with Biology …via Linked Data

Digital Enterprise Research Institute www.deri.ie

21st Century will be the Age of Biology

Climate Change

Nutritious Food

Sustainable Energy

Disease and Ageing

Digital Enterprise Research Institute www.deri.ie

The most amazing molecule

4 letter code

2 chains, exact mirrors!

Same genetic code for all living cells!

- Adenosine

- Timine

- Citosine

- Guanine

- Adenosine

- Timine

- Citosine

- Guanine

Able to make copies of itself!

Digital Enterprise Research Institute www.deri.ie

Making a human

Digital Enterprise Research Institute www.deri.ie

Biology explained

Digital Enterprise Research Institute www.deri.ie

Creating Synthetic Biology

Genetic engineering… oversimplified

DNA!

Bio-fuel producing gene

Biofuel

CO2

Digital Enterprise Research Institute www.deri.ie

BioHacking = Do-it-yourself Biology by amateurs!

Bio

Bio

Digital Enterprise Research Institute www.deri.ie

Executable Cell Biology

Cell and computers are not that different

Src

: htt

p:/

/gen

e-t

hera

py.

yola

site

.com

/pro

cess

.php

Activator genes

Repressor genes

Digital Enterprise Research Institute www.deri.ie

Where does LD fit in all of this?

Let’s make a “virtual” experiment

Which gene?

Digital Enterprise Research Institute www.deri.ie

?gene

biofuel

CO2

Non-toxic

Not-soluble H2O

Digital Enterprise Research Institute www.deri.ie

Not that simple…

U de Lichtenberg et al. Science 2005;307:724-727

?sugar

Biofuel

? ?gene

?

?

Digital Enterprise Research Institute www.deri.ie

The Linked Data Cloud“Life sciences will drive adoption of the Semantic Web, just as high-energy physics drove the early Web.” - BioIT World, 2005

Digital Enterprise Research Institute www.deri.ie

Linked Data for Understanding Cancer

Digital Enterprise Research Institute www.deri.ie

Link the Data, cure the disease

What your doctor is not telling you! Drugbank ClinicalTrialDiseasome

Digital Enterprise Research Institute www.deri.ie

The diseasome project

Digital Enterprise Research Institute www.deri.ie

Biosurveillance!! Today!

Digital Enterprise Research Institute www.deri.ie

Linked Data to track E. coli infection

UKE. coli

GermanyE. coli

Digital Enterprise Research Institute www.deri.ie

Sou

rce:

htt

p:/

/ww

w.n

yti

mes.

com

/im

ag

ep

ag

es/

20

07

/01

/22

/sci

en

ce/2

00

70

12

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ILLO

.ht

ml

Nothing in Biology Makes Sense Except in the Light of Evolution (Dobzhansky, 1973)

Digital Enterprise Research Institute www.deri.ie

Toss the details, understand the patterns Navigating the genetic landscape with simplified

views

Source: http://www.sciencemag.org/content/327/5964/425.full

… IN THE CELL

IN CANCER OR …

Digital Enterprise Research Institute www.deri.ie

Where is the data?

http://linkeddata.org

http://sindice.comhttp://www.w3.org/wiki/HCLSIG/LODD/Data

Digital Enterprise Research Institute www.deri.ie

21st Century Biology belongs to BioHackers!