Copyright 2010 Digital Enterprise Research Institute. All rights reserved.

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Helena F. Deus

A little semantics … can go a long way!

What is the Semantic Web and how can it be used to accelerate translational research and biological discovery

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Data is what you find on the Web

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Microarrays Sequences

In vitro experiments

Electrophoresis

Chrystalography

Data, data everywhere

What pathways is my protein involved in?

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Building bridges

If you could have only 3 apps to do all your work, which ones would they

be?

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Building bridges

Statistics

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Building bridges

species

cc5

sub-type

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Biological Knowledge Continuum

Knowledge Continuum

Proteome

Genome

Microbiome

Metabolome

Medical Records

Sequences

Microarrays

Protein Gels

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Enabling Translational Research

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Writing the story

??

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!!

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Computers can make life easier!

Statistics

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A Little Semantics

Strain1 hasGene

mecA

causes “resistance to met”

Sample1

pneumondiseaseSample1

mecA

Strain1 origin

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A Little Semantics

http://Strain1

hasGene

http://mecA

causes “resistance to met”

Sample1

pneumondiseaseSample1

mecA

http://Strain1 origin

Principle #1 Use URL to name

things

Principle #2 Organize data in Triples

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A Little Semantics

http://Strain1

hasGene

http://mecA

pneumondiseaseSample1

causes “resistance to met”

http://mecA

Sample1

http://Strain1 origin

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... a lot of knowledge networking!

nih:EGFR

epidermal growth factor receptor

Homo sapiens

CCCCGGCGCAGCGCGGCCGCAGCAGCCTCCGCCCCCCGCACGGTGTGAGCGCCCGACGCGGCCGAGGCGG …

nih:EGF

nci:has_description

nih:sequence

nih:organism

nih:interacts

nih:organism

nih:EGFR

rea:Membrane

rea:Receptor

rea:Transferase

rea:keyword

rea:keyword

rea:keyword

NCBI Reactome

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Linked Data Cloud – the Story so Far

Src: http://linkeddata.org/

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Staphylococcus

Clonal Complex

5

PortugalDate of

Collection

How to make use of that data?

What are the microbial Staphylococcus strains, belonging to clonal complex 5 and collected in Portugal? And when were they collected?

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Linking genomes

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Linking Diseases

Src: Kwang-Il Goh et al. The human disease network PNAS 2007 104 (21)

Digital Enterprise Research Institute www.deri.ie

Sourc

e:

Sci

ence

 22

Janu

ary

20

10

: Vol. 3

27

 no. 5

96

4 p

p. 4

25

-43

1 

Genetic Landscape

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How about the statistics?

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Plugging data to the Web of the Future