Download pptx - Itqb talkslideshfd deritemplate

Copyright 2010 Digital Enterprise Research Institute. All rights reserved.

Digital Enterprise Research Institute www.deri.ie

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


Data is what you find on the Web


Microarrays Sequences

In vitro experiments

Electrophoresis

Chrystalography

Data, data everywhere

What pathways is my protein involved in?


Building bridges

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

be?


Building bridges

Statistics


Building bridges

species

cc5

sub-type


Biological Knowledge Continuum

Knowledge Continuum

Proteome

Genome

Microbiome

Metabolome

Medical Records

Sequences

Microarrays

Protein Gels


Enabling Translational Research


Writing the story

??


!!


Computers can make life easier!

Statistics


A Little Semantics

Strain1 hasGene

mecA

causes “resistance to met”

Sample1

pneumondiseaseSample1

mecA

Strain1 origin


A Little Semantics

http://Strain1

hasGene

http://mecA


Sample1


mecA

http://Strain1 origin

Principle #1 Use URL to name

things

Principle #2 Organize data in Triples


A Little Semantics

http://Strain1

hasGene

http://mecA



http://mecA

Sample1

http://Strain1 origin


... 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


Linked Data Cloud – the Story so Far

Src: http://linkeddata.org/

http://linkeddata.org/


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?


Linking genomes


Linking Diseases

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


Sourc

e:

Sci

ence

22

Janu

ary

20

10

: Vol. 3

27

no. 5

96

4 p

p. 4

25

-43

1

Genetic Landscape


How about the statistics?


Plugging data to the Web of the Future