itqb talkslideshfd deritemplate
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itqb slidesTRANSCRIPT
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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
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Digital Enterprise Research Institute www.deri.ie
Data is what you find on the Web
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Digital Enterprise Research Institute www.deri.ie
Microarrays Sequences
In vitro experiments
Electrophoresis
Chrystalography
Data, data everywhere
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What pathways is my protein involved in?
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Digital Enterprise Research Institute www.deri.ie
Building bridges
If you could have only 3 apps to do all your work, which ones would they
be?
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Digital Enterprise Research Institute www.deri.ie
Building bridges
Statistics
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Digital Enterprise Research Institute www.deri.ie
Building bridges
species
cc5
sub-type
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Digital Enterprise Research Institute www.deri.ie
Biological Knowledge Continuum
Knowledge Continuum
Proteome
Genome
Microbiome
Metabolome
Medical Records
Sequences
Microarrays
Protein Gels
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Digital Enterprise Research Institute www.deri.ie
Enabling Translational Research
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Digital Enterprise Research Institute www.deri.ie
Writing the story
??
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Digital Enterprise Research Institute www.deri.ie
!!
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Digital Enterprise Research Institute www.deri.ie
Computers can make life easier!
Statistics
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Digital Enterprise Research Institute www.deri.ie
A Little Semantics
Strain1 hasGene
mecA
causes “resistance to met”
Sample1
pneumondiseaseSample1
mecA
Strain1 origin
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Digital Enterprise Research Institute www.deri.ie
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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Digital Enterprise Research Institute www.deri.ie
A Little Semantics
http://Strain1
hasGene
http://mecA
pneumondiseaseSample1
causes “resistance to met”
http://mecA
Sample1
http://Strain1 origin
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Digital Enterprise Research Institute www.deri.ie
... 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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Digital Enterprise Research Institute www.deri.ie
Linked Data Cloud – the Story so Far
Src: http://linkeddata.org/
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Digital Enterprise Research Institute www.deri.ie
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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Digital Enterprise Research Institute www.deri.ie
Linking genomes
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Digital Enterprise Research Institute www.deri.ie
Linking Diseases
Src: Kwang-Il Goh et al. The human disease network PNAS 2007 104 (21)
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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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Digital Enterprise Research Institute www.deri.ie
How about the statistics?
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Digital Enterprise Research Institute www.deri.ie
Plugging data to the Web of the Future