AIDA and Semantic Web for epigenetics
hypothesis formation
Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans
SWAT4LS, Edinburgh, November 28, 2008
Components controlling structure & function of DNA
2
Extending my biological model
Decondensed chromatin
HDAC
HAT
Histone
acetylation
Histone methylation at H3K9
DNA methylation
Condensed chromatin
3
My brain is too small!
4
Empower me with a ‘virtual brain’
*
My ws
Your ws
My ws
My ws
Your ws
5
* From P.J. Verschure, Journal of Cellular Biochemistry 2006, vol. 99(1), pg 23-34
Workflow and Semantic Web
Quer
y
Decondensed chromatin
HDAC
Add query to
semantic model
Retrieve documents
from Medline
HAT
Histone
acetylation
Histone methylation at H3K9
DNA methylation
Condensed chromatin
Add documents (IDs)
to semantic model
Extract gene or
protein names
Add proteins to
semantic model
Extract gene or
protein interactions
Add gene or protein
interactions to semantic model
Calculate
ranking scores
Add scores to
semantic model
Create biological
cross references
Add cross references
to semantic model
Convert to
table (html)
6
Separation of models and instances in
OWL
BiologicalModel
Proteins or genes
association
assertion
isComponentOf some
Document
isComponentOf some
relates some
relatesBy some
Association
Protein
term
Protein
or gene
PMID:
15298701
“HDAC1”
Interaction
term
“p68 and p72
associate with
histone
deacetylase 1
(HDAC1)”
“p68”
“associate”
isComponentOf
HDAC1-PCAF
interaction
PCAF
HDAC1
isComponentOf
Retrieved
document
Document
search query
Protein
or gene
Discovered
protein term
Discovered
interaction
term
Text mining
process
Document
search query
PMID:
15298701
Discovered
protein term
Chromatin
condensation
hypothesis
HDAC1-p68
association
“HDAC1”
HDAC1
“p68”
“interacts”
“DNMT3B
also interacts
with histone
deacetylase 1
(HDAC1)”
discoveredBy
searchesWith
discoveredBy
discoveredBy
discoveredBy
Discovered
association
assertion
Interaction
Discovered
interaction
assertion
AIDA based
extraction
process
relates
relates
BiologicalModel
“HDAC1 AND
chromatin”
relatesBy
isComponentOf
Chromatin
condensation
hypothesis
p68
“p68”
“p68 and p72
associate with
histone
deacetylase 1
(HDAC1)”
7
AIDA and Semantic Web for epigenetics
hypothesis formation
Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans
SWAT4LS, Edinburgh, November 28, 2008