Components controlling structure & function of DNA
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AIDA and Semantic Web for epigenetics hypothesis formation Marco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. Adriaans SWAT4LS, Edinburgh, November 28, 2008
description
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. Decondensed chromatin. Histone methylation at H3K9. HDAC. HAT. - PowerPoint PPT Presentation
Transcript of Components controlling structure & function of DNA
AIDA and Semantic Web for epigenetics hypothesis formationMarco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. AdriaansSWAT4LS, Edinburgh, November 28, 2008
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Components controlling structure & function of DNA
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Decondensed chromatin
Condensed chromatin
Histone methylation at H3K9
DNA methylation
HDAC HAT
Histoneacetylation
Extending my biological model
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My brain is too small!
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Empower me with a ‘virtual brain’
My ws
Your ws
My ws
Your ws
My ws
* From P.J. Verschure, Journal of Cellular Biochemistry 2006, vol. 99(1), pg 23-34
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Workflow and Semantic Web
Query
Retrieve documents from
Medline
Extract gene or protein names
Calculate ranking scores
Create biological cross references
Convert to table (html)
Add documents (IDs) to semantic
model
Add proteins to semantic model
Add scores to semantic model
Add cross references to semantic model
Add query to semantic model
Extract gene or protein interactions
Add gene or protein interactions to semantic
model
Decondensed chromatin
Condensed chromatin
Histone methylation at H3K9
DNA methylation
HDAC HAT
Histoneacetylation
Decondensed chromatin
Condensed chromatin
Histone methylation at H3K9
DNA methylation
HDAC HAT
Histoneacetylation
HDAC HAT
Histoneacetylation
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Separation of models and instances in OWL
Protein or gene
Association
BiologicalModel
HDAC1 PCAF HDAC1-PCAF interaction
Chromatin condensation
hypothesis
Protein term
Proteins or genes associationassertion
Document
“HDAC1” “p68”
“p68 and p72 associate with
histonedeacetylase 1
(HDAC1)”
PMID: 15298701
Interaction term
“associate”
isComponentOf some
relates some
relatesBy some
isComponentOf
relatesrelatesisComponentOf
isComponentOf
relatesBy
isComponentOf some
Discovered protein term
Text mining process
AIDA based extraction process
“p68”“p68”
“DNMT3B also interacts with histone
deacetylase 1 (HDAC1)”
“DNMT3B also interacts with histone
deacetylase 1 (HDAC1)”
Discovered interaction
term
“interacts”“interacts”
discoveredBy
searchesWith
Document search query Discovered
interactionassertion
Retrieved document
“HDAC1 AND chromatin”
PMID: 15298701
PMID: 15298701
discoveredBy
discoveredBy
discoveredBy
Discovered protein term
“p68”“p68”“p68 and p72
associate with histone
deacetylase 1 (HDAC1)”
“p68 and p72 associate with
histonedeacetylase 1
(HDAC1)”
Document search query
Discovered associationassertion
“HDAC1”“HDAC1”
Protein or gene
BiologicalModel
Chromatin condensation
hypothesis
Chromatin condensation
hypothesis
HDAC1HDAC1
p68p68
HDAC1-p68 associationHDAC1-p68 association
Interaction
AIDA and Semantic Web for epigenetics hypothesis formationMarco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. AdriaansSWAT4LS, Edinburgh, November 28, 2008
