AIDA and Semantic Web for epigenetics hypothesis formationMarco Roos, M. Scott Marshall, Andrew P. Gibson, Pieter W. AdriaansSWAT4LS, Edinburgh, November 28, 2008

2

Components controlling structure & function of DNA

3

Decondensed chromatin

Condensed chromatin

Histone methylation at H3K9

DNA methylation

HDAC HAT

Histoneacetylation

Extending my biological model

4

My brain is too small!

5

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

*

6

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

7

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