1. MCW Driving Biological Project
Simon Twigger, PhD
1
Monday, September 27, 2010

2. Rat Genome Database
2
Monday, September 27, 2010

3. Whats the problem?
• large scale repositories
with unused or
inaccessible information
• How can these
databases be made
more useful?
• How to help researchers
find and use this
information to connect
genes to disease?
3
Monday, September 27, 2010

4. Rat researchers ask...
What tissue is this gene expressed in?
What expression data is Are any of these genes
known for SD (aka SD/NHsd,
Harlan Sprague Dawley, associated with my
Sprague Dawley) rats? phenotype?
Has this gene been seen in the brain?
What rat expression studies have been done on
Mammary Cancer(aka breast neoplasms/breast
cancer/cancer of the breast, breast carcinoma...)?
Monday, September 27, 2010

5. What's the strategy?
• Focus on GEO
GEO Records
(microarray) Create Annotation
Jobs & Queue Up
Q-Out
• Use NCBO annotator
1..n Annot. Workers
to markup text, RabbitMQ Index text
review annotations at OBA
and then use for tools Q-In
Parse
Results
and visualization
Results saved to Put results in to
GMiner database queue for save
• Combine annotations
with biological data
to derive new
insights.
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Monday, September 27, 2010

6. Current Ontologies
http://bioportal.bioontology.org/
Monday, September 27, 2010

7. 7
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8. 8
Monday, September 27, 2010

9. Progress
Monday, September 27, 2010

10. Linking annotations to data
Tm2d1
RGD1306410
Svs4
Hbb
Scgb2a1
Alb
Monday, September 27, 2010

11. Linking annotations to data
Tm2d1
RGD1306410
Svs4
Hbb
Scgb2a1
+
Alb
Hbb is_expressed_in rat kidney
Tm2d1 is_expressed_in rat kidney
Human (U133, U133v2.), Mouse (430, U74, U95) and Rat
(U34a/b/c, 230, 230v2)
62,000 samples x ca. 25,000 genes/sample = 1.5B data points
Monday, September 27, 2010

12. Probeset results on GMiner
Probeset L08490cds_at for
Gabra1 - gamma-aminobutyric
acid (GABA) A receptor, alpha 1
Hs GABRA1
Monday, September 27, 2010

13. QTL
Hypertensive
G G G
Phenotype
Pathway Strain 1 != Strain 2
G
Anatomy
G
(Kidney)
Component
Function
Process
Hypertension
Monday, September 27, 2010

14. QTL Gene ‘Highlighter’
QTL
G G G
AllegroGraph
Disease/Pheno.
GMiner RGD OBO etc
Monday, September 27, 2010

15. RDF/OWL sources
Cell Ontology
http://www.berkeleybop.org/ontologies/obo-all/cell/cell.owl
Mouse Adult Gross Anatomy
http://www.berkeleybop.org/ontologies/obo-all/adult_mouse_anatomy/
adult_mouse_anatomy.owl
Mammalian Phenotype
http://www.berkeleybop.org/ontologies/obo-all/mammalian_phenotype/
mammalian_phenotype.owl
GO Function
http://www.berkeleybop.org/ontologies/obo-all/molecular_function/molecular_function.owl
GO Process
http://www.berkeleybop.org/ontologies/obo-all/biological_process/biological_process.owl
GO component
http://www.berkeleybop.org/ontologies/obo-all/cellular_component/cellular_component.owl
Monday, September 27, 2010

16. Rat Genome Database
Wide variety of data types - genomic and physiological
many with corresponding ontologies
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Monday, September 27, 2010

17. Monday, September 27, 2010

18. RGD->RDF
Existing RGD ‘object types’ &
mappings to SO
Monday, September 27, 2010

19. RGD Gene
Monday, September 27, 2010

20. RGD QTL
Monday, September 27, 2010

21. QTL Highlighter
• Rails source code will be available on GitHub
• RDFizer (ruby) http://github.com/simont/MCW-RDF
Monday, September 27, 2010

22. Next Steps
• Register PURL for RGD
• Create RGD core object ontology (OWL/RDF)
• Select appropriate URIs for RGD data
• Ontology annotations - how best to represent in triple store?
• Export GMiner data to RDF-> Triple Store
• Document & refine biological use cases related to candidate gene selection/evaluation
• Identify additional data required for candidate gene selection, RDFize as appropriate,
load into triple store.
• Connections to other RDF collections/LOD, etc.?
Monday, September 27, 2010