1. The New ArkDB Database
Andy Law et al.

2. The History ArkDB – designed to handle genetic linkage mapping data
Written as cgi using webintool and ingres

3. The plan Rewrite in java over postgres Build: A web application
An applet to draw the maps
A webstart application
An API to the data model

4. The demo

5. The new Use Case
Use the power of comparative genomics to investigate quantitative trait loci

6. The new Use Case Linkage Map Radiation Hybrid Map Cytogenetic Pig
EST2
EST1
Linkage
Map
Radiation
Hybrid Map
Cytogenetic
Pig
Human
Chicken
BAC1
BAC2
BAC3
Physical
Mapping
Expression
Analysis
Trait
location
Fat
Linked
References

7. The parallel project
ComparaGRID

8. The bits that it’s built on
There are ‘things’
Markers, clones, maps, sequences, arrays, chromosomes, phenotypes…
There are ‘relationships’
Sequence similarity, mappings, hybridisations, linkage disequilibrium…

9. RDF subject-predicate-object
e.g. ([{The Sky} {has_colour} {blue}])
Aim to represent all our relationships using this pattern

10. Extensions
In our system, the objects carry attribution/publication sources
([{The Sky} {is} {falling}] [Chicken Licken])
... and the assertions are objects too
([Assertion1] [{GeneX} {has_orthologue} {GeneY}] [PubMed:1234])
So we can represent
([Assertion2] [{Assertion1} {is} {false}] [Andy Law])

11. Pre-requisites Need to define the relationships – an ontology
“The only thing that ontologists agree on is that they disagree with each other (and everyone else). They reserve the right to disagree over what it is they disagree over.”

12. The new Use Case Linkage Map Radiation Hybrid Map Cytogenetic Pig
EST2
EST1
Linkage
Map
Radiation
Hybrid Map
Cytogenetic
Pig
Human
Chicken
BAC1
BAC2
BAC3
Physical
Mapping
Expression
Analysis
Trait
location
Fat
Linked
References

13. Pre-Requisites II Is my trait the same as yours?
E.g. Fat
Back fat depth
Marbling
Abdominal fat pad
Tri-glyceride metabolism

14. Tuesday 16th Advert Dover Room 1pm to 5pm
Animal Trait Ontology Discussion
Part of the Animal QTL Database Meeting
Tuesday 16th
1pm to 5pm
Dover Room

15. The new Use Case Linkage Map Radiation Hybrid Map Cytogenetic Pig
EST2
EST1
Linkage
Map
Radiation
Hybrid Map
Cytogenetic
Pig
Human
Chicken
BAC1
BAC2
BAC3
Physical
Mapping
Expression
Analysis
Trait
location
Fat
Linked
References

16. It’s all about relationships
Immensely complex to define
But, from the user’s perspective it’s all about ducks
If it looks like a duck…
There’s a lot going on under the surface

17. More info and feedback ArkDB ComparaGRID Roslin Bioinformatics
ComparaGRID
Roslin Bioinformatics