1. Gramene Technical Improvements
Gramene Technical Improvements
Chengzhi Liang

2. Goals Support Complex Queries Better Genome Annotation
Diversity Visualization
Biochemical Pathways
Better Comparative Views

3. Complex Query Examples
Find all rice genes/QTL that control a trait, eg, height
Find all rice genes in the syntenic region of a Maize QTL

4. Complex Data View Primary Evolution Protein Family Gene Ontology
Reference
Tool
Chromosome
Clone (BAC)
Synteny
Marker
Chromosome
Marker
Locus
Allele
Gene/QTL
Diversity
Trait
Trait Option

5. Current Gramene Schema
Portable, modular, etc, many advantages, but not well-suitable for complex queries
The previous query examples need to access to multiple modules, including QTL, Genome Browser, CMap, Ontology
Several ways, but usually steps
To do it better, we will use…

6. BioMart Data warehousing technology for complex queries
Well developed, part of GMOD
Simple, query optimized, generic schema
Portable, easily integrated with Gramene

9. New Personnel Will Spooner Former Ensembl employee BioMart Developer
Many years of experience in developing/deploying/using those programs

10. Better Genome Annotation
Need consistent, reproducible gene predictions across the cereal genomes
Software that is being used…

11. BioPipe Portable Easy to grasp -- close cousin to Ensembl technolgy
Simple to use – works with Ensembl schema
Data consistency -- using for Gramene alignment annotation

12. Portable, Standalone tools
To search
Interpro
Go annotation
Trans-membrane Prediction
Sequence mapping

13. New Personnel Kiran Kumar Payan Canaran From Biopipe project
From Merck’s pipeline project

14. Diversity Visualization
For fast-accumulating diversity data
Dr. Ed Buckler will discuss this in details

15. Biochemical Pathways To fully utilizing data of Trait Diversity
Expression
Make static data dynamic (both spatial and temporal)

16. Pathway Tools
From Peter Karp, eg, EcoCyc
Well developed/supported

19. To Be Released
Liya Ren attended the Cyc short course, and is setting it up for rice and other cereals.
Expected date: Fall 2005

20. Better Comparative Viewer
Many web UI improvements to CMap (Ken Clark & Ben Faga)
Multiple Genomes in Ensembl via Compara (Will Spooner)

21. Graphical Summary Web Web Web Web Raw Ensembl CMap BioMart DAS Data
Objects
API
Objects
API
Objects
API
Objects
API
Raw
Ensembl
CMap
BioMart
DAS
Diversity
Data
Gramene
Dump