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Gramene Technical Improvements

Gramene aims to support complex queries and improve genome annotation, diversity visualization, and comparative views. New personnel and tools, such as BioMart and BioPipe, are being added to enhance data accessibility and analysis. Additionally, the incorporation of Biochemical Pathways and a better comparative viewer will provide a more comprehensive and interactive experience.

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Gramene Technical Improvements

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  1. http://www.gramene.org 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 10-15 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

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

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

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

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

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

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

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

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

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

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

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

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