New PomBase website features
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The document discusses upcoming new features and pages for the Pombase website including publication details, genotype descriptions, phenotype annotations, and building curated networks that connect genes and gene products through their biological activities and processes to represent pathways in a visual format. It also outlines current limitations and plans to further develop network displays and features to better represent curated gene interaction and regulation data.
New PomBase website features
- 1. Welcome to pombase- preview.babraham.ac.uk/ New features Arriving soon Example pages Feedback Antonia’s poster P132
- 2. ● New website pages & features to display existing content ● New displays from novel approaches to curation to build networks Overview
- 3. Current System - Slow development - Large Bug fix:New feature ratio - Long update cycle Unnecessary Architecture Lots of “moving parts” Large maintenance Overhead (e.g. Drupal web content management) Redundancy
- 4. Simplified Removed unnecessary infrastructure: ● Increased robustness (fewer bugs) ● Easy to implement new features ● Nightly updates
- 6. New Pages Genotype Name(description) Allele type, expression Annotations, filters
- 7. ● Single/Multi-allele ● Population/Cell New Features ● Filter on term “class” ● Non redundant annotation display in summary view (click the gene page to play the movie) Phenotypes
- 8. Building Curated Networks Traditionally annotations/gene/gene pages unconnected. We grouped gene products by common activities and processes - accessible via linked lists e.g. Pom1 protein kinase activity Pom1 regulation of G2/M Cdr2 protein kinase activity Etc But how these were connected biologically was not evident
- 9. Pom1 Cdr2 Wee1 Cdc2 Cell size pathway involved in negative regulation of G2/M Pom1 ---------- Cdr2 Wee1 ----------- Cdc2 Cell size pathway involved in positive regulation of G2/M P P P By capturing gene product “inputs” and “outputs” we can represent pathways and processes as biological network diagrams. Building Curated Networks
- 10. Pom1 Cdr2 Wee1 Cdc2 Cdr2 Wee1 We now capture inputs and outputs to provide “functional” connections between genes (pages). PomBase is the first MOD to make use of these curated connections between effectors and substrates to build networks. Making Connections
- 11. Moving towards detailed network displays P P P P P Building Networks
- 12. Making Connections Making connections between effectors and substrates (click the gene page to play the movie)
- 13. Making Connections Processes and Subprocesses (click the gene page to play the movie)
- 14. Currently generate networks for GO slim terms only. Will gradually fill in for all terms with enough curated data. Add more notation. (click the gene page to play the movie)
- 15. Currently generate networks for “GO slim” processes only Future ● All processes ● Inhibition and activation ● Activities, modifications (Annotation practice supports this, we are working on the display) Future Displays P P P P P P
- 16. Future JBrowse Protein feature viewer New Query interface Network viewer
- 17. Acknowledgements Website Developer: Kim Rutherford Curators: Midori Harris, Antonia Lock, Jacky Hayles, Val Wood The community curators (212 of you!) PIs: Jürg Bähler, Steve Oliver