WormBase-Caltech Weekly Calls

2011 Meetings

Gene ID mapping problems (as discussed in site-wide call)

Does CIT need to worry about consistency of gene IDs over database builds?
Hyper-linking entities in papers could be an issue
Acquire an ID for every gene for every new genome?
When mark a paper, separate into two different types of genes :stable vs unstable
- Stable genes map to stable ID
- Unstable genes map with a version number
WormBase communicate/work with DCC personnel for data wrangling during post-DCC era?

Updating Predicted Gene Interactions

Wei wei asking about how to update with WormBase
WormBase predicted interaction objects can be updated simply via link to Gene Orienteer
If we want a live interaction browser, we would need to pull the data into the build process
Do we want a single object per pair of genes? One object per instance of evidence (per paper)?

Worm Publication is under review

NAR paper is published - has DOI

Citace, Development Release

Cron-jobs/scrips used to update the database, but now requires manual manipulation
Manual versus automated updating of database
Need a plan for the future
Migration to EBI affecting the process; will things change again
Where will WS release files exist

SVM

Motifs in WormBase

Interaction Model

Discuss with Todd the integrated model of 4 types (physical, genetic, predicted, regulatory)
Change WBID names (WBInteraction versus WBPhysicalInteraction, WBGeneticInteraction, WBRegulatoryInteraction, WBPredictedInteraction)
Put together series of example data objects; send to Todd/Paul to test out
Need Interaction_type tag to distinguish the 4 basic types
Types will need to be parsed/extracted after the build for FTP download etc.

Human Disease Relevance Descriptions