Difference between revisions of "WormBase-Caltech Weekly Calls"
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*If we want a live interaction browser, we would need to pull the data into the build process | *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)? | *Do we want a single object per pair of genes? One object per instance of evidence (per paper)? | ||
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| + | == November 10, 2011 == | ||
| + | |||
| + | |||
| + | Worm Publication is under review | ||
| + | |||
| + | |||
| + | NAR paper is published - has DOI | ||
| + | *Williams et al has to be added to bibliography | ||
| + | |||
| + | |||
| + | 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 | ||
| + | *Collecting feedback from curators | ||
| + | *Curators need to review results | ||
| + | |||
| + | |||
| + | Motifs in WormBase | ||
| + | *Xiaodong working on it | ||
| + | |||
| + | |||
| + | 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 | ||
| + | *Started going in from last build | ||
| + | *Ranjana will discuss with Web Team | ||
| + | *Disease-paper connections | ||
Revision as of 19:45, 10 November 2011
2011 Meetings
November 3, 2011
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)?
November 10, 2011
Worm Publication is under review
NAR paper is published - has DOI
- Williams et al has to be added to bibliography
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
- Collecting feedback from curators
- Curators need to review results
Motifs in WormBase
- Xiaodong working on it
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
- Started going in from last build
- Ranjana will discuss with Web Team
- Disease-paper connections
