WormBase-Caltech Weekly Calls
From WormBaseWiki
2011 Meetings
July 7, 2011
Root Passwords for all machines
- Send to Paul for emergency access
Issue Trackers
- All code in production use in BitBucket or equivalent
- Textpresso - Subversion (code can be shared)
- WormBase - Bitbucket, GitHub (can commit code)
- Todd says Github for code is best
Alex Bishop Help Desk E-mail
- Interolog Finder
- FlyBase will include links soon
- Is WormBase interested connecting to it?
- Can it be sustainably maintained?
- We should make a link under the Tools section of WormBase
- Interolog Finder provides cytoscape files
- Does Cytoscape have a web interface?
Elbrus is currently working stably
- Raymond stabilized Elbrus
- Elbrus is a frankenstein now
- Sanger/EBI taking over the RNAi mappings
- Will discuss with Igor once we determine the remaining issues
- Elbrus still needed for RNAi scripts to generate ACE files
Oliver Hobert correcting expression patterns occasionally
- Ask Oliver to point out what is missing
- Also ask Shawn Lockery
- Cell-specific markers
- Curated as transgenes
- Can link to specific promoters if transgenes present
- Bottom of every transgene page has a link to the static Marker table
- Check on new Beta version of WormBase website
Changing language of e-mail to authors to confirm data
- Non-nematode papers in WormBase via Cecilia?
- Authors sending all papers in their CV
Expression Cluster data curation
- Including GO terms, life stage, etc.
- Link to process pages?
Expression Cartoons
- Attempting to depict expression patterns by separate images for each tissue
- Would be nice to have a consolidated image with the option to expand to see individual tissue images
- Will maintain consolidated and expandable images for each gene as well as each expression pattern for each gene
- Trying to capture "Certain", "Uncertain", and "Partial" curation tags
Molecule curation
- Will need a molecule page on WormBase at some point
- Need a way to handle molecules that do not have a Mesh IDs
- Will replace WBMolecule IDs with Mesh IDs when they become available
- WBMolecule ID will be made a synonym of the molecule name alongside the Mesh ID
- Need to consider how the data will be stored and referred to in the long term (via ACE files etc.)
July 14, 2011
Concise descriptions
- OA being developed for concise descriptions
- Wiki page for concise descriptions
- User Community involvement - individual user curation/annotation
Diseases
- Managing disease relevance tags in appropriate models
- Relating human disease genes to C. elegans orthologous genes
- Developing an integrated view for users to browse human disease relevance
- Manual vs Automated curation processes
Worm Breeder's Gazette mass e-mails
- Users complained about e-mails going to old e-mail addresses
- Will only e-mail the most current e-mail on a user's profile
GitHub
- WormBase curation repository
- Should Juancarlos put postgres (and other) cgi's there?
- Make a separate Tazendra repository?
- Generate symbolic links for flat files (non-code)?
- Are we limited in the number of repositories we can have? Cost-dependent
- We could pay more for more repositories; is it worth it?
- Make another account separate from Todd's? Probably not; should keep consolidated in one account
- Do different dependencies cause problems?
- We will ask Todd about what he thinks is best
- OA code could eventually go to GitHub as well Code already in github -- J
- Textpresso code can go to GitHub as well
Ontology Browser
- Aldrin installing Amigo
- How long should installing Amigo take?
- Get some input from GO Consortium
Genetic Interactions from Textpresso
- Where are relevant paper sentences stored?
- Should we pull out sentences used by Andrei for interactions curation?
- Alternatively, redo a Textpresso search for relevant gene names, etc.
- Can we adequately find allele information?
Interolog Finder
- How to incorporate Interolog Finder into relevant gene pages?
- Maybe make a database object for each C. elegans Interolog Finder interaction
- Can we display our own data in Cytoscape? Interolog Finder data?
- Are Wei-wei's data being updated?
Rearrangements
- Want to change the variation auto-complete file
- Dead allele objects
- Problem: some Rearrangment objects are considered alleles/variations, others are dead or are not considered alleles
- How do we define/distinguish between Rearrangements/Deficiencies and Alleles?
- All are variations
- Do we make alleles and rearrangements mutually exclusive?
- Since all are variations, we handle each generically as a WBVar### object
- The distinction would just need to be made at the point of object creation
Anatomy Ontology
- Obsolete terms dumped from the Anatomy Ontology
- Will flag obsolete terms or try to remove from dump
