WormBase-Caltech Weekly Calls July 2011
July 7, 2011
Root Passwords for all machines
- Send to Paul for emergency access
- 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?
- 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
- 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
- OA being developed for concise descriptions
- Wiki page for concise descriptions
- User Community involvement - individual user curation/annotation
- 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
- 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
- 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? on tazendra /home/postgres/work/pgpopulation/genegeneinteraction/<date>/ggi_<something> -- J
- 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?
- 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?
- 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
- Obsolete terms dumped from the Anatomy Ontology
- Will flag obsolete terms or try to remove from dump
July 28, 2011
- No one is using
- Juancarlos will remove
Concise Description OA
- Almost done
- Can this be of use for other nematode (other species) groups?
- Those studying other nematode are collecting functionally relevant information for genes
Life Stage tags
- Do we need a species tag for Life Stages?
- How closely do different nematode species have similar or the same life stages (and stage names)?
- Example, Infective Juveniles (IJs) (analogous to dauer?)
- Example, are all "L1"s the same across species?
- Let's leave out the species tag for now
Tracking Gene Name Changes
- Juancarlos fixed script for tracking and updating gene names in the OA
- Names will still not be updated (in the OA) until the new release, so there will be a lag
- Solution for now is to look up WBGeneID in WormBase and query the OA using that
- (This came up because the official name of a gene changed and the OA hadn't caught up yet)
Concise Description records with no genes?
- Some invalid genes disappeared from the name server all together, but should have stayed in tagged as "obsolete"
Author First Pass forms for transgene
- Overexpression phenotype
- Transgene phenotype
Streamlining Molecule curation
- Karen gave Michael a list of molecules to run through Textpresso
- Can save sentences related to molecules
- FlyBase linking moving forward
- GO-term linking
- 3 Papers have come through pipeline
- Curators will discuss once gone through
Outline for NAR paper in the works
WormBase paper for "Worm" journal
- "Fun" paper
- Discuss who we are and what is being done
Worm Breeder's Gazette
- WormBase can use Worm Breeder's Gazette as a forum for discussion
- We should have a presence for every Gazette
- Replacement for the news letter?
- SPELL related article? Virtual Worm?
- Ruihua will be here until late September
- We have an opportunity to update and tighten up the SVM code/process
- FlyBase interested in implementing
- Will take some effort to convert for fly
Expression Cluster Model
- Last week Wen finished processing Array Express microarray data
- Not a problem to keep up importing data from Array Express and GEO into SPELL
- Some authors do not provide spot IDs or respond to e-mails
- Gene IDs used rather than spot IDs
- New model will accommodate data from RNA-seq and tiling arrays (not just microarrays)
- Tag the Expression Cluster with applicable WormBase build/release for reference
- Capture treatment conditions (temperature, molecules, pathogens, etc.)