WormBase-Caltech Weekly Calls

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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? 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?

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

July 28, 2011

Condition Form

• 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

GSA

• 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?

SVM

• 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.)

August 4, 2011

Leak in office

• Emergency showers don't necessarily have drains
• We need to make sure that things in offices are prepared for potential water leaks
• Production server still running
• Mangolassi down for the time being; will be back up when dry
• Should call physical plant 24-hour emergency line (ext. 4717)
• Feel free to check offices/labs above ours to assess risk of leak

Testing concise description OA on sandbox

• Community annotation form needs to be very simple (e.g. gene name and empty box only)

Transgenomics pictures

• Daniela spoke with Mihail about getting pictures from their database
• We should know exactly what the clone is (sequence)
• What are they using for anatomy annotation?
• Linking to Yuji Kohara's database (NEXTDB)?

Gene file from Hinxton to populate Gene Tables

• Kimberly working with Mary Ann Tuli and Michael Paulini to make sure each gene names are cleaned up

Raymond

• Trying to install Amigo (for Ontology browsing)
• Working on SPELL

SVM

• Karen using author first pass list for priority
• 2 out of 3 papers have not been flagged for phenotype; Why?
• Michael setup a way to tag papers on Textpresso Dev if they've been processed by SVM
• How do we make sure all papers go through SVM pipeline?

Replacing power supply on conference phone

• Probably cannot fix
• Need to buy new one