WormBase-Caltech Weekly Calls

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2012 Meetings

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March 1, 2012

GO Meeting

• Focused on annotation pipelines; improving efficiency/effectiveness
• How to make GO annotations more 'expressive'
• GO would like to move towards more expressive statements
• Example: If a gene is involved in a function or process, where in the cell does this take place
• Common Annotation Framework
• Current/future members of the GO network can annotate using the same version of GO, same tools and standards
• Quality controls checks: e.g. do you have all the fields necessary to make an annotation
• GO hopes to centralize all of the data handling, formatting
• LEGO - Logical Extensions of GO
• We should pilot how we want to handle this; similar to how concise descriptions are constructed
• WormBase curates phenotypes, pathways, etc.
• Defining useful relationships to curate/annotate: Cross-products with defined relations
• Pilot: Take subdomains, pathways, try extended version of curation on these
• How do we capture that fly eye development is relevant to human biology?
  • Humans don't have compound eyes - not the point
  • The pathways are the same or similar; EGF signaling
• WormBase Process curation could really benefit from GO's adoption of this strategy
• Need to consider what the "right" way to approach this issue; need good pilot
• Where is the value? How do we focus on this?
• Another annotation pipeline: Phylogenetic Annotation and INference Tool (PAINT)
  • How best to make these inferences?
  • What kind of inferences can you make about organismal- or organ-specific processes?
    • Uberon has framework for interspecies anatomical comparisons
  • PAINT tool for nematodes?

Upload for WS231

• Interaction file upload took several hours
• Check if virtual memory is being used
• Likely culprit is the extra data and XREFs in the Interactor_info hash
• Can objectify the Interactor_info to be a tag in the main ?Interaction model
• We should warn EBI/Hinxton about this

WormBase Curator Interview next Thursday

Migration of Reporter_gene object annotations from Expr_pattern OA to Transgene OA

• Everything seems OK

SPELL

• Papers with less than three experiments, statistics calculations cause slow-down, memory limitations
• Now can bypass this problem
• We are now operating SPELL on our local machines
• Do Amazon instances function/behave differently than local server?
  • Need to compare; find benefits & drawbacks
• Use Amazon server as a dynamic name server
• Users shouldn't notice a difference
• We won't need to ask Todd for anything; we can fix it ourselves

GO Meeting breakout session

• Software architecture for upcoming GO expansion (CAT - Common Annotation Tool)
• How does Textpresso integrate?
• What kind of annotation would GO expect Textpresso to do?
• User will be able to do guided text mining operations
  • Example: regular expressions, then HMM, then export to CAT
• No forseeable roadblocks
• Maybe standardize all of the text mining types and methods behind them
• Develop paper-viewer? Apart from CAT, text mining flow? Separate module

March 15, 2012

RNAi clone mappings

• Can we submit PCR primers to Hinxton for genome mapping?
  • They say so, we'll have to test
  • Usually we deal with PCR_product objects like sjj_* or mv_*

PCR construction of transgenes

Should we make a standard submission format for authors?

• Maybe, authors should have to submit explicit sequences for RNAi probes, transgenes, etc.
• Enforce standards at what level? Editors, reviewers, journal, user community, etc...
• Submit PCR primers?