WormBase-Caltech Weekly Calls March 2012

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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_*


Transgene sequences

  • Authors explain PCR construction of transgenes; provide explicit sequence?


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?
  • We will draft a letter to community/editors to request explicit sequences for RNAi experiments


Should we perform sequencing of Ahringer (and other) clones ourselves?

  • Write grant, perform sequencing?


New website release

  • We will draft an e-mail/blog post about official release of new website at end of March


SVM Precision/Recall

  • Standardize methods of calculating precision and recall on SVM results?
  • True Positive = a positive identified by SVM that is actually positive
  • False Positive = a positive identified by SVM that is actually negative
  • True Negative = a negative identified by SVM that is actually negative
  • False Negative = a negative identified by SVM that is actually positive
  • Precision Rate (Positive Predictive Value) - how many SVM-identified positives are true positives? = True Positives/(True Positives + False Positives)
  • Recall Rate (Sensitivity) = True Positives/(True Positives + False Negatives)
  • Specificity = True Negatives/(True Negatives + False Positives)
  • NPV (Negative Predictive Value) = True Negatives/(True Negatives + False Negatives)


Curator Candidates


March 22, 2012

New website release

  • Sending around mass e-mail to WormBase community (9960 e-mail addresses) announcing release
  • Will notify that old site will still be available (at legacy.wormbase.org?)
  • Provide link to old website on new website homepage?


Browsable worm model

  • Implemented by Open Worm project team


SPELL

  • Monitoring to see if it is up and running
  • Had a few shutdowns that we weren't aware of
  • Would like to be ahead of the users so we can restart it
  • Trying to figure out how to be made aware of any shutdowns
  • Yeast SPELL has set it up such that a user could paste in a URL to get results
    • Worm SPELL cannot do this; not setup in the same way
    • Wen will contact yeast SPELL team; already contacted Michael Cherry
  • http://imperio.princeton.edu - has nice functionality
  • Kimberly will ask around


RNAi OA

  • Working on the new RNAi OA
  • Will take advantage of Igor's RNAi processing script for dumping from the OA
  • Would be good if we had a working tool (locally) to map primer sets and clones to DNA text


Interaction and Gene Regulation OAs

  • Need to be updated (OA and dumping script) to accommodate the new ?Interaction model


March 29, 2012

BioCurator Meeting

  • QC Fast poster looks good
  • Wen presenting poster on SPELL
  • Kimberly has multiple presentations
    • WormBase workflow
    • CCC for Dictybase
    • Another presentation
  • Michael and Yuling going; will meet with collaborators
  • Text-linking groups (Reflect)
  • Keep an eye out for PDF(paper) viewers/editors/annotators


SPELL upgrade

  • Upgraded to newer version of software
  • Automatically keep track of whether or not it is functioning
    • Regular test query every 30 min to 1 hr
  • Still using Amazon server as a forwarding service


OA edits

  • Interaction and Gene_regulation OAs under modification for new ?Interaction model
  • RNAi OA, generating OA and dumping
  • Configuring OAs so that single objects exist on a single row in the OA
    • Is it necessary to map interaction objects (Transgene, Antibody, etc.) to a core interaction entity (Gene, Protein, etc.)