Difference between revisions of "WormBase-Caltech Weekly Calls"

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*The "Under Testing" tag on GitHub issues is applied when something needs to be tested
 
*The "Under Testing" tag on GitHub issues is applied when something needs to be tested
 
*Curators can filter for "Under Testing" issues and close them as they determine they are resolved
 
*Curators can filter for "Under Testing" issues and close them as they determine they are resolved
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= March 21, 2013 =

Revision as of 15:36, 21 March 2013

2009 Meetings

2011 Meetings

2012 Meetings


2013 Meetings


January

February


March 7, 2013

Grant

  • Grant gets reviewed next week
  • Should hear results in ~two weeks


Gene Concise Description form

  • Ranjana, Kimberly working on form layout
  • Easy to use form, simple drop down menus to select, e.g., Species
  • Can users follow references for info?
  • Citing references in concise descriptions has, in the past, greatly increased workload/time to write
  • Prepopulated, precanned Textpresso info?
  • Send out to targeted members of the community, get feedback; Who should we ask for other species?
  • Curators could each try using form to make at least one concise descriptions, give feedback
  • Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
  • Can promote form at the International meeting


Galaxy Workshop

  • Screencast videos capturing use of Galaxy available
  • Chris will send around


Genetic Interaction Ontology

  • Perhaps add "what is expected" info during curation?
  • Good to have a comparison of curation with core set of common papers
    • Cross check for consistency of curation (at least terms should lay in same lineage, if not at same depth)


March 14, 2013

Cleaning up Citace Minus

  • Stemming from Paul Davis' GitHub ticket pointing out small-scale data problems
  • Bogus molecule objects (Chris will take care of)
  • Homol_data from RNAi (and the housing RNAi objects) can be removed
  • Ghost Expr_pattern objects, Wen taking care of (Xiaodong will remove from the Gene_regulation OA)
  • Will need to create a better (more robust) pipeline (with SOPs) for converting, for example, object names to WBID#'s
    • Once a conversion has been made, we need to check Postgres and Citace (& Citace Minus) for consistency
    • Need to minimize the burden on Wen to perform quality and consistency checks
    • Curators need to clean up/fix their data before a big change
    • Scenarios to foramlize:
      • Whole-class name changing
      • Model changes
  • Is there a list of classes (and objects?) that are held in Citace Minus?
    • Cross-references create complexity
  • We will suggest shifting the phase of the model proposal cycle: Propose to freeze all models one month before upload


Queries

  • AQL vs WQL vs AcePerl
  • We may consider working out more formal pipelines for submitting queries (maybe to Wen?)
  • AQL and WQL convenient but not necessarily efficient
  • AcePerl efficient, but has a learning curve
  • Todd highly recommends learning AcePerl as it has many advantages:
    • Learning AcePerl will provide skills to handle other generic queries
    • Whereas AQL and WQL will be obsolete when we leave ACeDB, AcePerl will still be useful (even if the details need updating)
    • Curators have GitHub access to all the AcePerl scripts, including those that generate FTP files


Under Testing

  • The "Under Testing" tag on GitHub issues is applied when something needs to be tested
  • Curators can filter for "Under Testing" issues and close them as they determine they are resolved


March 21, 2013