WormBase-Caltech Weekly Calls

From WormBaseWiki
Revision as of 17:36, 13 March 2014 by Raymond (talk | contribs) (→‎Agenda)
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings



March 6, 2014


  • ?Construct model


  • WS242 started to have miRNA datasets; very short probes, not uniquely mapped
  • Wen made modifications to SPELL to accommodate
  • Wen has started separating datasets from papers
  • miRNA analyses have used completely different platforms than protein-coding genes, so requires a different dataset for each
  • Wen started loading WB topics into SPELL
  • Wen would like assign ~100 papers in SPELL to WB topics
  • Wen also modified SPELL script to annotate datasets applicable to specific tissues or cells
  • Wen may/will co-opt Juancarlos' SPELL instance for testing

?Construct model

  • New ?Construct model will be vetted and approved for early in the WS244 curation cycle
  • Some changes to the ?Construct model proposed over last week
  • Still discussing how to handle plasmids/vectors, whether they should go in the ?Clone class (there is precedence)
  • We should defer to the Sequence Ontology, wherever possible, for definitions and relationships
  • We will go ahead with considering including all plasmids and vectors (e.g. AddGene & Fire vectors) to the ?Clone class which can then be referenced within the ?Construct class
  • Will change the "Identical_transgene"/"Identical_variation" tags to "Corresponding_transgene"/"Corresponding_variation"
  • If necessary, we will consider adding a ?Construct tag to the ?Interaction model to accommodate annotation of constructs used in in vitro physical interaction experiments; this is pending curation of (sufficient amounts of) the relevant data

March 13, 2014


  • ?Infection_assay model
  • ?Construct model (do we need to discuss?)

From my side there no need to discuss further if we can keep the Clone tag in the ?Construct model and as far as plasmids are continued to be curated in the ?Clone class. -Daniela

  • Database Future Mtg report

Write up <https://www.dropbox.com/s/fr9qrsbup9djx4z/DatabaseFutureMeetingatOICR.pdf>. Working group from three sites will test candidate technologies against metrics, considerations and requirements and report by Oct 2014.