WormBase-Caltech Weekly Calls

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2014 Meetings

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March 6, 2014

Agenda

• ?Construct model
• SPELL

SPELL

• 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

Agenda

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