WormBase-Caltech Weekly Calls
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Previous Years
2014 Meetings
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?)