WormBase-Caltech Weekly Calls
September 1, 2016
Working group discussions
- More clear about issues surrounding orthology sets
- ZFIN has protein curation that may be becoming a bit out of date
Single-cell RNA profiling
- We've been curating some data, but not clear how to display the data
- Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
- Genes that are detected at convincing levels (present call) in cell/tissue
- Should we display expression data that we do not (or cannot) update differently from other data
- Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
- Could capture quantitative assessments; transcripts per million, etc.
- Should we provide an analysis of raw data to users to perform their own comparative analyses
- Bob Goldstein's group prepared software tools in their paper; could we make use of them?
- Big question: how do we handle divergent (expression) data?
- David (Angeles) working on an expression data analysis pipeline
- Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
- There's difficulty in reconciling small and large datasets (or different data types)
- Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
- In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage
September 8, 2016
- TransgeneOme import -Daniela:
adding a Community_curator tag or Curator tag in the Expression model to acknowledge the community curators that annotated/will annotate the data.
-for the records- documentation on the import here http://wiki.wormbase.org/index.php/TransgeneOme_import