WormBase-Caltech Weekly Calls
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Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
February 1, 2018
Automated gene descriptions - orthology
- Some genes have human orthology mentioned in automated descriptions, even though the orthology call has not been called in DIOPT
- WormBase uses EnsemblCompara and other methods (not aggregate method like DIOPT)
- Orthology synchrony is a challenge; WormBase and FlyBase may need to pay special attention to orthology calls and discrepancies
- DIOPT is purely automated, does not consider other information about orthology evidence
- We should be clear about how the orthology calls are made
Next upload
- Unclear of exact date
- Probably end of March
SimpleMine issue
- Redundant genes in input list are merged
- Should SimpleMine provide an option to keep redundancies?
- Give option up front? Provide submission step to point out redundancies? Ask for choice?
- We can default to show row-by-row correspondence, and display the number of redundant entries
- Conclusion: Make an option for users to indicate if they want row-by-row correspondence or a merged list
Cell type expression
- Waterston paper
- 40,000 random cells, clusters sequenced individually to a depth of 20,000 reads; ~1000 genes per cell; cluster data; make judgement call as to what cell types they likely are
- For now, we can do a simple annotation: significantly expressed genes for each cell type
- Supplemental table S5 for neurons
- Maybe just ignore the hybrid calls like AQM/PVM, etc.
- It may be good to isolate the single cell data from other expression data
- We should annotate/capture the expression clusters
- Would be good to be able to do enrichment analysis on the clusters; compare data sets
- Data has not been placed in SPELL yet, Gary considered the data a work in progress
- We can communicate with Waterston group; are they collecting more data?
- Wen will take another look at the data
- Gary W. concerned about the reported/assumed/inferred identity of the cells in the paper
- Probably cannot curate to individual cells, but we can annotate to a higher level term
- We want to annotate and display expression enrichment as well as presence/absence calls
February 8, 2018
Release schedule
- Wen will ask Hinxton to update the published release schedule (for next data upload)
New York Worm Meeting
- Wen and Kimberly will present a WormBase tutorial on March 24
GO curation
- New simple input form for Noctua, being developed at USC
- Not very much GO curation happening at WB right now
- Protein-2-GO pipeline
- Do we have a good Phenotype-2-GO(Process) mapping pipeline? We have our old mappings; not very reliable; would need to spend more time expanding the worm phenotype ontology and GO to improve
- Cellular component curation will come in from WB expression curation
- Don't have pipeline for Interactions-2-GO
- Textpresso Molecular Functions pipeline?
- geneprod and catalyticact data types for molecular function pipeline
- Textpresso can send molecular function annotations to Noctua
- For high-level pathway curation; we should probably read WormBook chapters (or other reviews) and develop pathways (using non-experimental evidence codes)
- We could potentially seed Noctua models from Reactome
- We would like to have complete curation for major pathways for gene enrichment analysis
