WBConfCall 2020.04.16-Agenda and Minutes
- 1 Agenda and Minutes
- 1.1 Reproducing or reworking the "protein schematic" in protein pages
- 1.2 Calculating potential interologs based on Alliance orthology
- 1.3 GO-CAM model/pathway curation with orthology data
- 1.4 User survey for feedback, ideas and feature requests
- 1.5 Curation program for Summer undergraduate students
- 1.6 Help-desk issue
Agenda and Minutes
Reproducing or reworking the "protein schematic" in protein pages
As we winnow down the number of items at WormBase.org that directly depend on ACEDB (and there are very few left), we have the graphic generated for protein homology like in the UNC-26, isoform a page While we can reproduce that image with JBrowse like this, it does require jumping through some hoops. So the question is, do we keep this functionality and jump through those hoops, or should we rework it to be more useful, or do we pitch it altogether?
- It is very useful. Should keep this.
Calculating potential interologs based on Alliance orthology
- Predicted Protein-Protein interactions from multiple species' orthology data in AGR
- Need to do minor model change for WS277 or WS278
- Hosting data at AceDB and automatic update from AGR update
GO-CAM model/pathway curation with orthology data
- molecular activity and regulatory pathway can be curated from orthology based data with evidence codes.
- reactome has some fuctions for pathway prediction from orthology data.
User survey for feedback, ideas and feature requests
Curation program for Summer undergraduate students
- molecular region/ sequence feature curation project for students (supervised courses)
1. Looking for AVB-specific promoter of C. Elegans
- Old data set available for maker and reporters
- single cell RNA-seq data available for the cell-specific gene or reporter expression pattern
- In anatomy page, we need to curate tissue-specific marker genes combining with its multiple expression data.
2. FTP site search for basement membrane related genes/proteins
- GO term data will address this issue
3. REST API issues