WBConfCall 2022.09.01-Agenda and Minutes
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Help desk issues
- Fosmid and clone availability #8649
- No availability seems to be the word- most replies were negative
- Urgently need to update pages https://wiki.wormbase.org/index.php/Fosmids and https://wiki.wormbase.org/index.php/Cosmids/YACs to reflect real lack of availability
- Sanger is now providing clones (after being closed for a long time for the pandemic). We should publish a blog post and update our wiki
- Magda is working on it. We have the data
- Raymond looked into the variant data but we don't have additional info. In terms of the deletion we don't have seq info so it's not on the seq browser. Magda can help but she will need to study the paper
- pseudo gene sequences should be on the website. Magda will investigat
- Check if the reply to #8755 was sent to the user via email
- check https://github.com/WormBase/website/issues/8756 (for webteam)
- phosphoproteomic dataset and rnai dataset - Magdalena is working on it. There's a lot of data and a lot of work to integrate it.
- Grant progress & questions
- Data/classes already harmonized in Alliance
https://docs.google.com/spreadsheets/d/1ZsxGlMHvWxPjRwI2jtIys-sQgZY602cf/edit#gid=284571688 - please all refresh/check
- New RNA-Seq processing pipeline towards Y4/Y5 of the grant? - okay, mention it
- Data on productivity over time (which releases to count, which data)?
- Do we need to add progress report? No - we don't think so, but we can double-check with NIH support? And we can add some progress data in the text
- Do references add to page count? No - we don't think so
- Model single-cell data, and Highlight genes, markers and reagents for that cell/type
- Venn diagrams? Fold changes?
- Need to modify the schema of expression_cluster - then calculate the numbers
- Magdalena will work on new data models soon. Ranjana is working on the disease model. Alliance IDs in the disease model are not yet included in it but currently there's no data to populate. The main use case would be to link WB pages to Alliance disease section on gene pages.
- Grant discussion
- Grant is coming along very well. The doc is too long and needs to be cut
- Magdalena started to draft a count of all classes that have been harmonized. Chris is asking what the definition of "harmonized" is in this context. Todd: there's not much room for class by class analysis and an high level overview of the data will be good. Paul: we can give an example to show the level of detail of the work. We could add a project plan and some goals for these metrics.
- Todd: we should wipe out comments and start working on a final draft. Paul: create a new version without comments. To make it more scientific, we could expand section B and shrink the other sections. Progress report section? Paul will ask the PO. One or two sentences for progress will probably be fine.
- New copy of the grant: Magdalena created a backup copy with comments. We can directly delete comments from the main copy (same link). Unshortened version - snapshot https://docs.google.com/document/d/1fkVTsWY0ts4dG3y1lTqorhSJPWa4wst10e_ev5zz7Nw/edit?usp=sharing
- References - Ranjana: how many references do we need to add? Ref don't count as page numbers so add as many as we need.
- Sarah: Adding a gantt is important. We can make it very compact with just enough info
- Add a chart with the roles of the personnel. Could be linked to the gantt with institutions.
- Add a number on the amount of curation we are going to do
- Add a couple of sentences on progress (last 5 years)
- Are there worm specific datasets/features we need to move to Alliance that are not going to be harmonized? We mentioned something in the last section but it should be more prominent. Do we have a list of these WB-specific features? E.g., soba graph, expression clusters.
- Phenotype community curation part added by Daniela but numbers are missing. Chris will add them.
- Future plans part is a bit light on the draft. Discuss new data types + examples on how we are going to respond to community needs for new data.
- Innovation - should be highlighted
- Productivity over time as part of section A. It could be good to discuss what we can do and add something short but impactful.
- Paul prefers author and year refs
- We can also add figures. Maybe an overall graphical abstract on curation process or software (ML/community curation)
- New RNA-Seq processing pipeline is very different at the Alliance and we should talk about the differences.
- For single cell we should add a description on how we are going to model expression in cell by cell data. How are we going to serve our users with these data? Raymond: what we have right now is an expression profile. This matches with small scale expression pattern. A quantitative presentation would be more difficult because each dataset has specific features and sometimed they cannot be reproduced. Markers and reagents for each cell? We have Eduardo's tool but we should add lists of genes in WB based on single cell analyses but this is hard since there's no standard for thresholds. Wen: We need to store the data in better ways. Should we present the data to the Alliance for expression cluster single cell RNA Seq? Paul: the problem with other organisms is that the anatomy is not as well defined as C. elegans. Wen will add this to the grant.
- We decided to have sitewide calls every week for the next couple of weeks to work on the grant.