Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Sarah (Torres) could register all WB CIT participants | * Sarah (Torres) could register all WB CIT participants | ||
* Kimberly is helping organize | * Kimberly is helping organize | ||
| + | |||
| + | === AGR Portal Use Case working group update === | ||
| + | * Working on first use case, basic text search for genes, GO terms, diseases, and orthology groups | ||
| + | * Data is being collected into a "Portal Data" Google drive: https://drive.google.com/drive/u/1/folders/0B9qQtJIEUDEhRnJKWF9NTTVMVGs | ||
| + | * Some MODs providing more data than requested; That's OK, we just want to keep it simple for the first implementation | ||
| + | * We only want, for the first pass, to retrieve genes, GO terms (no GO-gene annotations), diseases (no disease-gene annotations), and orthology groups | ||
Revision as of 18:22, 13 October 2016
Contents
Previous Years
2016 Meetings
October 6, 2016
Citace upload
- Tuesday, October 25th, 2016
Automated descriptions
- Ranjana working with Juancarlos to run and update automated descriptions pipeline
Intellectual lineage
- First draft up on WormBase development site
Noctua
- Raymond trying to annotate axioms for anatomy function
- How to connect cell types in different organisms to those in C. elegans anatomy ontology?
- Maybe best way is to connect based on biological function, e.g. regulate osmolarity (kidney, excretory cell)
- Raymond attempting to use Noctua to draw relationships between anatomy terms and function
- There's a distinction between annotating to an instance vs. to a class
- Raymond worked on modeling a statement on excretory cell function from WormAtlas
- Question: how much redundancy might we end up with if we annotate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable
Expr_pattern model change
- Daniela proposed a CRISPR-Cas9 tag for the expression pattern class as an experiment type
- Would be inline with "Reporter gene", "In situ", "Antibody", etc.
- Probably want "Genome editing" instead of "CRISPR-Cas9" so as to be more generic
- Would a GFP knock-in via genome editing be distinct from "Reporter gene"?
- Could have a super tag "Genome_editing" and sub-tags "CRISPR-Cas9", "Zinc_fingers", "TALEN"
- Maybe we'll just stick with a "Genome_editing" tag
October 13, 2016
Strain requests
- Ranjana sending strain requests to Mary Ann
- Mary Ann processing published strains requested by Ranjana
GO meeting
- Registration is now setup
- Sarah (Torres) could register all WB CIT participants
- Kimberly is helping organize
AGR Portal Use Case working group update
- Working on first use case, basic text search for genes, GO terms, diseases, and orthology groups
- Data is being collected into a "Portal Data" Google drive: https://drive.google.com/drive/u/1/folders/0B9qQtJIEUDEhRnJKWF9NTTVMVGs
- Some MODs providing more data than requested; That's OK, we just want to keep it simple for the first implementation
- We only want, for the first pass, to retrieve genes, GO terms (no GO-gene annotations), diseases (no disease-gene annotations), and orthology groups
