Difference between revisions of "WormBase-Caltech Weekly Calls"
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* Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working | * Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working | ||
* Possibly SGD could run a worm instance on their machine(s) | * Possibly SGD could run a worm instance on their machine(s) | ||
+ | |||
+ | === Transgenome === | ||
+ | * Junacarlos finished parsing the transgenome data with Daniela | ||
+ | * Checking parse output numbers with the Transgenome group | ||
+ | * Will the expression data be dumped out in the expression GAF? Yes, should be | ||
+ | * Data from Transgenome are not necessarily peer-reviewed; need to make that clear in display | ||
+ | |||
+ | === Micropublications === | ||
+ | * Trial with uploading Nemametrix data; hopefully finished by end of month | ||
+ | * Added micropublication type in the ?Paper class |
Revision as of 18:34, 13 October 2016
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
- We likely already have enough data for a first pass implementation; not comprehensive data, but that is fine for now
- Disease data dumped from ACEDB, based on Disease Ontology; not comprehensive for OMIM disease list
- We'll eventually want to pull data directly from OMIM and GO
Extending SPELL virtual machine
- Has a lot of data; may be contributing to SPELL downtime
- Could possibly move to the cloud, but we would need a machine in the cloud
- Can only install SPELL on Ubuntu 8; SGD uses RedHat; we can ask them what they're using, how it's working
- Possibly SGD could run a worm instance on their machine(s)
Transgenome
- Junacarlos finished parsing the transgenome data with Daniela
- Checking parse output numbers with the Transgenome group
- Will the expression data be dumped out in the expression GAF? Yes, should be
- Data from Transgenome are not necessarily peer-reviewed; need to make that clear in display
Micropublications
- Trial with uploading Nemametrix data; hopefully finished by end of month
- Added micropublication type in the ?Paper class