Difference between revisions of "WormBase-Caltech Weekly Calls"
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**Ontology Annotator | **Ontology Annotator | ||
**Demo by Kimberly or Ranjana? | **Demo by Kimberly or Ranjana? | ||
− | **Relatively trivial to setup new OA for a new site (Juancarlos) | + | **Relatively trivial (depending on situation) to setup new OA for a new site (Juancarlos) |
**Discuss what's been proposed in the grant | **Discuss what's been proposed in the grant | ||
**What does the consortium want? Brainstorming/Fantasizing | **What does the consortium want? Brainstorming/Fantasizing | ||
Line 106: | Line 106: | ||
*Group met on Tuesday | *Group met on Tuesday | ||
*Made headway on genetic interaction organization | *Made headway on genetic interaction organization | ||
+ | *Add "Additive" type term and "No Apparent Interaction", etc. | ||
Line 132: | Line 133: | ||
*12,000 genes that are NOT represented in CGC | *12,000 genes that are NOT represented in CGC | ||
*Discrepancy wrt alleles; negative in AQL query, but present on site | *Discrepancy wrt alleles; negative in AQL query, but present on site | ||
+ | *Strains with LOTS of alleles; how to handle? | ||
+ | *Polymorphisms vs. alleles | ||
+ | |||
+ | |||
+ | Aldrin Montana working over the summer | ||
+ | *We invited him to visit | ||
+ | *We'll come up with projects | ||
+ | *Web team fully involved in web site | ||
+ | *Help with minor GO issues (Ranjana) | ||
+ | **Requires knowledge of Perl | ||
+ | **Non-C.elegans species | ||
+ | **InterPro-to-GO mapping | ||
+ | **Export pipelines for other species? | ||
+ | **Maybe small project; requires more communication than coding? | ||
+ | *Raymond could help provide projects | ||
+ | *Would be nice to use PAINT across the nematodes for annotation | ||
+ | |||
+ | |||
+ | New Web site (Todd) | ||
+ | *Web team wrapping up various projects | ||
+ | *Polishing user interface | ||
+ | *Abby working on user interface | ||
+ | *Todd working on production environment | ||
+ | *Norie working on code that interfaces with database | ||
+ | *Release beta version at International Worm Meeting | ||
+ | *Working with Kevin Howe to standardize formats of files used during build | ||
+ | *Can now host new data for new species |
Revision as of 19:03, 12 May 2011
2011 Meetings
May 5, 2011
Citace upload
- Using current citace release (WS226) for Progress Report
Pictures
- Daniela did not actually curate ~7000 pictures this month ;)
- Script to fetch pictures automatically
Snehal starts next week
- working on phenotype curation
- 90 genes >= 10 publications
- Of these 90, 54 with no annotated phenotype
- 20,000 genes with RNAi data
- Concise Descriptions? May be appropriate
- Prioritize by genes that currently have no description but have new papers
- Picture curation?
- Learning an ontology may be difficult, but she can stick to familiar material
Aldrin
- Karen, Raymond, Chris will talk to Todd
- Lineage browser for ontologies?
- Cell lineage browser? Capture multi-parentage issues
Ranjana - Preplanning WormBase side meetings at IWM?
Periodically sending someone to different sites
- E.g. Someone from Caltech goes to Hinxton, etc.
Practice Talks before International Worm Meeting
- on Monday before meeting
May 12, 2011
Example of Bandana for International Worm Meeting
- Looks good!
GO Consortium meeting next week
- Paul, Michael, Ranjana, and Kimberly going
- Discussion about tools (Juancarlos?)
- Section in meeting agenda to discuss curation
- Textpresso-based curation
- Ontology Annotator
- Demo by Kimberly or Ranjana?
- Relatively trivial (depending on situation) to setup new OA for a new site (Juancarlos)
- Discuss what's been proposed in the grant
- What does the consortium want? Brainstorming/Fantasizing
- People are likely partial to their own tools
- Make use of the best parts of everyone's tools
- Are others using flat/text files or web-based/java-based tools? Mostly web-based
- Phenote? Funding? Bio-Portal e-mail?
- PAINT tool (Phylogenetic Annotation and INference Tool) (http://wiki.geneontology.org/index.php/PAINT)
Progress Report
- Paul has received some reports, but not all, yet
Picture curation
- Started receiving permission from Elsevier!!
- Blanket-permission for 11 journals
- Publicly display list of cooperating journals online
Talks at the Int Worm Meeting
- Paul S listed for a Plenary talk during Workshop
- Two Wormbase Plenary talks
Snehal
- Concise descriptions
- Kimberly helping
- Will get into phenotypes soon
Juancarlos waiting to hear back from some people about OA
- People need more time to test
- Karen has encountered some issues; needs to reproduce
- Ranjana - loads slowly?
- Mangolassi issues?
Genetic Interactions
- Group met on Tuesday
- Made headway on genetic interaction organization
- Add "Additive" type term and "No Apparent Interaction", etc.
Paper pipeline
- Kimberly & Juancarlos working on
- Documented on Wiki
- CGI's still being used?
- Remove outdated or unused CGI's?
Rewriting script from Jack Chen
- Neuron connection search
- Inroad to working on more web-interface topics
Adding interaction datasets into WormMart (Xiaodong and Ruihua)
Gene interaction dumping script (Raymond/Todd)
Strain Display
- Karen doing queries at CGC
- How many genes represented in CGC strain list?
- Protein-coding genes with alleles in strains?
- 12,000 genes that are NOT represented in CGC
- Discrepancy wrt alleles; negative in AQL query, but present on site
- Strains with LOTS of alleles; how to handle?
- Polymorphisms vs. alleles
Aldrin Montana working over the summer
- We invited him to visit
- We'll come up with projects
- Web team fully involved in web site
- Help with minor GO issues (Ranjana)
- Requires knowledge of Perl
- Non-C.elegans species
- InterPro-to-GO mapping
- Export pipelines for other species?
- Maybe small project; requires more communication than coding?
- Raymond could help provide projects
- Would be nice to use PAINT across the nematodes for annotation
New Web site (Todd)
- Web team wrapping up various projects
- Polishing user interface
- Abby working on user interface
- Todd working on production environment
- Norie working on code that interfaces with database
- Release beta version at International Worm Meeting
- Working with Kevin Howe to standardize formats of files used during build
- Can now host new data for new species