Difference between revisions of "PAG 2011 Collaborators Workshop"
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'''who: ''' | '''who: ''' | ||
| − | * MaizeGDB: Carolyn Lawrence, Mary Schaeffer, Jack Gardiner. | + | '''* MaizeGDB: Carolyn Lawrence, Mary Schaeffer, Jack Gardiner.''' |
From Mary Schaeffer: | From Mary Schaeffer: | ||
We will be exploring the new PO release as working on term matching to some developmental stages for a Maize Gene Atlas. | We will be exploring the new PO release as working on term matching to some developmental stages for a Maize Gene Atlas. | ||
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I anticipate being able to provide associations for gene models expressed highly. There are 61 tissues, at various plant growth stages, so this will be a substantial number of associations. | I anticipate being able to provide associations for gene models expressed highly. There are 61 tissues, at various plant growth stages, so this will be a substantial number of associations. | ||
| − | '''PJ: Would you be mapping the RNAseq data and the Array data to gene/gene models | + | '''PJ: Would you be mapping the RNAseq data and the Array data to gene/gene models?''' |
MS: Initially they will be mapped to coordinates, and by inference then, to gene models. We are in close contact with CSH on the release of the | MS: Initially they will be mapped to coordinates, and by inference then, to gene models. We are in close contact with CSH on the release of the | ||
Revision as of 22:56, 29 October 2010
This page is under construction.....
When:
Proposed Time: Sunday Late Morning to include lunch
Time 10:30-1:00 pm (will wrap up in time to get to 1:30 sessions)
Where: Town and Country Hotel, Room TBA
What:
The plan will be to have about 5 speakers from groups that use the PO or send annotations to us. The goal is to show a range of types of uses and highlight the utility of the PO to the plant science community.
who:
* MaizeGDB: Carolyn Lawrence, Mary Schaeffer, Jack Gardiner. From Mary Schaeffer: We will be exploring the new PO release as working on term matching to some developmental stages for a Maize Gene Atlas.
The sequencing group is turning in a final set of models soon, that MaizeGDB will be guardians of, starting Jan 2011. We anticipate loading into MaizeGDB, both Nimblegen and RNA_Seq expression data from the same group for a Maize Gene Atlas.
I anticipate being able to provide associations for gene models expressed highly. There are 61 tissues, at various plant growth stages, so this will be a substantial number of associations.
PJ: Would you be mapping the RNAseq data and the Array data to gene/gene models?
MS: Initially they will be mapped to coordinates, and by inference then, to gene models. We are in close contact with CSH on the release of the new models.
About adequacy of the PO, my sense is that all seems cool. The current listing is a bit drafty in parts, and I am conferring as I work through the list with the authors. Perhaps of better utility to you, would be how each 'tissue' is annotated to the PO terms? Maybe I could present this in the workshop Laurel is organizing re use of PO?
In any case, I will have the 'mappings' soon.
- Solanaceae Genome network (SGN); Lukas Mueller + Naama Menda; see Solanaceae Workshop
- Gramene Gramene See: Gramene workshop at PAG
- TAIR email: curator@arabidopsis.org
- Plex DB who?
- Blake Meyer (meyers@dbi.udel.edu) see International Arabidopsis Informatics Consortium (IAIC) Workshop
- Physco group: Rensing and Lang see Non-seed plant workshop
- Genome Database for Roseae (GDR), Univ of Washington see Fruit and Nut workshop
- Brian Smith White- NCBI NCBI Workshop
- Helen Parkinson- Array Express EBI
- Genevestigator: contact ? (support@genevestigator.com) Ontologies
- VirtualPlant who, use their "contact us" form? Virtual plant
Michael Barker see
Others:?
- Nottingham Arabidopsis NASC Ontology page
- SoyBase- Rex Nelson?
- OryzaBase: to: Yukiko Yamazaki
- PlantTribes: to: PI: Claude dePamphilis (Penn State) cwd3@psu.edu
- TraitNet: Coordinators Farshid Ahrestani (fa2260@columbia.edu) and Dan Bunker (dbunker@njit.edu)
- CIMMYT, Mexico Generation Challenge Program: Rosemary Shretha
- BRENDA to:project leader Prof. Dr. Dietmar Schomburg
- UniProt "contact us" page
- BAR: Nicholas Provert and Rohan Patel
- Trish Whetzel and BioPortal-
