Difference between revisions of "WormBase-Caltech Weekly Calls"
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**Anatomy ontology | **Anatomy ontology | ||
***Anatomy page is hub for data | ***Anatomy page is hub for data | ||
| + | ****We should strive for user friendly display of information | ||
| + | ****Cell functions, 10 or 100 highest/preferentially expressed genes, cell connections, cell signals | ||
***Upcoming challenge - male/female/hermaphrodite divergence | ***Upcoming challenge - male/female/hermaphrodite divergence | ||
| − | ***Anatomy with respect to life stage | + | ***Anatomy with respect to life stage (e.g. life-stage-specific cells) |
***Multiple species | ***Multiple species | ||
| − | ***[http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page Uberon] framework can be adapted for multiple species | + | ***[http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page Uberon] framework can be adapted for multiple (nematode) species |
| + | **Gene Function | ||
| + | ***RNAi, Allele-phenotype, etc. | ||
| + | **Interactions | ||
| + | ***Integrated interaction model, genetic interaction ontology | ||
| + | ***Can we estimate how many interactions are left to curate? Can use OA/Postgres, SVM, and first-pass author forms etc. to estimate | ||
| + | **Gene expression and Pictures | ||
| + | ***Need to update Gene expression model to accommodate Epic dataset (John Murray), 3D movies, and single-molecule FISH | ||
| + | ***Itai Yania dataset (embryo expression across several nematode species) | ||
Revision as of 16:48, 2 August 2012
2012 Meetings
August 2, 2012
Grant updates
- Topics
- Diseases
- Worm Phenotype ontology; attempt applying to other species? Some has been done already (e.g. C. briggsae)
- Benefit of curating phenotypes in other species? Particularly useful for genes not in C. elegans, for example
- Textpresso for nematodes
- >5000 papers now
- Complete set of papers by ~Labor Day
- Anatomy ontology
- Anatomy page is hub for data
- We should strive for user friendly display of information
- Cell functions, 10 or 100 highest/preferentially expressed genes, cell connections, cell signals
- Upcoming challenge - male/female/hermaphrodite divergence
- Anatomy with respect to life stage (e.g. life-stage-specific cells)
- Multiple species
- Uberon framework can be adapted for multiple (nematode) species
- Anatomy page is hub for data
- Gene Function
- RNAi, Allele-phenotype, etc.
- Interactions
- Integrated interaction model, genetic interaction ontology
- Can we estimate how many interactions are left to curate? Can use OA/Postgres, SVM, and first-pass author forms etc. to estimate
- Gene expression and Pictures
- Need to update Gene expression model to accommodate Epic dataset (John Murray), 3D movies, and single-molecule FISH
- Itai Yania dataset (embryo expression across several nematode species)
- Suggestions for future
- Better integration across data types
- How the OA can evolve and what it can be used for?
