Difference between revisions of "WormBase-Caltech Weekly Calls"
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***[http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page Uberon] framework can be adapted for multiple (nematode) species | ***[http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page Uberon] framework can be adapted for multiple (nematode) species | ||
**Gene Function | **Gene Function | ||
| − | ***RNAi, Allele-phenotype, etc. | + | ***RNAi, Allele-phenotype, Transgene-phenotype etc. |
**Interactions | **Interactions | ||
***Integrated interaction model, genetic interaction ontology | ***Integrated interaction model, genetic interaction ontology | ||
| Line 56: | Line 56: | ||
***Should let users download search results more easily (for single genes, for example) | ***Should let users download search results more easily (for single genes, for example) | ||
***Need to change SPELL database to incorporate new species | ***Need to change SPELL database to incorporate new species | ||
| − | + | ***Users should be able to run clustering on data | |
| − | + | ***Co-expression correlation; should recalculate each build (with flexible significance thresholds) | |
| − | + | ***Provide Cytoscape view of genes connected by co-expression | |
| + | **Pathways and Processes | ||
| + | ***Plan to work with Wikipathways | ||
| + | ***Vocabularies and annotation schemes like Systems Biology Graphical Notation (SBGN) | ||
| + | ***Trying to get data into BioPAX (Biological PAthway eXchange) format | ||
| + | ***BioPAX too detail oriented? Very biochemical? | ||
| + | ***Some databases dump BioPAX format, but won't read it in | ||
| + | **Paper and curation pipeline | ||
| + | **Concise description progress; coverage | ||
| + | ***Re-annotation efforts? | ||
| + | ***New concise description curation interface for easier writing and updating | ||
| + | **Annotating genes in the more expressive GO format | ||
| + | ***How would our data models need to change to curate with the new expressive GO | ||
| + | **SVMs | ||
*Suggestions for future | *Suggestions for future | ||
**Better integration across data types | **Better integration across data types | ||
**How the OA can evolve and what it can be used for? | **How the OA can evolve and what it can be used for? | ||
Revision as of 17:16, 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, Transgene-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 (Bill Mohler), and single-molecule FISH (van Oudenarden et al)
- Itai Yania dataset (embryo expression across several nematode species)
- Expression SVM won't catch isolated tissue/cells expression analysis or microarray data
- Incorporating the virtual worm and browser
- Microarray and SPELL
- Will incorporate microarray and RNA-Seq data sets for other species
- Should let users download search results more easily (for single genes, for example)
- Need to change SPELL database to incorporate new species
- Users should be able to run clustering on data
- Co-expression correlation; should recalculate each build (with flexible significance thresholds)
- Provide Cytoscape view of genes connected by co-expression
- Pathways and Processes
- Plan to work with Wikipathways
- Vocabularies and annotation schemes like Systems Biology Graphical Notation (SBGN)
- Trying to get data into BioPAX (Biological PAthway eXchange) format
- BioPAX too detail oriented? Very biochemical?
- Some databases dump BioPAX format, but won't read it in
- Paper and curation pipeline
- Concise description progress; coverage
- Re-annotation efforts?
- New concise description curation interface for easier writing and updating
- Annotating genes in the more expressive GO format
- How would our data models need to change to curate with the new expressive GO
- SVMs
- Suggestions for future
- Better integration across data types
- How the OA can evolve and what it can be used for?
