Difference between revisions of "WormBase-Caltech Weekly Calls"
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| − | + | AMIGO2 (Wormbase Ontology Browser) | |
*Raymond and Juancarlos have taken AMIGO2 infrastructure to make an ontology browser for integration into WormBase | *Raymond and Juancarlos have taken AMIGO2 infrastructure to make an ontology browser for integration into WormBase | ||
| − | * | + | *Graph view shows path to root (DAG view) |
| + | *Inferred tree view shows: | ||
| + | **Ancestor terms, no annotation numbers | ||
| + | **Main term and children, with annotation numbers (inferred, term and descendant annotations) | ||
| + | **Annotation numbers link to list of genes | ||
| + | **Will not show "direct" annotations, only inferred | ||
| + | *Sibling term displays | ||
| + | *Separate expandable/collapsible tree of ontology | ||
| Line 50: | Line 57: | ||
**We chose papers from the Author First Pass list with 'stress' | **We chose papers from the Author First Pass list with 'stress' | ||
** | ** | ||
| − | * | + | *Todd suggests for paper pages on WormBase: |
| − | ** | + | **Show a table of flagged data types for a paper? |
| + | **Give users a sense of where paper is in the curation pipeline | ||
Revision as of 17:30, 1 August 2013
2013 Meetings
August 1, 2013
Quarterly Progress Reports
- Capturing curation stats from the Curation Status form
- What data types do we want to capture that we are not currently?
- We have frequent database dumps that can be read for stats
- We can capture the stats table statically on a regular basis (daily?)
RNA-Seq and Tiling Array data
- Data in SPELL
- Wen found a lot more non modENCODE data sets
- May use SVM for expression cluster data
- Gene IDs can be found from original paper or data set
- Up-to-date mapping to genes is not currently done
AMIGO2 (Wormbase Ontology Browser)
- Raymond and Juancarlos have taken AMIGO2 infrastructure to make an ontology browser for integration into WormBase
- Graph view shows path to root (DAG view)
- Inferred tree view shows:
- Ancestor terms, no annotation numbers
- Main term and children, with annotation numbers (inferred, term and descendant annotations)
- Annotation numbers link to list of genes
- Will not show "direct" annotations, only inferred
- Sibling term displays
- Separate expandable/collapsible tree of ontology
Paper Categorization
- Word frequency
- We chose papers from the Author First Pass list with 'stress'
- Todd suggests for paper pages on WormBase:
- Show a table of flagged data types for a paper?
- Give users a sense of where paper is in the curation pipeline
