Difference between revisions of "Talk:Data Jamboree 2"
From phenoscape
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# Todd Vision suggested using auto composition of search terms | # Todd Vision suggested using auto composition of search terms | ||
# Monte Westerfield suggested using Boolean combinations of query parameters. Seconded by Judith Blake | # Monte Westerfield suggested using Boolean combinations of query parameters. Seconded by Judith Blake | ||
| + | |||
| + | == Hilmar's notes == | ||
| + | |||
| + | * option for hierarchical indexing of results (taxonomy, phylogeny, but also anatomy ontology) | ||
| + | * mapping characters on a tree: multiple phenotypes may match any particular query | ||
| + | ** map to different colors for indicators? use numbers as indexes? | ||
| + | ** mapping phenotypes onto trees cannot typically reconstruct character state changes, and hence traditional visualizations may be misleading? | ||
| + | * ability to prune species with no data (values) for export | ||
| + | * search interface: ability to combine taxon/entity/quality specifications (and, or, not) | ||
| + | * graph navigation: Dbgraphnav, Cytoscape | ||
| + | * clickable fish image for starting navigation | ||
| + | * most common entry point is likely to be a simple one-field form for entering terms | ||
| + | * phenotype query prototype: how do I get from here to the genes? | ||
| + | * ability to see correlations between phenotypes | ||
| + | |||
| + | MGI batch query demo | ||
| + | * users don't use complex query forms | ||
| + | * auto-detect type of input tokens | ||
| + | * allow download in different formats | ||
| + | * computationally savvy users | ||
| + | * pre-written SQL as available from GO website | ||
Revision as of 23:55, 28 September 2008
September 28, 2008 - Discussion on Query Prototype (Proto Alpha Version) of Phenoscape (Presented by Jim Balhoff)
- Visualization
- Jim Balhoff suggested enabling drill down from higher taxa to lower ones. Typically, query for annotations will yield more results at higher levels in the taxonomy. Drilling down into the lower levels will serve to prune the results and narrow down to users' exact requirements. Monte Westerfield, and Paula Mabee seconded.
- Mark Sabaj suggested using a fish landscape with different predefined areas for visualization of results and guiding the search. Paula Mabee and John Lundberg approved.
- Todd Vision suggests displaying only those nodes of a taxonomy that have been annotated
- Judith Blake suggested using Cytoscape to browse through various nodes in the tree
- Monte Westerfield suggested linking phenotypes to genes
- Todd Vision suggested character correlations
- Querying
- Todd Vision suggested using auto composition of search terms
- Monte Westerfield suggested using Boolean combinations of query parameters. Seconded by Judith Blake
Hilmar's notes
- option for hierarchical indexing of results (taxonomy, phylogeny, but also anatomy ontology)
- mapping characters on a tree: multiple phenotypes may match any particular query
- map to different colors for indicators? use numbers as indexes?
- mapping phenotypes onto trees cannot typically reconstruct character state changes, and hence traditional visualizations may be misleading?
- ability to prune species with no data (values) for export
- search interface: ability to combine taxon/entity/quality specifications (and, or, not)
- graph navigation: Dbgraphnav, Cytoscape
- clickable fish image for starting navigation
- most common entry point is likely to be a simple one-field form for entering terms
- phenotype query prototype: how do I get from here to the genes?
- ability to see correlations between phenotypes
MGI batch query demo
- users don't use complex query forms
- auto-detect type of input tokens
- allow download in different formats
- computationally savvy users
- pre-written SQL as available from GO website
