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| − | '''September 28, 2008 - Discussion on Query Prototype (Proto Alpha Version) of Phenoscape (Presented by Jim Balhoff)'''
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| − | * Visualization
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| − | # 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.
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| − | # 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.
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| − | # Todd Vision suggests displaying only those nodes of a taxonomy that have been annotated
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| − | # Judith Blake suggested using Cytoscape to browse through various nodes in the tree
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| − | # Monte Westerfield suggested linking phenotypes to genes
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| − | # Todd Vision suggested character correlations
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| − | * Querying
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| − | # Todd Vision suggested using auto composition of search terms
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| − | # Monte Westerfield suggested using Boolean combinations of query parameters. Seconded by Judith Blake
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| − | '''Hilmar's notes'''
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| − | * option for hierarchical indexing of results (taxonomy, phylogeny, but also anatomy ontology)
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| − | * mapping characters on a tree: multiple phenotypes may match any particular query
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| − | ** map to different colors for indicators? use numbers as indexes?
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| − | ** mapping phenotypes onto trees cannot typically reconstruct character state changes, and hence traditional visualizations may be misleading?
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| − | * ability to prune species with no data (values) for export
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| − | * search interface: ability to combine taxon/entity/quality specifications (and, or, not)
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| − | * graph navigation: Dbgraphnav, Cytoscape
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| − | * clickable fish image for starting navigation
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| − | * most common entry point is likely to be a simple one-field form for entering terms
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| − | * phenotype query prototype: how do I get from here to the genes?
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| − | * ability to see correlations between phenotypes
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| − | MGI batch query demo
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| − | * users don't use complex query forms
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| − | * auto-detect type of input tokens
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| − | * allow download in different formats
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| − | * computationally savvy users
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| − | * pre-written SQL as available from GO website
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| − | '''September 29, 2008 - Wasila's notes on Data Curation Session at Sylvan Lake Lodge Meeting Room'''
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| − | Comparative phenotypes
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| − | size comparison between taxa within a pub (e.g., broad vs. narrow bone) cannot be extended beyond the taxa within the study (e.g., Rick's size example: large, small, extremely small)
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| − | John's idea for recording size comparison within a study
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| − | *graded series of lengths, widths, etc.. give 1, 2, 3 ...
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| − | *least/smallest value is given 1
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| − | Eric example of incomplete/complete scute series:
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| − | *E: scute series; Q: in contact RE: skull
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| − | *E: scute series; Q: in contact RE: dorsal fin
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| − | *E: scute series; Q: separated from RE: skull
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| − | *E: scute series; Q: separated from RE: dorsal fin
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| − | Judy: important to separate tasks of anatomy ontology development and annotation
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| − | *suggested having ontology dev. workshops and curation workshops
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| − | *idea:- enter terms ahead of time and have experts fix it
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| − | Mark submitted TAO request on Weberian vertebra - relationships that don't hold for all taxa
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| − | Wasila: batching vs. one term request: ok to submit related terms in one request
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| − | Suzi: suggested having a small PATO workshop with ichthyologists, like anatomy workshop
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