Talk:Data Jamboree 2
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
September 29, 2008 (Monday) - Data Curation Session at Sylvan Lake Lodge Meeting Room
Wasila's notes Comparative phenotypes 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)
John's idea for recording size comparison within a study
- graded series of lengths, widths, etc.. give 1, 2, 3 ...
- least/smallest value is given 1
Eric example of incomplete/complete scute series:
- E: scute series; Q: in contact RE: skull
- E: scute series; Q: in contact RE: dorsal fin
- E: scute series; Q: separated from RE: skull
- E: scute series; Q: separated from RE: dorsal fin
Judy: important to separate tasks of anatomy ontology development and annotation
- suggested having ontology dev. workshops and curation workshops
- idea:- enter terms ahead of time and have experts fix it
Mark submitted TAO request on Weberian vertebra - relationships that don't hold for all taxa
Wasila: batching vs. one term request: ok to submit related terms in one request
Suzi: suggested having a small PATO workshop with ichthyologists, like anatomy workshop
September 30, 2008 (Tuesday) - Project Personnel Meeting
Wasila's notes: Advisor's feedback
- Suzi: curators need to be aware that if they don't find the most appropriate term, they should not settle for the closest term but request what they need
- Judy: curators should be aware of 2 jobs: annotation and ontology improvement
- Suzi: add Wasila as ontology writer to Pato
October 1, 2008 (Wed morning) Wrap-up discussion with curators
Wasila's notes Paula: suggestions for improving curation process?
- Terry: would like to go through a paper first to deal with needed terms
- John: some things, like joints, can be added in bulk
- All: visualization issues - how to know what is there, and their relationships
- Need large poster of all terms
- Paula: PDF mark-up tool that highlights terms matching to TAO; characters not highlighted would likely require new term
- Todd and Paula: use Phenex to highlight ontology terms because character and state descriptions from pub are pre-entered as free text
- Mark: how does a curator decide to precompose vs. postcompose
- Wasila: if entity will be used repeatedly (in single or multiple pubs) then add to TAO; if not, post-compose
- Mark: when post-composing, would be helpful if Phenex would autocomplete to pre-composed cross-product term (if present in TAO) so that curator can be aware of similar term in ontology
- Suzi: tough anatomy stuff: you can discuss as a group of curators then submit and enter in ontology
- Paula: need to set up svn for Phenex files - WD will send instructions to new curators
- Rick: can we break down single character into multiple characters
- Paula: these are multiple annotations - don't break down character
- Pubs with same characters
- Paula: curate it all separately
- Jim: duplicates will come together in database
Paula: non-curation of present entities
- curate for basal taxa or annotate presence for a higher level group with weak evidence code
- propogate by evolutionary inference
- Jim: phenotypes are exhibits; congregate exhibits to higher level seems to be ok to do (e.g., cypriniformes exhibit red and blue dorsal fin)
- inheritance vs. propagation
- might need more than one reationship between taxon and a phenotype; right now we have exhibits as the relationship
- Paula: This relates to character mapping
