Meetings/20080115/FlyData-review
From ImageWeb
Contents |
Review meeting
When: 15 Jan 2008, 15:00 Where: Helen's office
Present:
- Helen White-Cooper
- David Shotton
- Jun Zhao
- Graham Klyne
Note - internal telephone numbers:
- 71195 (Helen)
- 71193 (David)
- 81993 (Jun)
- 81991 (Graham)
Project page:
Demonstrate initial FlyData server
We showed Helen the functionality achieved so far (see https://milos2.zoo.ox.ac.uk/trac/FlyData/milestone/Phase%201%3A%20Affy%20data%20display).
Surprisingly, Helen seemed very happy with what was offered, and did not offer any specific requests for changing the functionality as provided. A fair amount of time was spent exploring some unexpected results from the Affymetrics array mapping tables used (but we didn't decide what to do about this).
We did discuss a number of additional facilities and/or investigations:
- Rank ordering, e.g.:
- Rank display by intensity of WT signal
- Store rank index as computed value for each gene in each dataset (Helen's preference)
- Click on gene or probe name to run new search
- Current genome annotation release is 5.4 - we should check what version is the reference for the array mapping tables used.
- Order of results - preferably the same as the input list.
- Access to descriptions from either of the Affymetrix array data files, or (preferably) from the original local data file.
- Seach term to be non-case-sensitive
- Search on partial gene name, or wildcard pattern
- Wider space between results from local data and flyatlas
- Description - trim to use less display space, and provide link to expand this
- Delete (wt ?) from column heading
- Link to or provide means to get access to local data standard error values
- Links to local PCR quantitation results
- On local data display, link to display PCR graphs, or CD ("Cycle Detected") values, or delta CD (difference CD between strains) - each cycle corresponds to approx 2x change in PCR product level. CD means the number of the PCR cycle in which the gene product was first detected.
- Provide means to show results for all FlyAtlas tissue types and all Helen's strains
- Bar chart display for array data results (w/ standard error bars?)
- Annotations
- Attach to/key by gene (not probe?)
- Facility to retrieve by text search on gene annotation
- Facility for standardizing common annotations, as in controlled vocabulary, etc., to provide some consistency of results when searching.
Priorities for next phase of development
- Display all FlyAtlas data - all tissue types (and more?)
- Display descriptions of Affymetrix probes from local data file
Likely priorities for future phases
- User annotation, with provenance data. Helen to provide a list of standard annotation phrases.
- Link to PCR data
Other thoughts raised
- Searching within search results
- Save search results list for later reference
- Similarity search; e.g. similar in-situ pattern?
- In discussion, the requirement was more along the lines that that researchers could record lists of genes exhibiting some pattern, described by key textual phrases, and record that for subsequent side-by-side display of corresponding raw results.
Future collaboration
Helen is moving to Cardiff in/after March, but is keen to continue collaborating on this and other related projects.
Publications
David asked Helen for a list of related publications and source text, for submission to ORA, so that we could demonstrate linkage between published papers in institutional repositories and supporting published datasets.
