Gene Page

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Meeting minutes, Gene Page review:

  • Overview
-- Keep WormBase ID
-- From ce 1 and 2 -- move to history? references?
-- Provisional description -- legacy 
-- Floating Box, how to link to protein info?
-- Action Items: ce 1 and 2 -> Make sure citations are expanded. History for now. 
   Kimberly and Ranjana 2 look into proper placement of provisional description. 
   Make Sequence Widget appear on clicking sequence link in floating box.
  • Location
-- explicitly note a genomic position
-- call genomic view?  
-- Action Item: Name with something more descriptive

  • History
-- actually curation history; unclear what it is.
-- rename as database history? check presentation options on sidebar listing
-- call Database history? -- Try first
-- selective viewing; details to curators only?
  • Expression
-- Tissues with color has expression (color standard representation in WormAtlas).
-- Descriptive statements needed - TH
-- List anatomy terms associated with the expression; 
-- Action Items:  Chris to provide legend for color/tissue correspondence. Work on "conservative" and "liberal" info representation
   Move chronogram further down.
   Provide tooltip for expression cluster link; Wen to provide description.
   Microarray results -> Microarray Spot ID(?)
   Move topology Map right below Expression cluster
   via Anatomy_function -> Experiments in table column headers
   General cleanup
  • Gene Ontology
-- Simplify info representation; focus on term less the method
-- Make into sortable table?
-- Action Items: Look into GO details page for ideas for rendering table; See SGDs 
  • Genetics
-- Pretty straight forward
-- Action Items:  Move strains to the top.
  • Homology
-- Need feedback from Hinxton (left).
-- Protein domains - used to be part of function; should it be there?
-- Action Item:  Move Protein Domains to the bottom.

  • Interaction
-- Action Items: Put data in table
   Evaluate other tools for graphic viewing (long term)
  • Phenotype
-- Action Item: Collapse not observed: especially RNAi; 
   emphasize NOT in label; 
   use term "perturbations" rather than "mutation" for RNAi
   move to WB2 data tables; move Phenotype column in RNAi to first
  • Reagents
-- Sage & Matching cDNAs: toggle list?
-- Action Item: clean up empty fields
   Relabel Microarray probes -> Microarray oligo sets
   Remove "Found" in data lines (through out site).
   Move cDNA and Antibody up.
   Group primer pairs and oligos
  • References
-- Working to separate via categories
-- Export citations? -- Not yet
  • Sequences
-- Need comments from Hinxton
-- Action Items:  Rearrange table to reflect Central Dogma
   Caltech to make other sequences descriptions