ePlant3 Chromosome View Blueprint and Requirements

[VinLau]

Chromosome View

Unlike our other views which require a GOI to be selected. A few modules like the chromosome view can be accessed directly without a gene selected. The chromosome viewer should correctly:

• Show the chromosomes and their relative sizes for their respective species (i.e. Humans have 23, Arabidopsis have 5), so dynamically space the SVG/CANVAS area to the page
• When the user selects a chromosomal locus (area), the genes located in around that locus should populate a tooltip
  • The tooltip should show the chromosome loci numbers
  • The tooltip will have hyperlinks to load those genes into ePlant sidebar directly into ePlant from a modal
• From the user selected GOIs, these GOIs should be denoted properly in this view
• From speaking with Nick (Product Owner), we will NOT need to re-implemenet the gene density function (red/yellow colouring seen below)

*Chromosome module displaying genes selected, with a tooltip to add more genes. Notice how the tooltip has a list of genes in that region and the chromosomal locations from start and end in that region. Note that gene density is turned on* *Modal that shows once a user clicks on a gene from the above tooltip. The user can then load a gene from the green button. She can also close this modal*

Technical notes: Note that the chromosomes are drawn dynamically. The webservice for chromosome size is (https://bar.utoronto.ca/eplant/cgi-bin/chromosomeinfo.cgi?species=Arabidopsis_thaliana). When a locus is selected, a query is made to this [webservice] (https://bar.utoronto.ca/eplant/cgi-bin/querygenesbyposition.cgi?chromosome=Chr3&start=15105497.767957352&end=15171733.452802815), therefore the chromosome event listener should retain locus information.

Popular endpoint: https://bar.utoronto.ca/eplant_poplar/cgi-bin/chromosomeinfo.cgi?species=Populus_trichocarpa

NB: We are refactoring the above endpoints, the structure may slightly change.

Creative Notes: Could we add additional filters to this module such as a functional annotation?