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ePlant3 eFP World View Blueprint and Requirements

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Vincent Lau edited this page Dec 12, 2024 · 1 revision

ePlant3 eFP World View Blueprint and Requirements

by V. Lau (reviewed by N. Provart)

Introduction

The eFP World View is an eFP (electronic Fluorescent Pictograph) view which features Arabidopsis an aerial view of greenhouse-grown Arabidopsis seedlings collected across the world, data provided by Lempe, J., Balasubramanian, S., Sureshkumar, S., Singh, A., Schmid, M., & Weigel, D. (2005). Aerial climate data can then simultaneously be overlaid to see if genetic variation correlates with climatic variation. Historical climate data is provided by Jones, P., and Harris, I. (2013). See below for a screenshot for the current eFP World View from ePlant2.

image

Current ePlant2 world eFP View, with precipitation overlay enabled. Notice the coloured Arabidopsis seedling icons

Purpose

Users will wish to see at a glance, for their gene of interest (GOI), how different Arabidopsis ecotypes express that GOI across the world. Additionally, if GOI expression varies with climatic and geographical variation.

Intended Audience

  • ePlant Users
    • Plant biologists
    • Bioinformaticians
    • Students

Product Scope and Value

The addition of this module to ePlant will allow users to see how gene expression varies across different geographical regions and climates. By overlaying multiple climate data, researchers can identify trends (if any) across climates.

Abbreviations

  • eFP: electronic Fluorescent Pictograph
  • GOI: Gene of Interest
  • GIS: Geographical Informational Systems

System and Functional Requirements

  • The module must load by default load a world atlas (e.g. Google Maps) panned out such that the entire world is visible
    • It will have Arabidopsis seedling icons which represent each collection point (note each collection can have 1 or more samples)
      • These icons will be coloured accordingly to the expression levels (see prior eFP views)
      • Each icon will be geographically positioned to their collection point
      • Each icon will have a tooltip upon hover which will reveal the following information: Sample Name, Latitude, Longtitude, Elevation, Mean Expression, Standard Error, Sample Size, see below:
      image
    • The module should have the standard eFP options: Relative/Absolute, Masking, Heat Scale/Expression Max Graph
  • Users can interact with a call-to-action (likely a dropdown) to select which climate overlay they wish to use (if any)
    • When enabled, a scale corresponding to that overlay shall be displayed (i.e. a temperature heat scale when a temperature overlay is selected).
  • Users can export their data in Geographical Informational Systems (GIS)-friendly (GeoJSON) and digestible formats (JSON, CSV)

External Interface Requirements

  • User Interface: The world view view should take up as much resolution of the available panel as possible. Call-to-actions can be overlaid on top on the map (similar to ePlant2)
  • Hardware Interface: Optimize this for desktop and large format tablet visualization (resolution >960px); mobile visualization on graphs is unrealistic.
  • Software Interface: Use your existing ePlant3 module logic to create this view. You will need to use our existing webservices such as this one to grab the expression data. You should use Google Maps as the atlas library. You will also need to use our climate overlay tile server (example)
  • Communication Interfaces: Standard communication on Github Issues, and weekly discussions. Please link to this issue for any features, bugs pertaining to the World eFP View and label it with the 'World eFP View' label on Github.
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