Generic protein expression view for Human Body

Rationale

neXtProt is a fast growing resource integrating human protein data from different databases. As far as expression is concerned, neXtProt integrates data from Bgee (at mRNA level) and the Human Protein Atlas (at protein level). This data must be visualized in a coherent and scientific manner for biologists.

Approach

  • Understand the data contained in neXtProt related to human body expression.
  • Understand human body different part and tissues (nervous, cardiovascular, ... systems; Fig. 1).
  • Elaborate state-of-the-art document with current viewers and their limitations.
  • Propose and implement a viewer that satisfy the need of biologists using neXtProt data.

Fig 1. Wikimedia's static image of Human Body with tissues

Challenges

  • The amount and granularity of the data to be represented in a coherent and user-friendly manner.
  • The technology involved and generic aspect of the viewer.

Involved toolkits or projects

  • JSON REST API
  • D3
  • NodeJS
  • AngularJS,

Needed skills

Interest for biology and new technologies, essentially JavaScript.

Mentors

Daniel Teixeira and Pierre-André Michel (both at CALIPHO SIB in Geneva)