Make Pathway Diagram Collections Accessible via the Systems Biology Graphical Notation

[cannin]

Background

Systems Biology Graphical Notation (SBGN; http://sbgn.org/) provides standard graphical languages for representing cellular processes, interactions, and biological networks. SBGN diagrams are encoded in the SBGNML format (https://pubmed.ncbi.nlm.nih.gov/32568733/). SBGN diagrams are available from a number of sources including Reactome (https://reactome.org/download-data).

Existing Work

• A small R package (sbgnvizShiny) was created to work with SBGNML files in R including coloring them.
• A Python package to render SBGNML to images

Getting Started

• Try out the Python render code; does it work or not?
• Try out the R sbgnvizShiny package; what works or not?
• Make sure you can run Python from R
• Try out services to map node labels to gene symbols: https://extract.jensenlab.org/ how can it be used to address the project goals (other solutions welcomed)?

Goal

The goal is to improve and expand the capabilities of the expand sbgnvizShiny package. The package has issues with rendering some SBGN components that the base https://github.com/iVis-at-Bilkent/sbgnviz.js has no issue with, for example, SBGN units of information The goal of the project is to fix the issues and expand the capabilities of the R package allowing users more facility to interact with the Javascript rendered diagrams.

This project would also address the following goals:

• Currently, sbgnvizShiny has no easy way of downloading SBGN diagrams as raster images (e.g., PNG) from R
• There is no available repository of SBGNML files accessible within sbgnvizShiny
• Diagram labels are not always approved gene symbols (https://www.genenames.org/); an attempt to map these would be made to map these to approved symbols to simplify mapping datasets to SBGNML files

Difficulty Level: Medium

Size and Length of Project

Size: 175 hours Length: 12 weeks

Skills

• Essential skills: R, Javascript, XML
• Nice to have skills: Python

Public Repository

• https://github.com/cannin/sbgnvizShiny
• https://github.com/iVis-at-Bilkent/sbgnviz.js/
• https://github.com/vincent-noel/SBGNRenderAPI

Potential Mentors

Augustin Luna Ugur Dogrusoz

[spursbyte]

Hello @cannin can i work on this?@ugurdogrusoz do you need any help?

[cannin]

@spursbyte Feel free to submit a GSOC proposal if interested.

[spursbyte]

ok sure

[khanspers]

Cleanup in preparation for GSoC 2022.

[khanspers]

NRNB has officially been accepted as a mentoring organization for GSoC 2022! Here are some useful links:

• Project proposal template
• GSoC contributor guide
• Program timeline

[khanspers]

A reminder that the application period opens on Monday April 4. Proposals to NRNB must be submitted on the official GSoC Site (https://summerofcode.withgoogle.com/) before April 19, 18:00 UTC to be considered, and contributors are encouraged to submit proposals in draft format early, so that mentors can give feedback directly at the GSoC site.

[khanspers]

Closing in preparation for GSoC 2023.