Mentors: Tom Gillespie <tgbugs@gmail.com> and Jeff Grethe <jeffrey.grethe@gmail.com>
Skill level: Novice, Intermediate or greater
Required skills: JavaScript/React
Time commitment: Flexible (175 hours)
Forum for discussion
About: Knowledge systems that support research in life science routinely need to represent data about a wide variety of different kinds of biological entities, from species, to cells, to genes, proteins, ion channels, and biological processes. Each of these types of entities has distinct relations that define them and distinct data that are collected to study them. Being able to visualize each type of entity is critical for helping experts and novices alike work with complex knowledge about biology.
Aims: In this project, you will work to develop a variety of visualizations for knowledge about specific biological entities. For example, visualization of cell types could include a simplified representation of their morphology, a map of their anatomical location(s), graphical representation of the genes they express etc. As part of this project you will learn about how to collect requirements and develop use cases for visualizing complex domains and how to obtain, convert, and present structured data in a way that is accessible (e.g., via small visualization apps and/or dashboards) to domain expert users who may be intimately familiar with the biology but may not be familiar with the inner workings of informatics systems. This work will be conducted in the context of InterLex, a terminology management system for life sciences. InterLex makes it possible to easily create and edit new technical terminology. As part of that it is critical for users to be able to determine whether a term already exists (e.g. for a known biological entity) and being able to visualize the complexity in an accessible way is often critical for helping them identify that the term they want already exists.
Websites:
Tech keywords: JavaScript, React, visualization, ontology, knowledge graph
Hi, I’m Abhinav Gupta, a B.Tech Computer Science student at MNIT Jaipur. I have experience with React, Next.js, Three.js, Node.js, and full-stack development and tools like Git, Docker. I’ve worked on projects like a passive bot detection system using AI/ML in Hackathons and build my college fest website that was visited by thousands of users. I’m passionate about creating interactive visualizations and would love to contribute to the Custom Visualizations/Dashboards for Semantically Described Biological Entities project. I’ve been exploring the project details but I had few questions that I’d like to clarify:
1)What type of visualizations do we want like 3d models or any other svg structures
2)Can you help me out finding the starting point of project from where to start like if there are any GitHub repositories I can contribute or any feature that I should work on to show my work
3)If we want to visually represent the biological entities, then from where I can get the structure or models of those entities
I can start contribution if you can tell about github repos through which i can contribute or any specific issues regarding this project that i should focus on.
Hi everyone,
I hope you’re doing well! I previously introduced myself via email regarding my interest in contributing to the “Custom Visualizations/Dashboards for Semantically Described Biological Entities” project for GSoC 2025. Now that the forum is set up for discussions, I wanted to follow up and better understand how I can start contributing effectively.
I’m excited about working on biological data visualization. I’ve reviewed the InterLex system and GitHub repository and would love some guidance on the best way to get started.
A few questions I have:
- What are the current priorities or challenges in the visualization aspect of InterLex?
- Is there a preferred data visualization library (D3.js, Recharts, Vis.js) for this project?
- Are there any recommended resources to better understand biological data structures in InterLex?
- How can I start contributing before the official application period begins?
Looking forward to hearing your insights! Thanks in advance for your guidance.
Best,
Suhaib Ilahi
Hi @aabhinavvvvv,
I think for your question #3 @arnab1896 has already provided the link
- InterLex is a terminology management system for life sciences and provides the content for the visualization(s): https://interlex.org .
Pardon me if I am wrong
yes I have seen that but I am not able to understand what we have to do exactly like when we search for any term it has a id with it and it opens up a page that has some information related to it…my doubt is how they are connected and what api calls are going to get that data as if I have to visualize the data then i will be needing that data first and in the github repo also there arent any specific issues it just has some bunch of branches
Hello @aabhinavvvvv,
I hope you’re all doing well.
From what I understand, our goal is to create a visual representation of biological entities to help users determine whether a term already exists. This visualization would also assist in understanding the complexity of the term through aspects like morphology, anatomical location, and other relevant details.
Could the mentors please confirm if this is the correct approach, or provide any guidance on how to refine this further?
Looking forward to your insights!
Thank you.
hey @aabhinavvvvv ,
I hope this message finds you well.
I am writing to provide you with information on how to access biological entities from InterLex, our comprehensive terminology management system for life sciences.
To access the desired terminology, please follow these steps:
- Visit the InterLex API Handbook: You can find detailed documentation and available endpoints at InterLex API Handbook
.
- Authentication: Depending on the data you wish to access, you may need to authenticate using an API key or token. Please refer to the documentation for instructions on obtaining the necessary credentials.
- Retrieve Terminology: Use the API to query and retrieve the specific biological entities you need. You can search for terms, categories, or related concepts.
- Data Conversion: If required, convert the retrieved data into a suitable format for your use. This might involve transforming JSON data into tables, graphs, or other visual elements.
correct me if I am wrong
Thank you
Thank you for the relevant information @Ruchit44