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
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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
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@SUHAIB_ILAHI yes let’s wait for mentors to confirm
thank you @Ruchit44 for the link its helpful
1 Like
I’m Yash Saraswat, a Computer Science student and an aspiring developer with experience in JavaScript and React. I’ve worked on building dynamic web applications using React, Tailwind CSS, and various backend technologies like Node.js and Express.js. I also actively contribute to open-source projects and have a strong interest in data visualization.
I find this project particularly fascinating because it combines visualization with structured biological knowledge, making complex data more accessible to researchers. Understanding how InterLex integrates terminology management with knowledge graphs sounds like a great learning opportunity.
To better understand the scope, I wanted to ask
How do you envision the ideal visualization for biological entities…Should it be more interactive, similar to knowledge graphs. How can I start contributing to the project. Is there any pre requisites or documentation to know it better.
Looking forward to your insights!
Yes @Ruchit44,Thank you for the link its helpful.
Hi everyone,
Myself Aastha Bhat, a very excited 2nd-year student. I am interested in the intersection of biology and computers, particularly in areas like bioinformatics. I am new to GSoC and would greatly appreciate any inputs and links to go through.
My current tech stack includes HTML, CSS, JavaScript, Node.js, MySQL, Flask, and Python. I’ve also learned data visualization with Tableau.
Specifically, I’d love to hear any insights regarding essential visualization tools for bioinformatics and what types of visualizations (graphs, trees, etc.) are most effective.
Thank you,
Aastha Bhat
Hi mentors,
I just wanted to have some clarification about the project
Does the project require us to do these visualizations within the InterLex codebase or is it a separate project which consumes InterLex data via their API.
Thank you for your time
Hi, I’m Suhani Ahirwar ,a B.Tech Computer science student. I have experience with JavaScript, React.js, Node js and data visualization and have been exploring the Custom Visualizations/Dashboards for Semantically Described Biological Entities project with great interest.
As I work on drafting my GSoC proposal, I want to ensure it aligns closely with your expectations and the project’s core goals. I’d love to hear your insights on:
-
Key Focus Areas: What aspects of the project would you like to see emphasized — for example, should I focus more on building interactive visualizations, integrating real biological data, or enhancing user accessibility?
-
Technical Depth: How can I best showcase my technical skills, especially with React.js and visualization libraries, to highlight my suitability for the project?
-
Contributions and Roadmap: Would you suggest including a specific feature or small contribution from the InterLex GitHub repo in my proposal to strengthen it?
Your feedback will be extremely helpful in improving my proposal.
Looking forward to your guidance!
Warm regards,
Suhani Ahirwar
Hello everyone!
@jgrethe
I’m Pawan Yadav, currently in my final year of B.Tech. I have experience in full-stack development, and I’ve been exploring InterLex and its GitHub repository. My development background aligns well with the project’s requirements, and I’m excited about the opportunity to contribute.
I had a few questions to get started:
- Are there any interactive features you’d like the visualizations to have?
- Will we be following any design guidelines or using existing UI components?
- Is there a Slack or chat group where we can connect and discuss the project?
Looking forward to learning and collaborating with you all!
Hi @Harish27 I hope this message finds you well. I am writing to provide you with information regarding your question as per my knowledge we have to create separate mini visualization apps and or dashboard for this project later on they can be integrate in the codebase. I gathered this information while reading aim of this project.
Pardon me if I am wrong.
Dear @arnab1896 ,
I hope you’re doing well. I am writing to express my sincere interest in participating in the project on developing visualizations for semantically described biological entities . I would appreciate your guidance on a few points to ensure I have deep knowledge about the project goals:
1.“Is it acceptable to use of tools—like Tableau for dashboards and D3.js for
custom visualizations”-- if not provide name of specific tool that has to be used.
Thank you. Your insights will be incredibly helpful as I move forward.
Best regards, Ruchit kumar
Hello everyone, 
My name is Lalit, and I’m excited about contributing to the Custom Visualizations/Dashboards for Semantically Described Biological Entities project for GSoC 2025. I have experience in JavaScript, React, and data visualization, and I enjoy building interactive UIs and dashboards.
I find this project fascinating because of its potential to make complex biological data more accessible through visualization. I’d love to understand more about the data structure, existing visualization challenges, and how I can start contributing .Are there any starter issues or documentation I should check out?
Looking forward to collaborating with the community and learning more! 
namdevlalit914@gmail.com
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Hi @jgrethe ,
I hope you’re doing well! As I dive deeper into the project on developing custom visualizations for biological entities, I wanted to get some clarity on a few key aspects. I’ve outlined some questions below to better understand the scope, technical implementation, and expectations:
- What biological entities should we prioritize for visualization? (Cells, genes, proteins, etc.)
2.Are there existing visualization tools or frameworks that we should consider leveraging?
3.Should we integrate directly into the InterLex codebase or build a separate web-based app using its API?