Similar Patient Discovery

[inodb]

Background:
The cBioPortal for Cancer Genomics is an open-source platform designed to provide a web interface for exploring, visualizing, and analyzing cancer genomics data, and has grown to be widely used by researchers and clinicians worldwide. The current interface provides comprehensive tools for individual patient data exploration, including mutations, copy number variations, and clinical information as well as cohort exploration, analytics, and cohort comparisons.

A user can find similar patients by using the interface to look for patients that e.g. are of the same cancer type, have similar mutations, or received the same treatment. There are currently however no similar patients proposed automatically; finding similar ones requires many manual steps. Here, we propose to develop a new web service that would recommend similar patients a user could explore given a patient's molecular and clinical profile. In oncology, where genetic mutations and biomarkers play critical roles in determining the most effective treatments, the ability to easily find and compare similar patient cases is invaluable. Moreover, a patient similarity function within cBioPortal would empower users to leverage the vast amounts of data available in the portal more effectively. By integrating sophisticated similarity search capabilities, users could identify cohorts of patients based on specific criteria, compare their genomic landscapes, and analyze their treatment outcomes.

Goal:
Develop a REST API that provides patient similarity information given a patient's molecular and clinical profile. For the similarity scoring we will use an existing algorithm

Approach:
We will develop a backend web service for an existing Python-based algorithm that generates a model for identifying similar patients. This web service will provide a RESTful API to allow for communication of the cBioPortal frontend with the patient similarity model. These endpoints will be designed to handle real-time data exchanges, leveraging JSON for its versatility and efficiency in data transmission.

To manage data updates to the patient similarity model whenever new cBioPortal data is added to the system we propose to leverage event-driven triggers. When new data enters the system, we rerun the pipeline to regenerate the model and redeploy the backend web service Whenever a user visits the frontend page it will be using this new backend web service. This ensures that the frontend displays the most current data, enhancing the user experience in exploring patient similarities. Additionally, to maintain system efficiency and prevent overload, it's crucial to optimize the data payload and update frequency based on user interaction and system capabilities

Need skills:
Understanding of RESTful APIs, Familiarity with Python

Possible mentors:
@Thahmina

[domgor11]

Hi @inodb ,
I'm a backend software engineer with 2 year of experience, and will be starting masters in Health Data Science this fall.
I have experience in building cloud backend services with APIs that focus on processing large volumes of incoming data.
The described approach sounds to me fairly straightforward, and I'm confident that I'm capable of creating this backend service.

LinkedIn: https://www.linkedin.com/in/dominika-gorgosz
Email: dominikagorgosz@icloud.com

It would be great to have a call, or discuss your precise expectations over email.

[DininduChamikara]

Hi @inodb,
I am a fresh graduate and like to contribute to this project as a participant in the GSoC 2024. I have worked with some Natural Language Processing tasks and in there, I have worked with clustering models as well. In this project, I need to clarify some details.
* Is this approach based on clustering or classification?
* "We will develop a backend web service for an existing Python-based algorithm that generates a model for identifying similar patients." what does this mean? Does it mean there is an existing algorithm and no need to implement that?
* Do we need to complete some machine learning part here?
* If not the only part to implement is when a patient enters some data find the relevant cluster they are in and update the data set with the newly entered data.

Email - dininduchamikara99@gmail.com

[mdkintu]

hi @inodb
where do i submit the proposal?

[Akshat1000Sharma]

Dear @inodb,

I hope this message finds you well. I am a second-year college student eager to contribute to your open-source project. This is my first time contributing to Open Source but I am confident in my skills as a developer.

I have completed multiple internships focusing on Python full-stack development, with extensive experience in creating REST APIs for various projects. I am confident in my skills as a Python Backend Developer and would love the opportunity to collaborate with you on this initiative.

You can find more about me on my LinkedIn profile, or feel free to reach out via email at as549@snu.edu.in. I would be delighted to connect on LinkedIn or discuss your specific expectations over email.

Looking forward to your response.

Best regards,
Akshat Sharma

[officialasishkumar]

Hi @inodb ,

I'm Asish. I have been a part of Google Summer of Code in 2024 where i worked with Python in TARDIS-SN organisation. I have also been a part of Linux foundation mentorship program 2024 (term 2) where i worked with Golang in KCL language organisation. I have a vast experience in working with python and developing REST APIs with frameworks such as Django, flask and fastAPI. I believe my OSS experience is crucial for this project.

I would like to know are there any pretasks for this project that is crucial for selection?

Thank you
Asish Kumar

[satyam969]

Hi Team,

I hope you’re doing well. My name is Priya Raj, and I am interested in contributing to the "Patient Similarity REST API" project as part of GSoC 2025. I have experience in Python, Django, and RESTful API development, and I have previously worked on sentiment analysis and recommendation systems.

I am excited about this project as it aligns with my expertise and interests. I would love to get involved and start contributing. Could you please guide me on how I can begin? If there are any initial tasks or issues I can work on, I’d be happy to take them up.

Looking forward to your guidance and feedback!

Best regards,
Priya Raj

[sarthakeash]

Hey, I am Sarthak Arora. I am a working professional in software development. I have years of experience via projects and internships in rest api development, python, django and other FE, and AI frameworks too. I have a very good sense on how to take up this project. I am open to discuss these ideas with mentors before submitting the proposal. Whats the best way to connect

[kshitijaucharmal]

Hello, I'm Kshitij Aucharmal. I'm a Prefinal Year of ENTC engineering from India. I have worked on many AI/ML projects and am proficient in Python. Also have some experience in writing RESTful APIs due to an ongoing internship. I have also contributed to supervision (roboflow) in Hacktoberfest, and so have decent open source experience. I hope to connect with the mentors for this projects, as this projects seems right up my alley, what would be the best way to get in touch?

[mannan-ab]

Hi @inodb , my name is Abdul Mannan, and I’m pursuing my Master’s in Computer Science at Binghamton University, New York. I developed a strong interest for biomedicine and bioinformatics last semester and have continued working on it. Currently, I am working on the application of Quantum Computing (Grover's Algorithm) in Biomedicine, while also working simultaneously on genomic datasets for my multimodal ml class. I find this project really fascinating and believe it’s exactly what I’ve been looking for beause I've been working on backend integration,API's and also some concepts of devops this semester. I’m getting familiar with the cBioPortal interface and tools currently, and I’m looking forward to submitting my final proposal and working with the organization.

[SamarAhwaz]

Hello, @Thahmina and @inodb ,

I’m Samar, a BCA student and an aspiring software developer with experience in Python, Django Rest Framework (DRF), and REST API development. I’m very interested in contributing to this project as part of GSoC 2025.

I have experience in:

Building REST APIs using Django Rest Framework.
Integrating backend services with frontend applications (React + DRF).
Handling JSON data efficiently in APIs.
I have gone through the project details, and I find it very exciting! While I’m familiar with API development, I would love to learn more about event-driven triggers and updating the similarity model dynamically.

Could you please provide guidance on how I can get started? Are there any beginner-friendly issues I can work on to familiarize myself with the cBioPortal codebase? Looking forward to your response! 😊

Thanks!
Samar