Visualize OncoKB annotation and generate sample/patient report

[zhx828]

Background:
OncoKB™(https://www.oncokb.org) is a precision oncology knowledge base developed at Memorial Sloan Kettering Cancer Center that contains biological and clinical information about genomic alterations in cancer. cBioPortal includes OncoKB annotation in it's result view, patient view to provide detailed biological effect and clinical implications for each variant.

OncoKB provides varies way for users to annotate alterations. We have standard APIs that can be used with high volume requests (https://api.oncokb.org). We also have a python package which builds on top the APIs to annotate MAF/CopyNumberAlteration/StructuralVariant. Even with these applications, portion of OncoKB users still have difficulty to get their variants annotated. Especially to the users that without any computational background.

Goal:

1. Create an standard alone npm package that can be imported as dependency to visualize sample/patient level OncoKB annotation. The tool should include the following components.

   • Component to visualize OncoKB annotation by mutation type
   • Download the annotation as a PDF report

2. Integrate with cBioPortal sample view

   • Convert all sample genomic data into OncoKB API format
   • Annotate genomic data through OncoKB API
   • Use the component created in step 1 to visualize

Mockup(subject to change)

Approach:

• Understand the project especially understand the input formats
• Work with team members to implement the components above

Need skills:

• Javascript, typescript, React

Possible mentors:
John Konecny, Hongxin Zhang(@zhx828 )
Mary Chapman @mlizchap

[Abinash-bit]

@zhx828 Hey... I am intrested in resolving this issue... Please guide me .

[chaitravi-ce]

@zhx828 @calvinlu3 I am deeply interested in contributing to this issue...Could you please guide me in the further steps I should follow

[tamal78]

Hi @zhx828 can i would like contribute to this project .I have gone through the codebase and all the guidelines.I am more than happy to contribute for CbioPortal for this project.Hoping for a reply from the community!

[zhx828]

Hi @Abinash-bit @chaitravi-ce @tamal78 , thank you for your interests. To create a successful proposal, I think you would need to do the following

• Get familiar with oncokb-public website and code base
• Understand what we do/not offer through API, api.oncokb.org
• Have a good understanding the data types, Mutation/Copy Number Alteration/Structural Variant
• Understand why we want to create the tool and find a valid use case
• (optional) grab a good first issue to work on. Please also comment on the ticket if you are actually working on it to avoid uncessary duplications. Feel free to reach out to me if you need clarification. https://github.com/oncokb/oncokb/labels/good%20first%20issue

[SalihuDickson]

Hello @zhx828. This project requires that you be familiar with the oncokb code base. And the description says you'll have to build a tool that will be integrated with the website. But the oncokb platform is built largely with java. Do we need to know java to work on this project, I know the listed requirements are javascript, typescript and react but can I please get a clarification on if java will be needed at all.

[zhx828]

Hello @zhx828. This project requires that you be familiar with the oncokb code base. And the description says you'll have to build a tool that will be integrated with the website. But the oncokb platform is built largely with java. Do we need to know java to work on this project, I know the listed requirements are javascript, typescript and react but can I please get a clarification on if java will be needed at all.

@SalihuDickson This project would only require frontend coding. Any data if you need through API, our team will help on that.

[SalihuDickson]

@zhx828 Okay that sounds great, thank you. I'm really looking forward to having the opportunity to work on this project.

[shrikant1809]

Hello @zhx828 ,
Myself Shrikant, currently working as a Program Manager with Medprime Technologies (patented digital microscope producers).
I have read the above project and find it resonating with my current working spectrum and I aim to contribute to the same.
I am proficient in handling projects with JavaScript, HTML, Cascading Style Sheets; also have worked with the framework of Node.js and Express.js with database management system like MySQL and JavaScript libraries like Redux and Angular.
I hope you find my above skills relevant for the project "Annotate cancer alterations and generate patient report" and accept my participation in GSoC'23.

Thank you,
Shrikant
Email- [email protected]
LinkedIn - https://www.linkedin.com/in/shrikantp1809/

[zhx828]

@shrikant1809 thank you for your interest! It's great to hear our thoughts are resonated with other community members. If I understand correctly, you are a full time employee now at Medprime Technologies? This project is designed for GSoC participants and mostly students. But if I misunderstand anything, please let me know.

[Ahmed89shaaban]

I'm interested to begin this project and have new ideas need to guide and discuss plz

[Beking0912]

Hi, @zhx828 ,
I'm Gloria, a first-year CS Master student at North Carolina State University, and I'm interested in this project.
With around two year of experience worked as a Front-end Engineer writing React application with JavaScript and TypeScript, I've found that my tech stack is a great match for oncokb-public codebase. As a newcomer to open-source projects, I am eager to have the opportunity to make a contribution.
Please let me know if this project has already been assigned. Thank you for your time.

[shrikant1809]

@shrikant1809 thank you for your interest! It's great to hear our thoughts are resonated with other community members. If I understand correctly, you are a full time employee now at Medprime Technologies? This project is designed for GSoC participants and mostly students. But if I misunderstand anything, please let me know.

Yes, I am a full time employee, but I can come up with arrangements for participating in GSoC and wish to contribute to community.
I hope you will consider my request.

[Ahmed89shaaban]

We cand collebrate to make good discussion and find good idea

[divz-codess]

Hi I am interested in working on this project under GSoC 2023. I am currently in my junior year of university and have about an year of experience working as a frontend developer in past internships using various tech stacks such as ReactJS, Flutter etc. Additionally I have a research paper published in the field of Biological sciences and have deep interest in Genomics and Healthcare. Therefore, I will be really grateful for any help and guidance for this project.
Looking forward to your reply @zhx828
Have a nice day :)

[Ahmed89shaaban]

Hi iam very happy to contribute with you and discuss all idea and to be team

[zhx828]

@Ahmed89shaaban @Beking0912 @shrikant1809 @divz-codess thank you all for your interests. The description on this project should have the info to get you started. When ready, feel free to slack me your proposal before submitting. I can provide some feedbacks. Please have it uploaded to google doc and enable the access. Thank you.

[shrikant1809]

Greetings @zhx828,
Hope you find this message well. As instructed I have written a proposal for GSoC 2023. I have included Project titles, vision, detailed approach and my contact information. I have create proposal similar to the template which was available on GitHub of cBioPortal and sent you on slack. I hope you will approve my request to contribute and give a favourable response and approve my candidature.
Thank you.

[Shashank2104125]

@zhx828 I am really interested in this project. Will this project open for GSoC 2024?

[zhx828]

@zhx828 I am really interested in this project. Will this project open for GSoC 2024?

Yes it will. Sorry about the late reply.

[heymitali]

Hello, my name is Mitali. I have a strong interest in this project and am eagerly anticipating the opportunity to contribute to it.