Create pipeline/interface to prioritize variants for OncoKB curation

[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 pipeline by fetch a list of genomic variants from a clinical cohort(MSK-IMPACT) that haven't been curated by OncoKB Hint:

   • OncoKB deploys through k8s on AWS
   • OncoKB uses AirFlow to manage dags

2. Create an interface to manage the list of variants from above on OncoKB Curation Platform. The interface will include the following features

   • List variants
   • Provide action buttons to either add variant to the list of Variants of Unknown Significance or to Mutations list
   • If to add to Mutations list, we should allow the curator to add the data elements in a modal

Curation Platform

Genes page

Gene page

Mutation Data Elements

Approach:

• Understand the project
• Try to come up the mockups with Figma
• Work with team members to implement the components above

Need skills:

• Python, Javascript, typescript, React

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

[Prathamesh111-netizen]

Hello, I'm Prathamesh from India. I am interested in contributing to this issue:

I am learning about the project background and trying figure out the specific details.

This is my resume for your reference: https://shorturl.at/nIY49

As of now, I am working on creating an interface and figma mockups for OncoKB Curation Platform to better understand the platform and its features.

[AminaEmin]

Hello, I'm Amina from Azerbaijan. I am writing to express my sincere interest in joining your program. As a student majoring in biotechnology with a keen interest in both biotechnology and IT, I believe I am well-suited to make meaningful contributions to this project. Here is my resume: https://drive.google.com/file/d/1-lBqIWbpi3xMS3z7DF8FPB__mgT3aQUb/view?usp=sharing I forgot to include this in my resume and to be honest, I don’t know if this will be useful to you, but I also have experience working in Linux

[chhsch]

Hello, I'm Hathaway. I'm intrigued by this project and eager to delve deeper into the specifics of the website, the type of data it handles, and to identify an appropriate initial task to contribute to. Could you please advise if the oncokb-public website and its code base are the right places to begin my exploration? Thank you for your guidance.

[zhx828]

Hello, I'm Hathaway. I'm intrigued by this project and eager to delve deeper into the specifics of the website, the type of data it handles, and to identify an appropriate initial task to contribute to. Could you please advise if the oncokb-public website and its code base are the right places to begin my exploration? Thank you for your guidance.

It will be https://github.com/oncokb/oncokb-transcript/tree/rc It requires some work to get the system set up. Feel free to join the cBioPortal Public Slack and send me a message for next steps.