Create clinical trial curation tool based on CTML from MatchMiner

[zhx828]

Background: cBioPortal will include the clinical trial suggestions based on sample genomic data and clinical data. To match the patient with clinical trial, we need to curate trials by going through the eligible criteria(inclusion/exclusion) and identify whether there is any genomic biomarker that trial requires.

To accurately curate/manage clinical trial biomarkers, we will follow the CTML format to curate all precision medicine trials on a platform. The CTML format is defined by MatchMiner. MatchMiner(https://matchminer.org/) is an open source computational platform developed by the Knowledge Systems Group at Dana-Farber Cancer Institute (DFCI) for matching patient-specific genomic profiles to cancer precision medicine trials. OncoKB™ has previously worked on the curation platform 4 years ago and it was written in Angular. Over the years, our tech stack has been updated and we need to refactor the component as a stand-alone react component so all other projects can utilize.

Goal: Create a react component for trial curation. The component will use firebase for realtime editing.

Approach:

• get familiar with CTML, MatchMiner, OncoKB
• get familiar wit React and Firebase
• look through the previous implementation and understand how the project works
• implement all logics in React

Need skills: Javascript, typescript

Possible mentors: Hongxin Zhang(@zhx828 )

[Player256]

Hey, @zhx828 @inodb @ckandoth @cannin I found this issue really interesting. Would love to hear back from you.

[aditygrg2]

Hey @zhx828 I want to contribute to this project. Please let me know how I can start and some issues to know the problem better. Thank you!

[VenkatMastercoder]

Hey, @zhx828 @inodb @ckandoth @cannin I found this issue to be very interesting. I am interested in contributing to this project, please let me know how I can start and what issues I need to address in order to better understand the problem. Thank you very much!

[zhx828]

Hi @Player256 @aditygrg2 @VenkatMastercoder , thank you for your interests. To work on this issue, the following links would be helpful to you.

• This is the original implementation of the tool using Angular https://github.com/oncokb/matchminer-curate
• This is the main website where CTML is defined and used https://matchminer.org/#ctml
• We want to develop this component in React and it should be used anywhere. You could consider set up your own react website using create-react-app, or create within oncokb-public website

[tamal78]

hey @zhx828 I am done with the above steps.Now are there any small good first issue i can contribute.Or should i start with the proposal?

[zhx828]

Since this will be an indepandant component, I don't think you need to get familiar with the main code base. But if you want to, here is the list of good first issues. https://github.com/oncokb/oncokb/labels/good%20first%20issue

[tamal78]

yeah right i am currently focusing on the matchminer ,CTML only so i can skip the issues.so we will refactor the angular to react component right so that other projects can use this.right?

[zhx828]

I created a branch of matchminer-curate for GSoC usage. It will only start a frontend component. To see the example trials, please slack me your google email. I will add you to the firebase playground. Then you just need to add an environment.ts file in this folder https://github.com/oncokb/matchminer-curate/tree/gsoc/src/main/webapp/app/environments I will provide all connection strings too to update this file.

[Coderner]

Hii @zhx828 I am Shreya Shukla, a pre final year student pursuing a bachelor's degree in Computer Science and Engineering. I am a ReactJs developer and love create interactive UIs. I have familiarised myself with CTML and Matchminer. I have started working with my proposal. Kindly suggest me if there is anything I am missing out or must do before submitting my proposal.

[zhx828]

@Coderner thank you for your interest. Feel free to slack me about your proposal before submitting. I can provide some feedbacks. Please have it uploaded to google doc and enable the access. Thank you.

[zhx828]

In light of https://github.com/cBioPortal/GSoC/issues/103 , this project is no longer active.