Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Reactome integration #699

Open
ugurdogrusoz opened this issue Apr 4, 2023 · 0 comments
Open

Reactome integration #699

ugurdogrusoz opened this issue Apr 4, 2023 · 0 comments
Labels
feature New feature or request

Comments

@ugurdogrusoz
Copy link
Contributor

ugurdogrusoz commented Apr 4, 2023 •
edited
Loading

As Reactome content is available in BioPAX format and we already have the necessary modules to make graph-based queries (e.g. paths between, common targets/regulators, etc.) on data in BioPAX format (via Paxtools), we should be able to make these queries available on Reactome content as well.

We need to be careful about the fact that the queries rely on the existence of ProteinReference objects. ProteinReference objects should have UnificationXrefs to UniProt and RelationshipXrefs to HGNC symbols. Otherwise, queries may not be able to identify sources and targets.

It is worth noting that PathwayCommons resource integration pipeline makes some modifications on Reactome BioPAX so that it is in sync with the preferred format. This here is the class doing that. The modifications don't seem necessary for the queries to work, but this is something to keep in mind.
@ugurdogrusoz ugurdogrusoz added the feature New feature or request label Apr 4, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
feature New feature or request
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@ugurdogrusoz