RFC: GeneBe Hub public repository, website and functionality

[pstawinski]

Introduction

GeneBe Hub is a publicly available repository for storing and sharing variant annotations in the GeneBe Hub format. Conceptually, it is similar to PyPI or Docker Hub, but instead of Python packages or Docker images, it focuses on variant annotations.

GeneBe Hub simplifies the process of discovering new annotations by providing a simple browser and an infrastructure that allows users to pull and push annotations using the GeneBe Client.

You can use GeneBe Hub to share databases as well as store private ones. It can also help keep datasets evergreen; for example, the ClinVar repository is updated weekly, ensuring access to the most up-to-date ClinVar database.

Design decisions

• Each annotation has it's unique id that it is referenced by. For example @genebe/clinvar:0.0.1. The first part of the id is a namespace, second part is a name, the third one is a version.
• Namespaces, that are assigned to owners. It can be an owner login or an organization name. In case of an organization it is prefixed with @ and changes withing the namespace can be done by all organization members. For example @genebe is a GeneBe namespace.
• GeneBe Hub is open, every GeneBe user can push his own database in his/hers namespace. One can also create an organization and publish as an organization.
• Version is formatted as Semantic Version
• Database name is lowercased
• Databases can be public (accessible to everyone) or private (visible and available only to the owners of the namespace)
• To upload and download (!) databases one need to have GeneBe account and API key generated. Anonymous downloading is not supported.
• Hub stores databases only in standard parquet format.
• There is an access to the Hub on https://genebe.net/hub , which allows users to browse and read basic information about the database

Try It Yourself

To see GeneBe Hub in action, simply browse it and follow the GeneBe Hub Getting Started Guide to download the client and annotations. You can also create your own database by following the Create Database Guide.

Call for Feedback

This is an early draft of GeneBe Hub. We welcome feedback, suggestions, and concerns before moving the implementation from alpha to beta. 😊

[pstawinski]

First Round of the RFC is Over – Thank You!

The first round of the RFC has officially concluded. A huge thank you to everyone who shared their ideas via private messages! Your input has been greatly appreciated.

While this round is over, the discussion remains open—if you still have suggestions, feel free to send them.

A summary of the first round will be shared soon. Stay tuned!