Model Coverage Matrix for Cell Types and Assays

Help & Support
1

Hi Alpha Genome Team,

First of all, I want to express my gratitude for the incredible work you are doing. The tools and insights Alpha Genome provides are a massive asset to the scientific community.

Currently, between the numerous cell and tissue types defined in Cell Ontology and Uberon, combined with the variety of available assays, it can be quite challenging to determine exactly which cell/tissue type × assay combinations Alpha Genome is currently able to predict.

To make the platform even more user-friendly and powerful, I have a suggestion: Would it be possible to provide a comprehensive coverage matrix?

Ideally, this would include:

  • Visual Access: A searchable table or heatmap on the website for quick viewing.

  • Programmatic Access: An endpoint or downloadable metadata file (e.g., JSON or CSV) so users can programmatically check model compatibility before starting a workflow.

Having this transparency would save significant time and help researchers better align their experimental designs with Alpha Genome’s capabilities.

Thanks again for all your hard work and for considering this feedback!

Best regards,

Wenjin

2

Hi @WenjinZhang, welcome to the forum!

We have the following navigating data ontologies Colab notebook that has a table of all our metadata, and you can programatically interact with this data using an API key, or indeed download as a CSV.

You can also look at our supplementary tables which includes more details such as experiment and file accession numbers.

Hope this helps!

3

Thanks for the quick response! The Colab notebook and API access are exactly what I was looking for to navigate the ontologies. I’ll also dive into the supplementary tables for those specific accession numbers.

Much appreciated!