How to Prepare Curated Alias

This guide explains how to prepare an alias file and use it as the Curated alias that will be displayed for a factor layer by default in CartoScope

Concepts

• Alias
• Alias Source

1. Prepare Your Alias File

Alias File Format

• The file must be a tab-separated file (.tsv) with one row per factor.
• It should contains two columns:
  • 1st column (header: either index or name): numeric factor indices.
  • 2nd column (header: alias): aliases names.

Example Alias File

index   alias
1   Tumor
2   Stroma
3   Immune

Prepare Alias File via CartoScope

CartoScope offers a solution to prepare your alias file during exploration.

1. Click "Load Layers" button to load the factor layer you want to annotate.
2. Open the factor drawer to display your target factor layer.
3. Review the Overview table to determine whether existing alias sources (e.g., curated or AI-inferred aliases)) are available.
4. To annotate a factor, double-click the corresponding cell and enter your desired label.
5. Once all annotations are finalized, click the “Alias” button at the top of the Overview table and select “Export alias” to generate and download the .tsv file.

2. Link You Alias File in catalog.yaml

If you would like this alias file to be displayed as the default in CartoScope, please:

1. specify it in catalog.yaml,
2. upload the file to the AWS S3 directory or Zenodo repository that hosts this dataset.

Example catalog.yaml with Alias Files

In the example, we want to provide the curated_alias.tsv to the target_layer factor layer in the example_data dataset.

id: example_data
title: example_data
...
assets:
...
factors:
    - id: target_layer
    name: target_layer
    ...
    alias: curated_alias.tsv

In this setup:

• alias is the curated default alias table used as the Curated source.