This repository contains documents and code used by cellxgene's curation team. Issues/suggestions pertaining to datasets and how they interact with cellxgene should be created here.
For information/issues about cellxgene and its portal please refer to:
The primary curation tool is the cellxgene-schema CLI. It enables curators to perform schema validation for datasets to be hosted on the cellxgene Data Portal.
It requires Python >= 3.8. It is available through pip:
pip install cellxgene-schema
It can also be installed from the source by cloning this repository and running:
make install
And you can run the tests with:
make unit-test
The CLI validates an AnnData file (*.h5ad) to ensure that it addresses the schema requirements.
Datasets can be validated using the following command line:
cellxgene-schema validate input.h5ad
If the validation succeeds, the command returns a zero exit code; otherwise, it returns a non-zero exit code and prints validation failure messages.
The data portal runs the following in the backend:
cellxgene-schema validate --add-labels output.h5ad input.h5ad
This execution validates the dataset as above AND adds the human-readable labels for the ontology and gene IDs as defined in the schema. If the validation is successful, a new AnnData file (output.h5ad) is written to disk with the labels appended.
This option SHOULD NOT be used by data contributors.
Scripts demonstrating how the cellxgene team has curated datasets for hosting on the portal are stored in this repository. They provide worked examples that provide additional demonstrations of how the tool can be used.
The datasets folder contains step-by-step curation instructions for each dataset we have curated, each dataset has its own independent folder and readme.
In theory, anyone should be able to reproduce our curation process by following the steps in the dataset's readme, which starts with downloading data (usually publicly available) and finishes by creating one or more *.h5ad files that address the schema requirements and are ready to be hosted on the cellxgene Data Portal.
The docs folder contains guides, general documents, files, or scripts that have been used or could be used in the future for curation or integration processes.
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