Generating citations for Census slices

This notebook demonstrates how to generate a citation string for all datasets contained in a Census slice.

Contents

  1. Requirements

  2. Generating citation strings

    1. Via cell metadata query

    2. Via an AnnData query

⚠️ Note that the Census RNA data includes duplicate cells present across multiple datasets. Duplicate cells can be filtered in or out using the cell metadata variable is_primary_data which is described in the Census schema.

Requirements

This notebook requires:

  • cellxgene_census Python package.

  • Census data release with schema version 1.3.0 or greater.

Generating citation strings

First we open a handle to the Census data. To ensure we open a data release with schema version 1.3.0 or greater, we use census_version="latest"

[1]:

import cellxgene_census

census = cellxgene_census.open_soma(census_version="latest")
census["census_info"]["summary"].read().concat().to_pandas()

[1]:
soma_joinid label value
0 0 census_schema_version 1.3.0
1 1 census_build_date 2024-01-01
2 2 dataset_schema_version 4.0.0
3 3 total_cell_count 75694072
4 4 unique_cell_count 45846761
5 5 number_donors_homo_sapiens 16292
6 6 number_donors_mus_musculus 2153

Then we load the dataset table which contains a column "citation" for each dataset included in Census.

[2]:

datasets = census["census_info"]["datasets"].read().concat().to_pandas()
datasets["citation"]

[2]:

0      Dataset Version: https://datasets.cellxgene.cz...
1      Dataset Version: https://datasets.cellxgene.cz...
2      Dataset Version: https://datasets.cellxgene.cz...
3      Dataset Version: https://datasets.cellxgene.cz...
4      Publication: https://doi.org/10.1002/ctm2.1356...
                             ...
695    Publication: https://doi.org/10.1038/s41586-02...
696    Publication: https://doi.org/10.1038/s41586-02...
697    Publication: https://doi.org/10.1016/j.isci.20...
698    Publication: https://doi.org/10.1371/journal.p...
699    Publication: https://doi.org/10.1016/j.isci.20...
Name: citation, Length: 700, dtype: object

And now we can use the column "dataset_id" present in both the dataset table and the Census cell metadata to create citation strings for any Census slice.

Via cell metadata query

[3]:

# Query cell metadata
cell_metadata = census["census_data"]["homo_sapiens"].obs.read(
    value_filter="tissue == 'cardiac atrium'", column_names=["dataset_id", "cell_type"]
)
cell_metadata = cell_metadata.concat().to_pandas()

# Get a citation string for the slice
slice_datasets = datasets[datasets["dataset_id"].isin(cell_metadata["dataset_id"])]
print(*slice_datasets["citation"], sep="\n\n")

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/4866a804-37eb-436f-8c87-9cd585260061.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/bfd80f12-725c-4482-ad7f-1ed2b4909b0d.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/e6df8a57-f54f-413a-9d4d-dee03294d778.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/8d599205-5c51-4b50-9d48-3dec31238587.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/f6065c51-bd26-4aa5-a05d-2805aeea48d9.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/8cdbf790-4d29-4f46-9aef-21adfb2e21da.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Via AnnData query

[4]:

# Fetch an AnnData object
adata = cellxgene_census.get_anndata(
    census=census,
    organism="homo_sapiens",
    measurement_name="RNA",
    obs_value_filter="tissue == 'cardiac atrium'",
    var_value_filter="feature_name == 'MYBPC3'",
    column_names={"obs": ["dataset_id", "cell_type"]},
)

# Get a citation string for the slice
slice_datasets = datasets[datasets["dataset_id"].isin(adata.obs["dataset_id"])]
print(*slice_datasets["citation"], sep="\n\n")

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/4866a804-37eb-436f-8c87-9cd585260061.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/bfd80f12-725c-4482-ad7f-1ed2b4909b0d.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/e6df8a57-f54f-413a-9d4d-dee03294d778.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/8d599205-5c51-4b50-9d48-3dec31238587.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/f6065c51-bd26-4aa5-a05d-2805aeea48d9.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

Publication: https://doi.org/10.1126/science.abl4896 Dataset Version: https://datasets.cellxgene.cziscience.com/8cdbf790-4d29-4f46-9aef-21adfb2e21da.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/e5f58829-1a66-40b5-a624-9046778e74f5

And don’t forget to close the Census handle

[6]:

census.close()