Open Problems in Single Cell Analysis

Info

cellxgene_census/hcla
Sikkema et al. (2023)
17.35 GiB
02-02-2024
584944 × 28024

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No related benchmarks found.

Description

The integrated Human Lung Cell Atlas (HLCA) represents the first large-scale, integrated single-cell reference atlas of the human lung. It consists of over 2 million cells from the respiratory tract of 486 individuals, and includes 49 different datasets. It is split into the HLCA core, and the extended or full HLCA. The HLCA core includes data of healthy lung tissue from 107 individuals, and includes manual cell type annotations based on consensus across 6 independent experts, as well as demographic, biological and technical metadata.

Preview

dataset is an AnnData object with n_obs × n_vars = 584944 × 28024 with slots:

obs: soma_joinid, dataset_id, assay, assay_ontology_term_id, cell_type, cell_type_ontology_term_id, development_stage, development_stage_ontology_term_id, disease, disease_ontology_term_id, donor_id, is_primary_data, self_reported_ethnicity, self_reported_ethnicity_ontology_term_id, sex, sex_ontology_term_id, suspension_type, tissue, tissue_ontology_term_id, tissue_general, tissue_general_ontology_term_id, batch, size_factors
var: soma_joinid, feature_id, feature_name, hvg, hvg_score
obsp: knn_connectivities, knn_distances
obsm: X_pca
varm: pca_loadings
layers: counts, normalized
uns: dataset_description, dataset_id, dataset_name, dataset_organism, dataset_reference, dataset_summary, dataset_url, knn, normalization_id, pca_variance

Reference

Name	Description	Type	Data type	Size
obs
`assay`	Type of assay used to generate the cell data, indicating the methodology or technique employed.	`vector`	`category`	584944
`assay_ontology_term_id`	Experimental Factor Ontology (`EFO:`) term identifier for the assay, providing a standardized reference to the assay type.	`vector`	`category`	584944
`batch`	A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc.	`vector`	`category`	584944
`cell_type`	Classification of the cell type based on its characteristics and function within the tissue or organism.	`vector`	`category`	584944
`cell_type_ontology_term_id`	Cell Ontology (`CL:`) term identifier for the cell type, offering a standardized reference to the specific cell classification.	`vector`	`category`	584944
`dataset_id`	Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes.	`vector`	`category`	584944
`development_stage`	Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase.	`vector`	`category`	584944
`development_stage_ontology_term_id`	Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Developmental Stages (`HsapDv:`) ontology is used. If the organism is mouse (`organism_ontology_term_id == 'NCBITaxon:10090'`), then the Mouse Developmental Stages (`MmusDv:`) ontology is used. Otherwise, the Uberon (`UBERON:`) ontology is used.	`vector`	`category`	584944
`disease`	Information on any disease or pathological condition associated with the cell or donor.	`vector`	`category`	584944
`disease_ontology_term_id`	Ontology term identifier for the disease, enabling standardized disease classification and referencing. Must be a term from the Mondo Disease Ontology (`MONDO:`) ontology term, or `PATO:0000461` from the Phenotype And Trait Ontology (`PATO:`).	`vector`	`category`	584944
`donor_id`	Identifier for the donor from whom the cell sample is obtained.	`vector`	`category`	584944
`is_primary_data`	Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data.	`vector`	`bool`	584944
`self_reported_ethnicity`	Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits.	`vector`	`category`	584944
`self_reported_ethnicity_ontology_term_id`	Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications. If the organism is human (`organism_ontology_term_id == 'NCBITaxon:9606'`), then the Human Ancestry Ontology (`HANCESTRO:`) is used.	`vector`	`category`	584944
`sex`	Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions.	`vector`	`category`	584944
`sex_ontology_term_id`	Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only `PATO:0000383`, `PATO:0000384` and `PATO:0001340` are allowed.	`vector`	`category`	584944
`size_factors`	The size factors created by the normalisation method, if any.	`vector`	`float32`	584944
`soma_joinid`	If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell.	`vector`	`int64`	584944
`suspension_type`	Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions.	`vector`	`category`	584944
`tissue`	Specific tissue from which the cells were derived, key for context and specificity in cell studies.	`vector`	`category`	584944
`tissue_general`	General category or classification of the tissue, useful for broader grouping and comparison of cell data.	`vector`	`category`	584944
`tissue_general_ontology_term_id`	Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types. For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`.	`vector`	`category`	584944
`tissue_ontology_term_id`	Ontology term identifier for the tissue, providing a standardized reference for the tissue type. For organoid or tissue samples, the Uber-anatomy ontology (`UBERON:`) is used. The term ids must be a child term of `UBERON:0001062` (anatomical entity). For cell cultures, the Cell Ontology (`CL:`) is used. The term ids cannot be `CL:0000255`, `CL:0000257` or `CL:0000548`.	`vector`	`category`	584944
var
`feature_id`	Unique identifier for the feature, usually a ENSEMBL gene id.	`vector`	`object`	28024
`feature_name`	A human-readable name for the feature, usually a gene symbol.	`vector`	`object`	28024
`hvg`	Whether or not the feature is considered to be a ‘highly variable gene’	`vector`	`bool`	28024
`hvg_score`	A ranking of the features by hvg.	`vector`	`float64`	28024
`soma_joinid`	If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature.	`vector`	`int64`	28024
obsp
`knn_connectivities`	K nearest neighbors connectivities matrix.	`sparsematrix`	`float32`	584944 × 584944
`knn_distances`	K nearest neighbors distance matrix.	`sparsematrix`	`float64`	584944 × 584944
obsm
`X_pca`	The resulting PCA embedding.	`densematrix`	`float32`	584944 × 50
varm
`pca_loadings`	The PCA loadings matrix.	`densematrix`	`float32`	28024 × 50
layers
`counts`	Raw counts	`sparsematrix`	`float32`	584944 × 28024
`normalized`	Normalised expression values	`sparsematrix`	`float32`	584944 × 28024
uns
`dataset_description`	Long description of the dataset.	`atomic`	`str`	1
`dataset_id`	A unique identifier for the dataset. This is different from the `obs.dataset_id` field, which is the identifier for the dataset from which the cell data is derived.	`atomic`	`str`	1
`dataset_name`	A human-readable name for the dataset.	`atomic`	`str`	1
`dataset_organism`	The organism of the sample in the dataset.	`atomic`	`str`	1
`dataset_reference`	Bibtex reference of the paper in which the dataset was published.	`atomic`	`str`	1
`dataset_summary`	Short description of the dataset.	`atomic`	`str`	1
`dataset_url`	Link to the original source of the dataset.	`atomic`	`str`	1
`knn`	Supplementary K nearest neighbors data.	`dict`		3
`normalization_id`	Which normalization was used	`atomic`	`str`	1
`pca_variance`	The PCA variance objects.	`dict`		2

Slot crossref data

`dataset.layers['counts']`

In R: dataset$layers[["counts"]]

Type: sparsematrix, data type: float32, shape: 584944 × 28024

Raw counts

`dataset.layers['normalized']`

In R: dataset$layers[["normalized"]]

Type: sparsematrix, data type: float32, shape: 584944 × 28024

Normalised expression values

`dataset.obs['soma_joinid']`

In R: dataset$obs[["soma_joinid"]]

Type: vector, data type: int64, shape: 584944

If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the cell.

`dataset.obs['dataset_id']`

In R: dataset$obs[["dataset_id"]]

Type: vector, data type: category, shape: 584944

Identifier for the dataset from which the cell data is derived, useful for tracking and referencing purposes.

`dataset.obs['assay']`

In R: dataset$obs[["assay"]]

Type: vector, data type: category, shape: 584944

Type of assay used to generate the cell data, indicating the methodology or technique employed.

`dataset.obs['assay_ontology_term_id']`

In R: dataset$obs[["assay_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Experimental Factor Ontology (EFO:) term identifier for the assay, providing a standardized reference to the assay type.

`dataset.obs['cell_type']`

In R: dataset$obs[["cell_type"]]

Type: vector, data type: category, shape: 584944

Classification of the cell type based on its characteristics and function within the tissue or organism.

`dataset.obs['cell_type_ontology_term_id']`

In R: dataset$obs[["cell_type_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Cell Ontology (CL:) term identifier for the cell type, offering a standardized reference to the specific cell classification.

`dataset.obs['development_stage']`

In R: dataset$obs[["development_stage"]]

Type: vector, data type: category, shape: 584944

Stage of development of the organism or tissue from which the cell is derived, indicating its maturity or developmental phase.

`dataset.obs['development_stage_ontology_term_id']`

In R: dataset$obs[["development_stage_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Ontology term identifier for the developmental stage, providing a standardized reference to the organism’s developmental phase.

If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Developmental Stages (HsapDv:) ontology is used.
If the organism is mouse (organism_ontology_term_id == 'NCBITaxon:10090'), then the Mouse Developmental Stages (MmusDv:) ontology is used. Otherwise, the Uberon (UBERON:) ontology is used.

`dataset.obs['disease']`

In R: dataset$obs[["disease"]]

Type: vector, data type: category, shape: 584944

Information on any disease or pathological condition associated with the cell or donor.

`dataset.obs['disease_ontology_term_id']`

In R: dataset$obs[["disease_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Ontology term identifier for the disease, enabling standardized disease classification and referencing.

Must be a term from the Mondo Disease Ontology (MONDO:) ontology term, or PATO:0000461 from the Phenotype And Trait Ontology (PATO:).

`dataset.obs['donor_id']`

In R: dataset$obs[["donor_id"]]

Type: vector, data type: category, shape: 584944

Identifier for the donor from whom the cell sample is obtained.

`dataset.obs['is_primary_data']`

In R: dataset$obs[["is_primary_data"]]

Type: vector, data type: bool, shape: 584944

Indicates whether the data is primary (directly obtained from experiments) or has been computationally derived from other primary data.

`dataset.obs['self_reported_ethnicity']`

In R: dataset$obs[["self_reported_ethnicity"]]

Type: vector, data type: category, shape: 584944

Ethnicity of the donor as self-reported, relevant for studies considering genetic diversity and population-specific traits.

`dataset.obs['self_reported_ethnicity_ontology_term_id']`

In R: dataset$obs[["self_reported_ethnicity_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Ontology term identifier for the self-reported ethnicity, providing a standardized reference for ethnic classifications.

If the organism is human (organism_ontology_term_id == 'NCBITaxon:9606'), then the Human Ancestry Ontology (HANCESTRO:) is used.

`dataset.obs['sex']`

In R: dataset$obs[["sex"]]

Type: vector, data type: category, shape: 584944

Biological sex of the donor or source organism, crucial for studies involving sex-specific traits or conditions.

`dataset.obs['sex_ontology_term_id']`

In R: dataset$obs[["sex_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Ontology term identifier for the biological sex, ensuring standardized classification of sex. Only PATO:0000383, PATO:0000384 and PATO:0001340 are allowed.

`dataset.obs['suspension_type']`

In R: dataset$obs[["suspension_type"]]

Type: vector, data type: category, shape: 584944

Type of suspension or medium in which the cells were stored or processed, important for understanding cell handling and conditions.

`dataset.obs['tissue']`

In R: dataset$obs[["tissue"]]

Type: vector, data type: category, shape: 584944

Specific tissue from which the cells were derived, key for context and specificity in cell studies.

`dataset.obs['tissue_ontology_term_id']`

In R: dataset$obs[["tissue_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Ontology term identifier for the tissue, providing a standardized reference for the tissue type.

For organoid or tissue samples, the Uber-anatomy ontology (UBERON:) is used. The term ids must be a child term of UBERON:0001062 (anatomical entity). For cell cultures, the Cell Ontology (CL:) is used. The term ids cannot be CL:0000255, CL:0000257 or CL:0000548.

`dataset.obs['tissue_general']`

In R: dataset$obs[["tissue_general"]]

Type: vector, data type: category, shape: 584944

General category or classification of the tissue, useful for broader grouping and comparison of cell data.

`dataset.obs['tissue_general_ontology_term_id']`

In R: dataset$obs[["tissue_general_ontology_term_id"]]

Type: vector, data type: category, shape: 584944

Ontology term identifier for the general tissue category, aiding in standardizing and grouping tissue types.

`dataset.obs['batch']`

In R: dataset$obs[["batch"]]

Type: vector, data type: category, shape: 584944

A batch identifier. This label is very context-dependent and may be a combination of the tissue, assay, donor, etc.

`dataset.obs['size_factors']`

In R: dataset$obs[["size_factors"]]

Type: vector, data type: float32, shape: 584944

The size factors created by the normalisation method, if any.

`dataset.obsm['X_pca']`

In R: dataset$obsm[["X_pca"]]

Type: densematrix, data type: float32, shape: 584944 × 50

The resulting PCA embedding.

`dataset.obsp['knn_connectivities']`

In R: dataset$obsp[["knn_connectivities"]]

Type: sparsematrix, data type: float32, shape: 584944 × 584944

K nearest neighbors connectivities matrix.

`dataset.obsp['knn_distances']`

In R: dataset$obsp[["knn_distances"]]

Type: sparsematrix, data type: float64, shape: 584944 × 584944

K nearest neighbors distance matrix.

`dataset.uns['dataset_description']`

In R: dataset$uns[["dataset_description"]]

Type: atomic, data type: str, shape: 1

Long description of the dataset.

`dataset.uns['dataset_id']`

In R: dataset$uns[["dataset_id"]]

Type: atomic, data type: str, shape: 1

A unique identifier for the dataset. This is different from the obs.dataset_id field, which is the identifier for the dataset from which the cell data is derived.

`dataset.uns['dataset_name']`

In R: dataset$uns[["dataset_name"]]

Type: atomic, data type: str, shape: 1

A human-readable name for the dataset.

`dataset.uns['dataset_organism']`

In R: dataset$uns[["dataset_organism"]]

Type: atomic, data type: str, shape: 1

The organism of the sample in the dataset.

`dataset.uns['dataset_reference']`

In R: dataset$uns[["dataset_reference"]]

Type: atomic, data type: str, shape: 1

Bibtex reference of the paper in which the dataset was published.

`dataset.uns['dataset_summary']`

In R: dataset$uns[["dataset_summary"]]

Type: atomic, data type: str, shape: 1

Short description of the dataset.

`dataset.uns['dataset_url']`

In R: dataset$uns[["dataset_url"]]

Type: atomic, data type: str, shape: 1

Link to the original source of the dataset.

`dataset.uns['knn']`

In R: dataset$uns[["knn"]]

Type: dict, data type: ``, shape: 3

Supplementary K nearest neighbors data.

`dataset.uns['normalization_id']`

In R: dataset$uns[["normalization_id"]]

Type: atomic, data type: str, shape: 1

Which normalization was used

`dataset.uns['pca_variance']`

In R: dataset$uns[["pca_variance"]]

Type: dict, data type: ``, shape: 2

The PCA variance objects.

`dataset.var['soma_joinid']`

In R: dataset$var[["soma_joinid"]]

Type: vector, data type: int64, shape: 28024

If the dataset was retrieved from CELLxGENE census, this is a unique identifier for the feature.

`dataset.var['feature_id']`

In R: dataset$var[["feature_id"]]

Type: vector, data type: object, shape: 28024

Unique identifier for the feature, usually a ENSEMBL gene id.

`dataset.var['feature_name']`

In R: dataset$var[["feature_name"]]

Type: vector, data type: object, shape: 28024

A human-readable name for the feature, usually a gene symbol.

`dataset.var['hvg']`

In R: dataset$var[["hvg"]]

Type: vector, data type: bool, shape: 28024

Whether or not the feature is considered to be a ‘highly variable gene’

`dataset.var['hvg_score']`

In R: dataset$var[["hvg_score"]]

Type: vector, data type: float64, shape: 28024

A ranking of the features by hvg.

`dataset.varm['pca_loadings']`

In R: dataset$varm[["pca_loadings"]]

Type: densematrix, data type: float32, shape: 28024 × 50

The PCA loadings matrix.

References

Sikkema, Lisa, Ciro Ramírez-Suástegui, Daniel C. Strobl, Tessa E. Gillett, Luke Zappia, Elo Madissoon, Nikolay S. Markov, et al. 2023. “An Integrated Cell Atlas of the Lung in Health and Disease.” Nature Medicine 29 (6): 1563–77. https://doi.org/10.1038/s41591-023-02327-2.