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Companion Website for “Constructing and Using Cell Type Populations of the Human Reference Atlas”
Andreas Bueckle1*, Bruce W. Herr II1*, Lu Chen2, Daniel Bolin1, Danial Qaurooni1, Michael Ginda1, Yashcardhan Jain1, Aleix Puig Barbé 3,Kristin Ardlie4, Fusheng Wang2, Katy Börner1*
1 Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
2 Department of Computer Science and Department of Biomedical Informatics, Stony Brook University, Stony Brook, 11794, NY, USA
3 European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
4 Broad Institute, Cambridge, 02142, MA, USA
* Corresponding authors
abueckle@iu.edu
bherr@iu.edu
katy@iu.edu
Links
General
- Link to HuBMAP Publication page: https://portal.hubmapconsortium.org/browse/publication/f53d60b5994333777a446dd7ad3b0304
- Link to paper on bioRxiv (forthcoming)
- Link to GitHub repository for Supporting Information
- Link to HRA Portal
Portals
Code
Data
Interactive Sankey Diagrams
In total, as of HRApop v0.11.1, there are 11,817 datasets in the HRApop Universe (107 of which are sc-proteomics), and they cover 27 organs. 619 datasets make up the HRApop Atlas. 3680 datasets have an extraction site but no cell summary. Inversely, 5075 datasets have a cell summary but no extraction site. 2324 datasets have neither. The total number of non-atlas datasets is 11,198. The Sankey diagrams below offer an overview of HRApop Universe and Atlas provenance.
Explore the Sankey diagram for the HRApop Universe below (embedded) or here.
Explore the Sankey diagram for the HRApop Universe below (embedded) or here.
Usage Examples
A notebook to run the HRA Workflows Runner on Windows with Windows Subsystem for Linux (WSL) is provided at https://github.com/cns-iu/hra-pop-notebooks/blob/main/annotations/hra-workflows-runner-local-run.ipynb.
HRApop Universe Extraction Sites
Assigning a spatial location via the Registration User Interface (RUI, https://apps.humanatlas.io/rui) is an essential requirement for a dataset to be included in HRApop. Below is an instance of the Exploration User Interface (EUI, see federated version with all registered tissue blocks here) that only shows extraction sites for datasets in the HRApop Universe.
z-scores for CTs per organ and AS
- High-resolution versions of the heatmaps are available here.
- The code to generate these heatmaps (exported to HTML) is here.
- The R Markdown notebook is here.
CTann Tree
Step-by-step Instructions
Goal: get Mean B Expressions for a given CT in HRApop Atlas Datasets
-
When opening https://apps.humanatlas.io/api/grlc/hra-pop.html#get-/datasets-with-ct, the first item shown is the SPARQL query running when the endpoint is called:
-
Below, you can specify your request. The only mandatory field is the
celltype, which must be a Persistent URL (PURL). You can click the FILL EXAMPLE button to prefill this field withhttp://purl.obolibrary.org/obo/CL_0000136, which isadipocyte. Clickt the TRY button to run the query.
-
Then, the response area presents the result of the query, which consists of a table with one CT-B record per row. You may copy the results to your clipboard with the COPY button.
-
You can also click the tabs in the response area to get the
CURLcommand to run the query for the same results:
Exemplary Cell Summaries
For a Dataset
Shown is a snippet from a cell summary for a dataset in the small intestine. For clarity, we only show four CTs in this cell summary, all assigned by CellTypist, and we only show the top 1- Bs for the last CT (Tuft).
{
"@id": "https://entity.api.hubmapconsortium.org/entities/1628b6f7eb615862322d6274a6bc9fa0",
"@type": "Donor",
"samples": [
{
"@id": "https://entity.api.hubmapconsortium.org/entities/0b43d8d0dbbc5e3923a8b963650ab8e3",
"@type": "Sample",
"datasets": [],
"sections": [
{
"@id": "https://entity.api.hubmapconsortium.org/entities/35e16f13caab262f446836f63cf4ad42",
"@type": "Sample",
"datasets": [
{
"@id": "https://entity.api.hubmapconsortium.org/entities/3de525fe3e5718f297e8d62e037a042d",
"@type": "Dataset",
"link": "https://portal.hubmapconsortium.org/browse/dataset/3de525fe3e5718f297e8d62e037a042d",
"technology": "RNAseq",
"cell_count": "6000",
"gene_count": "60286",
"organ_id": "http://purl.obolibrary.org/obo/UBERON_0002108",
"label": "Registered 11/3/2023, HuBMAP Process, TMC-Stanford",
"description": "Dataset Type: RNAseq [Salmon]",
"thumbnail": "assets/icons/ico-unknown.svg",
"summaries": [
{
"@type": "CellSummary",
"annotation_method": "celltypist",
"modality": "sc_transcriptomics",
"summary": [
{
"cell_id": "ASCTB-TEMP:enterocyte",
"cell_label": "Enterocyte",
"gene_expr": [
...
],
"count": 3600,
"@type": "CellSummaryRow",
"percentage": 0.6
},
{
"cell_id": "ASCTB-TEMP:paneth",
"cell_label": "Paneth",
"gene_expr": [
...
],
"count": 265,
"@type": "CellSummaryRow",
"percentage": 0.04416666666666667
},
{
"cell_id": "ASCTB-TEMP:cycling-b-cell",
"cell_label": "Cycling B cell",
"gene_expr": [
...
],
"count": 43,
"@type": "CellSummaryRow",
"percentage": 0.007166666666666667
},
{
"cell_id": "ASCTB-TEMP:tuft",
"cell_label": "Tuft",
"gene_expr": [
{
"gene_id": "HGNC:29349",
"gene_label": "CCSER1",
"ensembl_id": "ENSG00000184305.15",
"mean_gene_expr_value": 3.573841094970703
},
{
"gene_id": "HGNC:18695",
"gene_label": "ST18",
"ensembl_id": "ENSG00000147488.11",
"mean_gene_expr_value": 2.0579261779785156
},
{
"gene_id": "HGNC:4036",
"gene_label": "FYB1",
"ensembl_id": "ENSG00000082074.18",
"mean_gene_expr_value": 2.106393337249756
},
{
"gene_id": "HGNC:10471",
"gene_label": "RUNX1",
"ensembl_id": "ENSG00000159216.19",
"mean_gene_expr_value": 2.0352487564086914
},
{
"gene_id": "HGNC:8783",
"gene_label": "PDE4D",
"ensembl_id": "ENSG00000113448.19",
"mean_gene_expr_value": 3.152188539505005
},
{
"gene_id": "HGNC:1079",
"gene_label": "BMX",
"ensembl_id": "ENSG00000102010.15",
"mean_gene_expr_value": 1.6486668586730957
},
{
"gene_id": "HGNC:13726",
"gene_label": "KMT2C",
"ensembl_id": "ENSG00000055609.19",
"mean_gene_expr_value": 2.2729785442352295
},
{
"gene_id": "HGNC:9066",
"gene_label": "PLCG2",
"ensembl_id": "ENSG00000197943.10",
"mean_gene_expr_value": 2.123337507247925
},
{
"gene_id": "HGNC:27363",
"gene_label": "ITPRID1",
"ensembl_id": "ENSG00000180347.13",
"mean_gene_expr_value": 1.7490202188491821
},
{
"gene_id": "HGNC:17890",
"gene_label": "HPGDS",
"ensembl_id": "ENSG00000163106.11",
"mean_gene_expr_value": 1.5961321592330933
}
],
"count": 41,
"@type": "CellSummaryRow",
"percentage": 0.006833333333333334
}
}
For an AS
Shown is a snippet from the AS Cell Summary of the cortex of kidney, assgined by Azimuth.
{
"@type": "CellSummary",
"sex": "Female",
"cell_source": "http://purl.obolibrary.org/obo/UBERON_0002189",
"cell_source_label": "outer cortex of kidney",
"annotation_method": "azimuth",
"aggregated_summary_count": 37,
"aggregated_summaries": [
{
"aggregated_cell_source": "https://entity.api.hubmapconsortium.org/entities/367fee3b40cba682063289505b922be1",
"percentage": 0.981
},
{
"aggregated_cell_source": "https://entity.api.hubmapconsortium.org/entities/434fbc55d458dc4e06da9ba4961f3840",
"percentage": 0.343
},
...],
"modality": "sc_transcriptomics",
"summary": [
{
"@type": "CellSummaryRow",
"cell_id": "CL:1000692",
"cell_label": "Fibroblast",
"count": 10336.100000000002,
"percentage": 0.01925307293655101
},
{
"@type": "CellSummaryRow",
"cell_id": "CL:1001108",
"cell_label": "Medullary Thick Ascending Limb",
"count": 26758.349000000002,
"percentage": 0.04984282707778434
},
{
"@type": "CellSummaryRow",
"cell_id": "CL:4030013",
"cell_label": "Descending Thin Limb Type 2",
"count": 31925.262000000002,
"percentage": 0.05946724565401847
}
...
}