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Companion Website for “Cell Type Populations for 3D Anatomical Structures of the Human Reference Atlas”

Andreas Bueckle¹*, Bruce W. Herr II¹*, Lu Chen², Daniel Bolin¹, Danial Qaurooni¹, Michael Ginda¹, Yashvardhan Jain¹, Aleix Puig Barbe 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

• Preprint on bioRxiv
• GitHub repository for Supporting Information
• HuBMAP Publication page with links to all HuBMAP datasets, tissue, blocks, and donors used for HRApop v1.0
• HRA Portal

Portals

• HuBMAP Portal
• SenNet Portal
• GTEx Portal
• CELLxGENE Portal

Code

• CTann Tool Containers
• DCTA Workflow
• RUI2CTpop Workflow

Data

• HRApop graph data on HRA LOD server

Figures

Figure C1. Mean scores for cell types (x-axis) from sc-transcriptomics datasets across organs and AS (y-axis) for (a) Azimuth, (b) CellTypist, and (c) popV.

Figure C2. Mean scores for cell types (x-axis) from sc-proteomics datasets across organs and AS (y-axis).

Usage examples

Accessing HRApop data via HRA API

A Jupyter Notebook detailing easy access to cell type populations for AS, extraction sites, and datasets is available at https://github.com/cns-iu/hra-cell-type-populations-supporting-information/blob/main/notebooks/hra-pop-grlc-queries.ipynb.

Visualizing Cell Type Populations for AS, ES, and Datasets

The HRApop Visualizer enables users to visualize stacked bar graphs for AS, ES, and Datasets, separated by sex and CTann tool. A video tutorial is available on YouTube and embedded below:

Step-by-step instructions

Goal: get mean biomarker expressions for a given CT in HRApop Atlas Datasets

1. 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:

2. 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 with http://purl.obolibrary.org/obo/CL_0000136, which is adipocyte. Clickt the TRY button to run the query.

3. 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.

4. You can also click the tabs in the response area to get the CURL command to run the query for the same results:

Interactive Sankey diagrams

In total, as of HRApop v1.0, there are 16,293 datasets in the HRApop Universe (558 of which are sc-transcriptomics and 104 of which are sc-proteomics), and they cover 49 organs. 662 datasets make up the HRApop Atlas. 5,672 datasets have an extraction site but no cell type population. Inversely, 6,395 datasets have a cell type population but no extraction site. 3,564 datasets have neither. The total number of non-atlas datasets is 15,631. 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 Input for the RUI2CTpop Workflow below (embedded) or here.

HRApop Atlas Data 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. Here is an instance of the Exploration User Interface that only shows extraction sites for HRApop Atlas Data. And here is the federated version with all registered tissue blocks.

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.

Exemplary corridor

Exemplary cell type populations

For a dataset

Shown is a snippet from a cell type population for a dataset in the small intestine, taken from a Dataset and Extraction Site Cell Type Population (DESpop). For clarity, we only show four CTs in this cell type population, all assigned by CellTypist, and we only show the top 10 Bs one 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 extraction site

Shown is a cell type population for an extraction site, taken from a Dataset and Extraction Site Cell Type Population (DESpop). All mesh-based collisions are listed in the all_collisions field. The corresponding corridor is described and linked in the corridor field. The summaries key contains the cell type population.

"rui_location": {
      "@context": "https://hubmapconsortium.github.io/ccf-ontology/ccf-context.jsonld",
      "@id": "http://purl.org/ccf/1.5/e240c0a4-5e53-4464-8320-ad775f2c4bf7",
      "@type": "SpatialEntity",
      "ccf_annotations": [
       "http://purl.obolibrary.org/obo/UBERON_0002115",
       "http://purl.obolibrary.org/obo/UBERON_0002116"
      ],
      "creation_date": "2022-02-16",
      "creator": "Yiing Lin",
      "creator_first_name": "Yiing",
      "creator_last_name": "Lin",
      "dimension_units": "millimeter",
      "placement": {
       "@context": "https://hubmapconsortium.github.io/hubmap-ontology/ccf-context.jsonld",
       "@id": "http://purl.org/ccf/1.5/e240c0a4-5e53-4464-8320-ad775f2c4bf7_placement",
       "@type": "SpatialPlacement",
       "placement_date": "2022-02-16",
       "rotation_order": "XYZ",
       "rotation_units": "degree",
       "scaling_units": "ratio",
       "target": "http://purl.org/ccf/latest/ccf.owl#VHFSmallIntestine",
       "translation_units": "millimeter",
       "x_rotation": 0,
       "x_scaling": 1,
       "x_translation": 130.806,
       "y_rotation": 0,
       "y_scaling": 1,
       "y_translation": 111.09,
       "z_rotation": 86,
       "z_scaling": 1,
       "z_translation": 54.023
      },
      "x_dimension": 3,
      "y_dimension": 30,
      "z_dimension": 15,
      "all_collisions": [
       {
        "@type": "CollisionSummary",
        "collision_method": "MESH",
        "collisions": [
         {
          "@type": "CollisionItem",
          "reference_organ": "http://purl.org/ccf/latest/ccf.owl#VHFSmallIntestine",
          "as_3d_id": "https://purl.humanatlas.io/ref-organ/small-intestine-female/v1.2#VH_F_jejenum",
          "as_id": "http://purl.obolibrary.org/obo/UBERON_0002115",
          "as_label": "jejunum",
          "as_volume": 28523.456808180017,
          "percentage": 0.103
         }
        ]
       }
      ],
      "corridor": {
       "@type": "Corridor",
       "file_format": "model/gltf-binary",
       "file": "https://cdn.humanatlas.io/digital-objects/graph/hra-pop/v1.0/assets/corridors/e240c0a4-5e53-4464-8320-ad775f2c4bf7.glb"
      },
      "summaries": [
       {
        "@type": "CellSummary",
        "sex": "Female",
        "annotation_method": "celltypist",
        "aggregated_summary_count": 1,
        "aggregated_summaries": [
         {
          "aggregated_cell_source": "https://entity.api.hubmapconsortium.org/entities/3de525fe3e5718f297e8d62e037a042d",
          "percentage": 1
         }
        ],
        "modality": "sc_transcriptomics",
        "summary": [
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:enterocyte",
          "cell_label": "Enterocyte",
          "count": 3598,
          "percentage": 0.5996666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:paneth",
          "cell_label": "Paneth",
          "count": 265,
          "percentage": 0.04416666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:cycling-b-cell",
          "cell_label": "Cycling B cell",
          "count": 43,
          "percentage": 0.007166666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:tuft",
          "cell_label": "Tuft",
          "count": 41,
          "percentage": 0.006833333333333334
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:trgv2-gdt",
          "cell_label": "TRGV2 gdT",
          "count": 120,
          "percentage": 0.02
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stem-cells",
          "cell_label": "Stem cells",
          "count": 110,
          "percentage": 0.018333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:best4-epithelial",
          "cell_label": "BEST4+ epithelial",
          "count": 124,
          "percentage": 0.020666666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:goblet-cell",
          "cell_label": "Goblet cell",
          "count": 289,
          "percentage": 0.04816666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:myofibroblast",
          "cell_label": "myofibroblast",
          "count": 57,
          "percentage": 0.0095
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:eecs",
          "cell_label": "EECs",
          "count": 251,
          "percentage": 0.041833333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:activated-t",
          "cell_label": "Activated T",
          "count": 47,
          "percentage": 0.007833333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mature-arterial-ec",
          "cell_label": "Mature arterial EC",
          "count": 11,
          "percentage": 0.0018333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:branch-a1-imn-",
          "cell_label": "Branch A1 (iMN)",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:memory-b",
          "cell_label": "Memory B",
          "count": 13,
          "percentage": 0.0021666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mesoderm-1-hand1-",
          "cell_label": "Mesoderm 1 (HAND1+)",
          "count": 5,
          "percentage": 0.0008333333333333334
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stat1-naive-b",
          "cell_label": "STAT1+ Naive B",
          "count": 21,
          "percentage": 0.0035
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:microfold-cell",
          "cell_label": "Microfold cell",
          "count": 198,
          "percentage": 0.033
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:proximal-progenitor",
          "cell_label": "Proximal progenitor",
          "count": 106,
          "percentage": 0.017666666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stromal-1-ccl11-",
          "cell_label": "Stromal 1 (CCL11+)",
          "count": 23,
          "percentage": 0.003833333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:branch-b1-emn-",
          "cell_label": "Branch B1 (eMN)",
          "count": 31,
          "percentage": 0.005166666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stromal-2-npy-",
          "cell_label": "Stromal 2 (NPY+)",
          "count": 12,
          "percentage": 0.002
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:ec-cells-tac1-",
          "cell_label": "EC cells (TAC1+)",
          "count": 20,
          "percentage": 0.0033333333333333335
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:i-cells-cck-",
          "cell_label": "I cells (CCK+)",
          "count": 26,
          "percentage": 0.004333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:smc-part1-capn3-",
          "cell_label": "SMC (PART1/CAPN3+)",
          "count": 6,
          "percentage": 0.001
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:arterial-capillary",
          "cell_label": "arterial capillary",
          "count": 30,
          "percentage": 0.005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lyve1-macrophage",
          "cell_label": "LYVE1+ Macrophage",
          "count": 18,
          "percentage": 0.003
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:m-x-cells-mln-ghrl-",
          "cell_label": "M/X cells (MLN/GHRL+)",
          "count": 12,
          "percentage": 0.002
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:tfh",
          "cell_label": "Tfh",
          "count": 33,
          "percentage": 0.0055
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stromal-3-kcnn3-",
          "cell_label": "Stromal 3 (KCNN3+)",
          "count": 18,
          "percentage": 0.003
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mlto",
          "cell_label": "mLTo",
          "count": 5,
          "percentage": 0.0008333333333333334
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lec6-adamts4-",
          "cell_label": "LEC6 (ADAMTS4+)",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:glia-1-dhh-",
          "cell_label": "Glia 1 (DHH+)",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:cycling-ec",
          "cell_label": "cycling EC",
          "count": 20,
          "percentage": 0.0033333333333333335
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:d-cells-sst-",
          "cell_label": "D cells (SST+)",
          "count": 10,
          "percentage": 0.0016666666666666668
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:myofibroblast-rspo2-",
          "cell_label": "myofibroblast (RSPO2+)",
          "count": 30,
          "percentage": 0.005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:contractile-pericyte-pln-",
          "cell_label": "Contractile pericyte (PLN+)",
          "count": 20,
          "percentage": 0.0033333333333333335
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:t-reticular",
          "cell_label": "T reticular",
          "count": 5,
          "percentage": 0.0008333333333333334
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:colonocyte",
          "cell_label": "Colonocyte",
          "count": 4,
          "percentage": 0.0006666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:cd8-tmem",
          "cell_label": "CD8 Tmem",
          "count": 7,
          "percentage": 0.0011666666666666668
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:cycling-plasma-cell",
          "cell_label": "Cycling plasma cell",
          "count": 28,
          "percentage": 0.004666666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lec4-stab2-",
          "cell_label": "LEC4 (STAB2+)",
          "count": 10,
          "percentage": 0.0016666666666666668
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:dz-gc-cell",
          "cell_label": "DZ GC cell",
          "count": 16,
          "percentage": 0.0026666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:angiogenic-pericyte",
          "cell_label": "angiogenic pericyte",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:fdc",
          "cell_label": "FDC",
          "count": 4,
          "percentage": 0.0006666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stromal-3-c7-",
          "cell_label": "Stromal 3 (C7+)",
          "count": 13,
          "percentage": 0.0021666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:progenitor-neurog3-",
          "cell_label": "Progenitor (NEUROG3+)",
          "count": 12,
          "percentage": 0.002
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:pdc",
          "cell_label": "pDC",
          "count": 5,
          "percentage": 0.0008333333333333334
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mature-venous-ec",
          "cell_label": "Mature venous EC",
          "count": 21,
          "percentage": 0.0035
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lti-like-ncr-ilc3",
          "cell_label": "LTi-like NCR- ILC3",
          "count": 6,
          "percentage": 0.001
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mait-cell",
          "cell_label": "MAIT cell",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:trdv2-trgv9-gdt",
          "cell_label": "TRDV2/TRGV9 gdT",
          "count": 19,
          "percentage": 0.0031666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:nk-cell",
          "cell_label": "NK cell",
          "count": 25,
          "percentage": 0.004166666666666667
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:glia-3-bcan-",
          "cell_label": "Glia 3 (BCAN+)",
          "count": 7,
          "percentage": 0.0011666666666666668
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:activated-cd8-t",
          "cell_label": "Activated CD8 T",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:neuroblast",
          "cell_label": "Neuroblast",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:distal-progenitor",
          "cell_label": "Distal progenitor",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:macrophages",
          "cell_label": "Macrophages",
          "count": 15,
          "percentage": 0.0025
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mast-cell",
          "cell_label": "Mast cell",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:trgv4-gdt",
          "cell_label": "TRGV4 gdT",
          "count": 22,
          "percentage": 0.0036666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:icc",
          "cell_label": "ICC",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:k-cells-gip-",
          "cell_label": "K cells (GIP+)",
          "count": 8,
          "percentage": 0.0013333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:pre-b",
          "cell_label": "Pre-B",
          "count": 7,
          "percentage": 0.0011666666666666668
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:l-cells-pyy-",
          "cell_label": "L cells (PYY+)",
          "count": 11,
          "percentage": 0.0018333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:smc-plpp2-",
          "cell_label": "SMC (PLPP2+)",
          "count": 16,
          "percentage": 0.0026666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:adult-glia",
          "cell_label": "Adult Glia",
          "count": 10,
          "percentage": 0.0016666666666666668
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:th1",
          "cell_label": "Th1",
          "count": 4,
          "percentage": 0.0006666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:branch-b3-ipan-",
          "cell_label": "Branch B3 (IPAN)",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:ta",
          "cell_label": "TA",
          "count": 13,
          "percentage": 0.0021666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:sell-cd4-t",
          "cell_label": "SELL+ CD4 T",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:branch-a2-ipan-in-",
          "cell_label": "Branch A2 (IPAN/IN)",
          "count": 8,
          "percentage": 0.0013333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:immature-pericyte",
          "cell_label": "Immature pericyte",
          "count": 4,
          "percentage": 0.0006666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:clp",
          "cell_label": "CLP",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:cycling-stromal",
          "cell_label": "cycling stromal",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:transitional-stromal-3-c3-",
          "cell_label": "Transitional Stromal 3 (C3+)",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:branch-a4-in-",
          "cell_label": "Branch A4 (IN)",
          "count": 5,
          "percentage": 0.0008333333333333334
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lec1-ackr4-",
          "cell_label": "LEC1 (ACKR4+)",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lec3-adgrg3-",
          "cell_label": "LEC3 (ADGRG3+)",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:monocytes",
          "cell_label": "Monocytes",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:sell-cd8-t",
          "cell_label": "SELL+ CD8 T",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:-cells-ins-",
          "cell_label": "β cells (INS+)",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mesothelium-rgs5-",
          "cell_label": "Mesothelium (RGS5+)",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:nk-t-cell",
          "cell_label": "NK T cell",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:activated-cd4-t",
          "cell_label": "Activated CD4 T",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:pericyte",
          "cell_label": "Pericyte",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:fetal-venous-ec",
          "cell_label": "Fetal venous EC",
          "count": 4,
          "percentage": 0.0006666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:fcrl4-memory-b",
          "cell_label": "FCRL4+ Memory B",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:cdc1",
          "cell_label": "cDC1",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lz-gc-cell",
          "cell_label": "LZ GC cell",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:gc-b-cell",
          "cell_label": "GC B cell",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:venous-capillary",
          "cell_label": "venous capillary",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:cldn10-cells",
          "cell_label": "CLDN10+ cells",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lymphoid-dc",
          "cell_label": "Lymphoid DC",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:mmp9-inflammatory-macrophage",
          "cell_label": "MMP9+ Inflammatory macrophage",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:pro-b",
          "cell_label": "Pro-B",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:branch-b2-emn-",
          "cell_label": "Branch B2 (eMN)",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:naive-b",
          "cell_label": "Naive B",
          "count": 3,
          "percentage": 0.0005
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:treg",
          "cell_label": "Treg",
          "count": 2,
          "percentage": 0.0003333333333333333
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stromal-2-ch25h-",
          "cell_label": "Stromal 2 (CH25H+)",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:best2-goblet-cell",
          "cell_label": "BEST2+ Goblet cell",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:lec2-madcam1-",
          "cell_label": "LEC2 (MADCAM1+)",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:ilc2",
          "cell_label": "ILC2",
          "count": 1,
          "percentage": 0.00016666666666666666
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "ASCTB-TEMP:stromal-1-adamdec1-",
          "cell_label": "Stromal 1 (ADAMDEC1+)",
          "count": 1,
          "percentage": 0.00016666666666666666
         }
        ]
       },
       {
        "@type": "CellSummary",
        "sex": "Female",
        "annotation_method": "popv",
        "aggregated_summary_count": 1,
        "aggregated_summaries": [
         {
          "aggregated_cell_source": "https://entity.api.hubmapconsortium.org/entities/3de525fe3e5718f297e8d62e037a042d",
          "percentage": 1
         }
        ],
        "modality": "sc_transcriptomics",
        "summary": [
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:1000334",
          "cell_label": "enterocyte of epithelium of small intestine",
          "count": 5408,
          "percentage": 0.9016338779593198
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:1000343",
          "cell_label": "paneth cell of epithelium of small intestine",
          "count": 192,
          "percentage": 0.032010670223407804
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:1000495",
          "cell_label": "small intestine goblet cell",
          "count": 215,
          "percentage": 0.035845281760586864
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0009006",
          "cell_label": "intestinal enteroendocrine cell",
          "count": 44,
          "percentage": 0.007335778592864288
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0009012",
          "cell_label": "transit amplifying cell of small intestine",
          "count": 10,
          "percentage": 0.0016672224074691564
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0009080",
          "cell_label": "intestinal tuft cell",
          "count": 26,
          "percentage": 0.004334778259419807
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0000057",
          "cell_label": "fibroblast",
          "count": 41,
          "percentage": 0.006835611870623541
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0000131",
          "cell_label": "gut endothelial cell",
          "count": 14,
          "percentage": 0.002334111370456819
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0000775",
          "cell_label": "neutrophil",
          "count": 38,
          "percentage": 0.006335445148382794
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0000624",
          "cell_label": "CD4-positive, alpha-beta T cell",
          "count": 1,
          "percentage": 0.00016672224074691563
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0000625",
          "cell_label": "CD8-positive, alpha-beta T cell",
          "count": 6,
          "percentage": 0.0010003334444814939
         },
         {
          "@type": "CellSummaryRow",
          "cell_id": "CL:0000786",
          "cell_label": "plasma cell",
          "count": 3,
          "percentage": 0.0005001667222407469
         }
        ]
       }
      ]
     }

For an AS

Shown is a snippet from the AS Cell Type Population of the cortex of kidney, assigned by Azimuth, taken from a AS Cell Type Population (ASpop).

  {
      "@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
        }
        ...
	}

Dataset counts

as_label_organ	tool	sex	dataset
Set of lactiferous glands in left breast - Interlobar adipose tissue of left mammary gland	popv	Female	2
Set of lactiferous glands in left breast - main lactiferous duct	popv	Female	2
Set of lactiferous glands in left breast - mammary lobe	popv	Female	2
Set of lactiferous glands in right breast - Interlobar adipose tissue of right mammary gland	popv	Female	3
Set of lactiferous glands in right breast - main lactiferous duct	popv	Female	3
heart - Posteromedial head of posterior papillary muscle of left ventricle	azimuth	Female	6
heart - Posteromedial head of posterior papillary muscle of left ventricle	celltypist	Female	6
heart - heart left ventricle	azimuth	Female	28
heart - heart left ventricle	azimuth	Male	37
heart - heart left ventricle	celltypist	Female	28
heart - heart left ventricle	celltypist	Male	37
heart - heart right ventricle	azimuth	Female	14
heart - heart right ventricle	azimuth	Male	16
heart - heart right ventricle	celltypist	Female	14
heart - heart right ventricle	celltypist	Male	16
heart - interventricular septum	azimuth	Female	7
heart - interventricular septum	azimuth	Male	8
heart - interventricular septum	celltypist	Female	7
heart - interventricular septum	celltypist	Male	8
heart - left cardiac atrium	azimuth	Female	7
heart - left cardiac atrium	azimuth	Male	7
heart - left cardiac atrium	celltypist	Female	7
heart - left cardiac atrium	celltypist	Male	7
heart - right cardiac atrium	azimuth	Female	9
heart - right cardiac atrium	azimuth	Male	8
heart - right cardiac atrium	celltypist	Female	9
heart - right cardiac atrium	celltypist	Male	8
large intestine - ascending colon	celltypist	Female	6
large intestine - ascending colon	celltypist	Male	8
large intestine - ascending colon	popv	Female	6
large intestine - ascending colon	popv	Male	8
large intestine - caecum	celltypist	Female	3
large intestine - caecum	celltypist	Male	1
large intestine - caecum	popv	Female	3
large intestine - caecum	popv	Male	1
large intestine - descending colon	celltypist	Female	4
large intestine - descending colon	celltypist	Male	7
large intestine - descending colon	popv	Female	4
large intestine - descending colon	popv	Male	7
large intestine - hepatic flexure of colon	celltypist	Female	3
large intestine - hepatic flexure of colon	celltypist	Male	1
large intestine - hepatic flexure of colon	popv	Female	3
large intestine - hepatic flexure of colon	popv	Male	1
large intestine - rectum	celltypist	Female	3
large intestine - rectum	popv	Female	3
large intestine - sigmoid colon	celltypist	Female	7
large intestine - sigmoid colon	celltypist	Male	8
large intestine - sigmoid colon	popv	Female	7
large intestine - sigmoid colon	popv	Male	8
large intestine - transverse colon	celltypist	Female	3
large intestine - transverse colon	celltypist	Male	5
large intestine - transverse colon	popv	Female	3
large intestine - transverse colon	popv	Male	5
left kidney - hilum of kidney	azimuth	Male	2
left kidney - kidney capsule	azimuth	Female	3
left kidney - kidney capsule	azimuth	Male	2
left kidney - outer cortex of kidney	azimuth	Female	17
left kidney - outer cortex of kidney	azimuth	Male	19
left kidney - renal column	azimuth	Female	10
left kidney - renal column	azimuth	Male	2
left kidney - renal papilla	azimuth	Female	5
left kidney - renal pyramid	azimuth	Female	37
left kidney - renal pyramid	azimuth	Male	31
left ureter - Left ureter	azimuth	Female	4
left ureter - Left ureter	azimuth	Male	8
liver - capsule of the liver	celltypist	Female	1
liver - capsule of the liver	celltypist	Male	1
liver - capsule of the liver	popv	Female	1
liver - capsule of the liver	popv	Male	1
liver - diaphragmatic surface of liver	celltypist	Female	1
liver - diaphragmatic surface of liver	celltypist	Male	1
liver - diaphragmatic surface of liver	popv	Female	1
liver - diaphragmatic surface of liver	popv	Male	1
liver - gastric impression of liver	celltypist	Female	1
liver - gastric impression of liver	celltypist	Male	1
liver - gastric impression of liver	popv	Female	1
liver - gastric impression of liver	popv	Male	1
male reproductive system - Verumontanum	popv	Male	2
male reproductive system - apex of prostate	popv	Male	2
male reproductive system - central zone of prostate	popv	Male	6
male reproductive system - peripheral zone of prostate	popv	Male	6
male reproductive system - seminal vesicle	popv	Male	2
male reproductive system - transition zone of prostate	popv	Male	2
pancreas - Neck of pancreas	azimuth	Female	1
pancreas - Neck of pancreas	azimuth	Male	1
pancreas - Neck of pancreas	celltypist	Female	1
pancreas - Neck of pancreas	celltypist	Male	1
pancreas - Neck of pancreas	popv	Female	1
pancreas - Neck of pancreas	popv	Male	1
pancreas - body of pancreas	azimuth	Female	1
pancreas - body of pancreas	azimuth	Male	1
pancreas - body of pancreas	celltypist	Female	1
pancreas - body of pancreas	celltypist	Male	1
pancreas - body of pancreas	popv	Female	1
pancreas - body of pancreas	popv	Male	1
pancreas - head of pancreas	azimuth	Female	1
pancreas - head of pancreas	azimuth	Male	1
pancreas - head of pancreas	celltypist	Female	1
pancreas - head of pancreas	celltypist	Male	1
pancreas - head of pancreas	popv	Female	1
pancreas - head of pancreas	popv	Male	1
pancreas - tail of pancreas	azimuth	Female	1
pancreas - tail of pancreas	azimuth	Male	1
pancreas - tail of pancreas	celltypist	Female	1
pancreas - tail of pancreas	celltypist	Male	1
pancreas - tail of pancreas	popv	Female	1
pancreas - tail of pancreas	popv	Male	1
pancreas - uncinate process of pancreas	azimuth	Female	1
pancreas - uncinate process of pancreas	azimuth	Male	1
pancreas - uncinate process of pancreas	celltypist	Female	1
pancreas - uncinate process of pancreas	celltypist	Male	1
pancreas - uncinate process of pancreas	popv	Female	1
pancreas - uncinate process of pancreas	popv	Male	1
respiratory system - Cartilage of segmental bronchus	azimuth	Female	1
respiratory system - Cartilage of segmental bronchus	azimuth	Male	4
respiratory system - Cartilage of segmental bronchus	celltypist	Female	1
respiratory system - Cartilage of segmental bronchus	celltypist	Male	4
respiratory system - Cartilage of segmental bronchus	popv	Female	1
respiratory system - Cartilage of segmental bronchus	popv	Male	4
respiratory system - Lateral segmental bronchus	azimuth	Female	1
respiratory system - Lateral segmental bronchus	azimuth	Male	2
respiratory system - Lateral segmental bronchus	celltypist	Female	1
respiratory system - Lateral segmental bronchus	celltypist	Male	2
respiratory system - Lateral segmental bronchus	popv	Female	1
respiratory system - Lateral segmental bronchus	popv	Male	2
respiratory system - Left Medial Basal Bronchopulmonary Segment	azimuth	Male	1
respiratory system - Left Medial Basal Bronchopulmonary Segment	celltypist	Male	1
respiratory system - Left Medial Basal Bronchopulmonary Segment	popv	Male	1
respiratory system - Left anterior segmental bronchus	azimuth	Male	1
respiratory system - Left anterior segmental bronchus	celltypist	Male	1
respiratory system - Left anterior segmental bronchus	popv	Male	1
respiratory system - Left apical segmental bronchus	azimuth	Male	1
respiratory system - Left apical segmental bronchus	celltypist	Male	1
respiratory system - Left apical segmental bronchus	popv	Male	1
respiratory system - Left lateral basal segmental bronchus	azimuth	Male	1
respiratory system - Left lateral basal segmental bronchus	celltypist	Male	1
respiratory system - Left lateral basal segmental bronchus	popv	Male	1
respiratory system - Left medial basal segmental bronchus	azimuth	Male	1
respiratory system - Left medial basal segmental bronchus	celltypist	Male	1
respiratory system - Left medial basal segmental bronchus	popv	Male	1
respiratory system - Left posterior basal segmental bronchus	azimuth	Female	8
respiratory system - Left posterior basal segmental bronchus	azimuth	Male	21
respiratory system - Left posterior basal segmental bronchus	celltypist	Female	8
respiratory system - Left posterior basal segmental bronchus	celltypist	Male	21
respiratory system - Left posterior basal segmental bronchus	popv	Female	8
respiratory system - Left posterior basal segmental bronchus	popv	Male	21
respiratory system - Left posterior bronchopulmonary segment	azimuth	Male	1
respiratory system - Left posterior bronchopulmonary segment	celltypist	Male	1
respiratory system - Left posterior bronchopulmonary segment	popv	Male	1
respiratory system - Right Anterior Bronchopulmonary Segment	azimuth	Female	1
respiratory system - Right Anterior Bronchopulmonary Segment	celltypist	Female	1
respiratory system - Right Anterior Bronchopulmonary Segment	popv	Female	1
respiratory system - Right Lateral Bronchopulmonary Segment	azimuth	Male	3
respiratory system - Right Lateral Bronchopulmonary Segment	celltypist	Male	3
respiratory system - Right Lateral Bronchopulmonary Segment	popv	Male	3
respiratory system - Right Medial Bronchopulmonary Segment	azimuth	Male	8
respiratory system - Right Medial Bronchopulmonary Segment	celltypist	Male	8
respiratory system - Right Medial Bronchopulmonary Segment	popv	Male	8
respiratory system - Right Posterior Basal Bronchopulmonary Segment	azimuth	Female	7
respiratory system - Right Posterior Basal Bronchopulmonary Segment	azimuth	Male	9
respiratory system - Right Posterior Basal Bronchopulmonary Segment	celltypist	Female	7
respiratory system - Right Posterior Basal Bronchopulmonary Segment	celltypist	Male	9
respiratory system - Right Posterior Basal Bronchopulmonary Segment	popv	Female	7
respiratory system - Right Posterior Basal Bronchopulmonary Segment	popv	Male	9
respiratory system - Right anterior basal bronchopulmonary segment	azimuth	Male	1
respiratory system - Right anterior basal bronchopulmonary segment	celltypist	Male	1
respiratory system - Right anterior basal bronchopulmonary segment	popv	Male	1
respiratory system - Right superior segmental bronchus	azimuth	Male	1
respiratory system - Right superior segmental bronchus	celltypist	Male	1
respiratory system - Right superior segmental bronchus	popv	Male	1
respiratory system - Superior lingular bronchopulmonary segment	azimuth	Female	1
respiratory system - Superior lingular bronchopulmonary segment	celltypist	Female	1
respiratory system - Superior lingular bronchopulmonary segment	popv	Female	1
respiratory system - left Lateral Basal Bronchopulmonary Segment	azimuth	Male	1
respiratory system - left Lateral Basal Bronchopulmonary Segment	celltypist	Male	1
respiratory system - left Lateral Basal Bronchopulmonary Segment	popv	Male	1
respiratory system - left anterior basal bronchopulmonary segment	azimuth	Male	1
respiratory system - left anterior basal bronchopulmonary segment	celltypist	Male	1
respiratory system - left anterior basal bronchopulmonary segment	popv	Male	1
right kidney - kidney capsule	azimuth	Female	2
right kidney - outer cortex of kidney	azimuth	Female	5
right kidney - outer cortex of kidney	azimuth	Male	75
right kidney - renal papilla	azimuth	Female	2
right kidney - renal papilla	azimuth	Male	2
right kidney - renal pyramid	azimuth	Female	13
right kidney - renal pyramid	azimuth	Male	4
right ureter - Right ureter	azimuth	Female	1
right ureter - Right ureter	azimuth	Male	2
skin of body - skin	celltypist	Female	1
skin of body - skin	celltypist	Male	6
skin of body - skin	popv	Female	1
skin of body - skin	popv	Male	6
small intestine - ascending part of duodenum	celltypist	Female	3
small intestine - ascending part of duodenum	celltypist	Male	8
small intestine - ascending part of duodenum	popv	Female	3
small intestine - ascending part of duodenum	popv	Male	8
small intestine - descending part of duodenum	celltypist	Female	4
small intestine - descending part of duodenum	celltypist	Male	7
small intestine - descending part of duodenum	popv	Female	4
small intestine - descending part of duodenum	popv	Male	7
small intestine - distal part of ileum	celltypist	Female	3
small intestine - distal part of ileum	celltypist	Male	7
small intestine - distal part of ileum	popv	Female	3
small intestine - distal part of ileum	popv	Male	7
small intestine - duodenal ampulla	celltypist	Female	2
small intestine - duodenal ampulla	popv	Female	2
small intestine - horizontal part of duodenum	celltypist	Female	3
small intestine - horizontal part of duodenum	celltypist	Male	7
small intestine - horizontal part of duodenum	popv	Female	3
small intestine - horizontal part of duodenum	popv	Male	7
small intestine - ileum	celltypist	Female	5
small intestine - ileum	celltypist	Male	1
small intestine - ileum	popv	Female	5
small intestine - ileum	popv	Male	1
small intestine - jejunum	celltypist	Female	4
small intestine - jejunum	celltypist	Male	8
small intestine - jejunum	popv	Female	4
small intestine - jejunum	popv	Male	8
small intestine - superior part of duodenum	celltypist	Female	2
small intestine - superior part of duodenum	celltypist	Male	1
small intestine - superior part of duodenum	popv	Female	2
small intestine - superior part of duodenum	popv	Male	1
spleen - diaphragmatic surface of spleen	popv	Male	6
spleen - hilum of spleen	popv	Female	2
spleen - hilum of spleen	popv	Male	2
thymus - left thymus lobe	popv	Female	2
thymus - left thymus lobe	popv	Male	2
thymus - right thymus lobe	popv	Female	2
thymus - right thymus lobe	popv	Male	2
urinary bladder - fundus of urinary bladder	popv	Female	2
urinary bladder - fundus of urinary bladder	popv	Male	5
urinary bladder - trigone of urinary bladder	popv	Male	4

Outlook

To improve coverage and quality of HRApop, the following steps are planned:

Long-term sustainability: The HRA and, by extension, HRApop is currently funded via the HuBMAP, SenNet, KPMP, Common Fund Data Ecosystem (CFDE), GTEx, and NIDDK. Funding that has been acquired since HRApop v1.0 was released comes via the Whole Person Reference Physiome Research and Coordination Center (WPP, 1U24AT013504-01), the Canadian Institute for Advanced Research (CIFAR) MacMillan Multiscale Human (cifar.ca/research-programs/cifar-macmillan-multiscale-human), and the Stiftung Charité via Berlin Institute of Health at Charité (BIH). This funding supports regular HRApop releases, with data products made available via Zenodo¹ and the HRA KG² (lod.humanatlas.io/graph/hra-pop).

Increase number of RUI registered datasets: As of January 2026, the HuBMAP and SenNet portals list 908 and 172 datasets with 3D extraction sites that are currently in QA/QC status but will be published soon. Outreach efforts to authors of peer-reviewed, published papers are ongoing to register their data for use in the DCTA Workflow. The HRApop effort will also integrate data from Tabula Sapiens³, KPMP, the Helmsley Gut Cell Atlas⁴, and the Deeply Integrated human Single-Cell Omics (DISCO) database⁵, which has a total of 21,330 datasets, out of which 32.8% of the total data is from a healthy human body, across 166 unique ASs. Other potential sources for high-quality datasets have been captured in Hemberg et al.’s recent article on large cell atlases⁶.

Scale up tissue registration via millitomes: A millitome⁷ (from Latin mille, meaning “thousand,” and the Greek temnein, meaning “to cut”) is a device designed to hold a freshly procured organ and facilitate cutting it into many small tissue blocks of well defined size for usage in sc-analysis and HRA construction. It is used to produce uniformly sized slices or cubes of tissue material that can be registered to 3D reference objects. Using a millitome improves efficiency by enabling consistent, high-throughput sampling. Recently, 209 brain tissue blocks have been added and will be included in the next HRApop run after the 10th HRA release.

Improve generalizability: The 104 sc-proteomics datasets in HRApop v1.0 were presented as a generalization from sc-transcriptomics datasets. In the future, and in synergy with HRA Vasculature Common Coordinate Framework (VCCF) construction efforts^8,9 around endothelial cell environments¹⁰, more CODEX¹¹ datasets and new modalities, such as the Spatial Multiomics Single-Cell Imaging platform CosMx¹², will be added to HRApop. A recent paper¹⁰ analyzed 399 spatially resolved omics datasets from 14 studies comprising 12 tissue types with a total of 47,349,496.

Increase number of CTann tools used to enable more benchmarking: Currently, HRApop uses three well-established CTann tools backed by scientific publications describing the methods, results, and validations for each tool. Results are presented as CT populations by CTann tool—users can pick their favorite tool and data or perform comparisons and benchmarks between CTann tools¹³. Future HRA releases will feature additional CTann tools such as FR-Match¹⁴ and Pan-Human Azimuth (satijalab.org/pan_human_azimuth) in support of improved cell type annotation, CTann tool comparisons and benchmarking.

Add biomarker sets: For HRApop v1.0, the top biomarkers per CT per dataset were computed using scanpy’s rank_gene_groups() method (scanpy.readthedocs.io/en/stable/generated/scanpy.tl.rank_genes_groups.html). In future HRApop releases, additional sets of top biomarkers will be provided to the user by running, e.g., NS-Forest¹⁵ during the annotation phase of the DCTA.

Decrease run time for HRApop code: As explained in the manuscript, for HRApop v1.0, the DCTA Workflow started on Thu, May 15, 2025, ran for about 10 days, and finished on Sunday, May 25, 2025. It averaged 87.63 dataset annotation runs per hour. Annotations took about 8.59 days to finish. This long runtime is primarily due to the complexity of the annotation pipeline, including annotation, crosswalking, and mean gene expression per cell type, to cover over 10,000 datasets and tens of millions of cells. Targeted optimization of the algorithms and workflows combined with more hardware resources and re-using annotations from prior runs will be required to reduce runtime. Work is underway to save annotations between runs to skip the re-annotation step. After a 22-day QA phase, the RUI2CTpop Workflow started on June 16 at 5:55:27 PM EDT and finished about four hours later at 10:07:11 PM EDT the same day. A full log is linked in Table S1. In the future, the run time for the DCTA Workflow will be decreased by using high performance computing (HPC), e.g., Big Red at Indiana University (kb.iu.edu/d/brcc). Also, the crosswalking will be moved to the RUI2CTpop Workflow, which will decrease runtime and increase the modularity of both workflows.

References

1. Bueckle, A., Herr II, B. W. & Börner, K. HRApop v1.0. Zenodo https://doi.org/10.5281/zenodo.15603820 (2025). https://doi.org/10.5281/zenodo.15603820.
2. Bueckle, A. et al. Construction, Deployment, and Usage of the Human Reference Atlas Knowledge Graph. Sci. Data 12, 1100 (2025). https://doi.org/10.1038/s41597-025-05183-6.
3. The Tabula Sapiens Consortium* et al. The Tabula Sapiens: A multiple-organ, single-cell transcriptomic atlas of humans. Science 376, eabl4896 (2022). https://doi.org/10.1126/science.abl4896.
4. Zilbauer, M. et al. A Roadmap for the Human Gut Cell Atlas. Nat. Rev. Gastroenterol. Hepatol. 20, 597–614 (2023). https://doi.org/10.1038/s41575-023-00784-1.
5. Li, M. et al. DISCO: a database of Deeply Integrated human Single-Cell Omics data. Nucleic Acids Res. 50, D596–D602 (2022). https://doi.org/10.1093/nar/gkab1020.
6. Hemberg, M. et al. Insights, opportunities, and challenges provided by large cell atlases. Genome Biol. 26, 358 (2025). https://doi.org/10.1186/s13059-025-03771-8.
7. Börner, K. et al. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nat. Methods 1–16 (2025). https://doi.org/10.1038/s41592-024-02563-5.
8. Weber, G. M., Ju, Y. & Börner, K. Considerations for Using the Vasculature as a Coordinate System to Map All the Cells in the Human Body. Front. Cardiovasc. Med. 7, (2020). https://doi.org/10.3389/fcvm.2020.00029.
9. Ghose, S. et al. 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging. Commun. Biol. 6, 718 (2023). https://doi.org/10.1038/s42003-023-04991-z.
10. Jain, Y. et al. Exploring endothelial cell environments across organs in spatially resolved omics data. 2025.09.23.678129 Preprint at https://www.biorxiv.org/content/10.1101/2025.09.23.678129v1 (2025). https://doi.org/10.1101/2025.09.23.678129.
11. Black, S. et al. CODEX multiplexed tissue imaging with DNA-conjugated antibodies. Nat. Protoc. 16, 3802–3835 (2021). https://doi.org/10.1038/s41596-021-00556-8.
12. He, S. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat. Biotechnol. 40, 1794–1806 (2022). https://doi.org/10.1038/s41587-022-01483-z.
13. Hu, J. et al. Benchmarking single cell transcriptome matching methods for incremental growth of reference atlases. 2025.04.10.648034 Preprint at https://www.biorxiv.org/content/10.1101/2025.04.10.648034v1 (2025). https://doi.org/10.1101/2025.04.10.648034.
14. Zhang, Y., Aevermann, B., Gala, R. & Scheuermann, R. H. Cell type matching in single-cell RNA-sequencing data using FR-Match. Sci. Rep. 12, 9996 (2022). https://doi.org/10.1038/s41598-022-14192-z.
15. Liu, A. et al. Discovery of optimal cell type classification marker genes from single cell RNA sequencing data. BMC Methods 1, 15 (2024). https://doi.org/10.1186/s44330-024-00015-2.