CCF Anatomical Structures, Cell Types and Biomarkers (ASCT+B) Tables

Overview

Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables aim to capture the nested part_of structure of anatomical human body parts, the typology of cells, and biomarkers used to identify cell types (e.g., gene, protein, lipid or metabolic markers). The tables are authored and reviewed by an international team of anatomists, pathologists, physicians, and other experts, see SOP.

Existing Tables

The below table lists for each organ the number of anatomical structures (#AS), the number of cell types (#CT), the number of biomarkers (#B), the number of part_of relationships between AS, the number of located_in links between CT and AS, and the number of CT and B, i.e., which B characterize a CT.

Organ #AS #CT #B Total #BG #BP #AS-AS #AS-CT #CT-B
Bone Marrow & Blood/Pelvis 3 46 327 201 126 2 70 710
Brain 187 127 254 254 0 187 127 330
Heart 52 25 48 48 0 61 164 78
Intestine, Large 65 69 94 88 6 389 1,361 197
Kidney 68 63 152 152 0 67 59 257
Lung 161 92 176 172 4 1,633 12,094 286
Lymph Node 41 49 266 108 158 62 135 544
Skin 16 42 70 0 70 17 19 105
Spleen 46 66 255 80 145 68 172 414
Thymus 25 41 511 388 123 38 180 657
Vasculature 870 2 1 1 0 869 606 2
Totals: 1,534 622 2,154 1,492 632 3,393 14,987 3,580

Explore Tables Visually

The CCF ASCT+B Reporter makes it possible to explore tables visually—per organ or across all organs in support of table authoring and review. It combines two different types of Angular visualizations: A partonomy tree of anatomical structures and bimodal networks that link anatomical structures to cell types and cell types to biomarkers.

Tables Under Development

There now exist initial ASCT+B table versions for 11 organs. We plan to publish another 11 tables by the end of 2021 bringing the total to 22. If you are interested in contributing to this effort, please complete this online form to receive relevant information and meeting invites. For questions, email infoccf@indiana.edu.

Acknowledgements

The very first ASCT+B table was published for the kidney by the Kidney Precision Medicine Project (KPMP) in "A Multimodal and Integrated Approach to Interrogate Human Kidney Biopsies with Rigor and Reproducibility: The Kidney Precision Medicine Project". Katy Börner (HuBMAP, KPMP), Peter Hunter (SPARC), and James Gee (BICCN) organized a CCF session at the 2020 Joint NIH-HCA Meeting that brought together experts from multiple consortia to develop ASCT+B tables in an effort to create a Human Reference Atlas. Mark Musen, Chris Mungall, and David Osumi-Sutherland provided expert guidance on linking ASCT+B tables to existing ontologies.

March 22, 2021