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.

Standard Operating Procedures (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 2 45 231 177 54 2 70 631
Brain 184 127 257 257 0 185 127 346
Heart 50 23 45 45 0 60 183 74
Intestine, Large 48 57 85 84 1 290 1,158 178
Kidney 61 62 150 150 0 62 60 257
Lung 146 87 258 258 0 911 1,658 722
Lymph Node 35 45 167 94 73 57 121 417
Skin 15 36 68 0 68 17 19 96
Spleen 27 66 163 72 91 55 413 372
Thymus 17 41 442 378 64 37 198 613
Vasculature 839 2 1 1 0 867 604 2
Totals: 1,424 591 1,867 1,516 351 2,543 4,611 3,708

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