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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.

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Organ #AS #CT #B Total #BG #BP #AS-AS #AS-CT #CT-B
Blood 1 30 159 112 47 1 30 506
Blood Vasculature 918 10 10 10 0 952 2030 11
Bone Marrow 1 47 262 198 64 1 47 838
Brain 183 127 257 257 0 183 127 346
Eye 26 53 140 61 75 27 58 404
Fallopian Tube 72 18 26 13 13 84 81 27
Heart 50 23 45 45 0 60 183 74
Kidney 57 67 184 184 0 72 75 300
Knee 33 41 12 0 12 33 21 47
Large Intestine 54 57 166 83 83 287 1156 360
Liver 17 31 85 29 56 17 32 116
Lung 76 76 280 191 89 121 168 456
Lymph Node 34 45 223 106 117 43 86 499
Lymph Vasculature 31 1 1 1 0 31 19 1
Ovary 77 16 12 0 12 126 30 11
Pancreas 32 34 51 49 2 153 228 126
Peripheral Nervous System 782 1 2 1 1 803 609 2
Placenta 25 22 44 43 0 32 44 74
Prostate 4 12 31 31 0 4 12 36
Skin 15 36 70 0 70 17 19 100
Small Intestine 39 48 89 43 46 69 178 131
Spleen 37 60 194 85 109 50 129 421
Thymus 17 51 394 318 76 28 39 603
Ureter 7 14 30 30 0 7 14 61
Urinary Bladder 16 15 30 30 0 16 16 63
Uterus 61 18 45 39 6 89 34 65
Totals: 2,665 953 2,842 1,959 878 3,306 5,465 5,678
Organ #AS #CT #B Total #BG #BP #AS-AS #AS-CT #CT-B
Blood 1 30 159 112 47 1 30 506
Blood Vasculature 841 2 1 1 0 869 606 2
Bone Marrow 1 47 262 198 64 1 47 838
Brain 183 127 257 257 0 183 127 346
Eye 26 53 136 61 75 27 58 404
Fallopian Tube 55 22 25 13 12 72 65 32
Heart 50 23 45 45 0 60 183 74
Kidney 61 62 150 150 0 62 60 257
Knee 32 19 14 0 14 32 8 17
Large Intestine 54 57 167 84 83 287 1,156 352
Liver 17 30 62 16 46 17 31 75
Lung 146 83 180 174 6 909 1065 267
Lymph Node 34 45 223 106 117 43 86 499
Lymph Vasculature 4 1 1 1 0 4 2 1
Ovary 71 7 13 7 6 109 12 5
Pancreas 32 32 44 42 2 162 229 101
Peripheral Nervous System 782 1 2 1 1 803 609 2
Prostate 4 12 31 31 0 4 12 36
Skin 15 36 70 0 70 17 19 101
Small Intestine 38 48 13 13 0 69 185 13
Spleen 37 61 194 85 109 50 129 424
Thymus 17 52 394 318 76 28 39 620
Ureter 7 14 30 30 0 7 14 61
Urinary Bladder 16 15 30 30 0 16 16 63
Uterus 58 19 45 39 6 73 28 65
Totals: 2,582 898 2,548 1,814 734 3,905 4,816 5,161
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

The initial release of ASCT+B table (v1.0) included 11 organs. In the 2nd release, 14 additional tables were published bringing the total to 25. In the 3rd release, several tables were updated and placenta was added resulting in 26 tables. 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.