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[Small intestine] Unmapped CL terms #47

Closed anitacaron closed 2 years ago

anitacaron commented 2 years ago

From the report listing CT terms without IDS: _2022-10-03 Release_

Some of the CL names in the report already exist in Cell Ontology:

N Terminal AS/ID Terminal AS/label Terminal AS/user_label CL Name CL term OLS link
1 UBERON:0008346 duodenal epithelium Epithelium tuft cell CL:0009080 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0009080
2 UBERON:0008346 duodenal epithelium Epithelium absorptive CL:0000212 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000212
3 UBERON:0008346 duodenal epithelium Epithelium enterocyte CL:0000584 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000584
4 UBERON:0008346 duodenal epithelium Epithelium stem cell CL:0000034 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000034
5 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) endothelial CL:0000115 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000115
6 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) myofibroblast CL:0000186 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000186
7 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) fibroblast CL:0000057 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000057
8 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) B cell CL:0000236 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000236
9 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) plasma CL:0000786 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000786
10 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) macrophage CL:0000235 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000235
11 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) eosinophil CL:0000771 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000771
12 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) mast cell CL:0000097 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000097
13 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) neutrophil CL:0000775 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000775
14 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) natural killer (NK) cell CL:0000623 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000623
15 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) dendritic cell (DC) CL:0000451 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000451
16 UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) innate lyphoid cell (ILC) CL:0001065 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0001065
17 UBERON:0003336 serosa of duodenum serosa mesothelial CL:0000077 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000077
18 UBERON:0003336 serosa of duodenum serosa fibroblasts CL:0000057 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000057
19 UBERON:0003336 serosa of duodenum serosa endothelial cells CL:0000115 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000115
20 UBERON:0000400 jejunal epithelium Epithelium Paneth CL:0000510 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000510
21 UBERON:0000400 jejunal epithelium Epithelium endocrine CL:0000163 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000163
22 UBERON:0000400 jejunal epithelium Epithelium absorptive CL:0000212 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000212
23 UBERON:0000400 jejunal epithelium Epithelium enterocytes CL:0000584 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000584
24 UBERON:0000400 jejunal epithelium Epithelium Tuft cells CL:0009080 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0009080
25 UBERON:0000399 jejunal mucosa mucosa endothelial CL:0000115 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000115
26 UBERON:0000399 jejunal mucosa mucosa myofibroblasts CL:0000186 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000186
27 UBERON:0000399 jejunal mucosa mucosa fibroblasts CL:0000057 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000057
28 UBERON:0000399 jejunal mucosa mucosa B cell CL:0000236 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000236
29 UBERON:0000399 jejunal mucosa mucosa macrophages CL:0000235 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000235
30 UBERON:0000399 jejunal mucosa mucosa eosinophils CL:0000771 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000771
31 UBERON:0000399 jejunal mucosa mucosa mast cells CL:0000097 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000097
32 UBERON:0000399 jejunal mucosa mucosa neutrophils CL:0000775 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000775
33 UBERON:0000399 jejunal mucosa mucosa NK cells CL:0000623 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000623
34 UBERON:0000399 jejunal mucosa mucosa DCs CL:0000451 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000451
35 UBERON:0000399 jejunal mucosa mucosa ILCs CL:0001065 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0001065
36 UBERON:0003333 submucosa of jejunum submucosa endoethlial CL:0000115 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000115
37 UBERON:0012377 muscle layer of jejunum muscularis externa Interstitial cells of Cajal CL:0002088 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002088
38 UBERON:0012377 muscle layer of jejunum muscularis externa fibroblasts CL:0000057 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000057
39 UBERON:0012377 muscle layer of jejunum muscularis externa endothelial CL:0000115 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000115
40 UBERON:0003337 serosa of jejunum serosa mesothelial CL:0000077 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000077
41 UBERON:0003337 serosa of jejunum serosa fibroblasts CL:0000057 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000057
42 UBERON:0003337 serosa of jejunum serosa endothelial cells CL:0000115 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000115
emquardokus commented 2 years ago

@anitacaron All cell types listed above were added to Small_Intestine_v1.1_DRAFT to be published in 4th HRA release Other cells also mapped by me that were not above are as follows:

M cell | M cell of gut | CL:0000682 epithelial stem cells | epithelial fate stem cell | CL:0000036

Remaining cells to be mapped for small intestine are as follows: will be working with NEW SMEs for both intestine tables for next release. Cell types too general, need to harmonize with Organ Mapping Antibody Panel cell types. CD4+ T regulatory CD4+ T CD8+ T nerve muscle

anitacaron commented 2 years ago

Thank you, Ellen!