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[Heart] Unmapped CL terms #55

Closed anitacaron closed 2 years ago

anitacaron commented 2 years ago

From the report listing CT terms without IDS: _2022-10-17 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 Mapped? OLS link
1 UBERON:0002078 right cardiac atrium right atrium lymphatic endothelial cell CL:0002138 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002138
2 UBERON:0002078 right cardiac atrium right atrium pericyte CL:0000669 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000669
3 UBERON:0002078 right cardiac atrium right atrium telocyte (interstitial like cell of cajal) CL:0017004 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0017004
4 UBERON:0002079 left cardiac atrium left atrium mast cell CL:0000097 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000097
5 UBERON:0002079 left cardiac atrium left atrium lymphatic endothelial cell CL:0002138 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002138
6 UBERON:0002079 left cardiac atrium left atrium B lymphocyte CL:0000945 CL:0000236 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000945
7 UBERON:0002079 left cardiac atrium left atrium ILC CL:0001065 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0001065
8 UBERON:0002079 left cardiac atrium left atrium endocardial CL:0002350 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002350
9 UBERON:0001982 capillary vasculature pericyte CL:0000669 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000669
10 UBERON:0001979 venule vasculature pericyte CL:0000669 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000669
11 UBERON:0002079 left cardiac atrium left atrium telocyte (interstitial like cell of cajal) CL:0017004 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0017004
12 UBERON:0006566 left ventricle myocardium myocardium Purkinje fiber cell CL:0002068 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002068
13 UBERON:0006566 left ventricle myocardium myocardium telocyte (interstitial like cell of cajal) CL:0017004 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0017004
14 UBERON:0006566 left ventricle myocardium myocardium mast cell CL:0000097 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000097
15 UBERON:0006566 left ventricle myocardium myocardium lymphatic endothelial cell CL:0002138 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002138
16 UBERON:0006566 left ventricle myocardium myocardium B lymphocyte CL:0000945 CL:0000236 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000945
17 UBERON:0006566 left ventricle myocardium myocardium ILC CL:0001065 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0001065
18 UBERON:0006566 left ventricle myocardium myocardium endocardial CL:0002350 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002350
19 UBERON:0002094 interventricular septum septum Purkinje fiber cell CL:0002068 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002068
20 UBERON:0002094 interventricular septum septum telocyte (interstitial like cell of cajal) CL:0017004 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0017004
21 UBERON:0002094 interventricular septum septum mast cell CL:0000097 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000097
22 UBERON:0002094 interventricular septum septum lymphatic endothelial cell CL:0002138 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002138
23 UBERON:0002094 interventricular septum septum B lymphocyte CL:0000945 CL:0000236 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000945
24 UBERON:0002094 interventricular septum septum ILC CL:0001065 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0001065
25 UBERON:0002094 interventricular septum septum endocardial CL:0002350 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002350
26 UBERON:0006567 right ventricle myocardium myocardium mast cell CL:0000097 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000097
27 UBERON:0006567 right ventricle myocardium myocardium lymphatic endothelial cell CL:0002138 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002138
28 UBERON:0006567 right ventricle myocardium myocardium B lymphocyte CL:0000945 CL:0000236 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000945
29 UBERON:0006567 right ventricle myocardium myocardium ILC CL:0001065 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0001065
30 UBERON:0006567 right ventricle myocardium myocardium endocardial CL:0002350 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002350
31 UBERON:0006567 right ventricle myocardium myocardium Purkinje fiber cell CL:0002068 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002068
32 UBERON:0002080 heart right ventricle right ventricle telocyte (interstitial like cell of cajal) CL:0017004 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0017004
33 UBERON:0002080 heart right ventricle right ventricle Purkinje fiber cell CL:0002068 Y https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002068
emquardokus commented 2 years ago

Josef Hardi [5:48 PM] November 8, 2022 Hi all, I'm revisiting my CCF pipeline code and found these invalid IDs: CL:0002542 - endothelial cell

  1. I tracked 20 instances of this to the Heart_v1.2_DRAFT table I double checked CL and this is an "has alternative id" for CL:1000413, replaced all 20 instances with CL:1000413.
emquardokus commented 2 years ago

@anitacaron 11-17-2011 updated Heart_v1.2_DRAFT 4 instances capillary endothelial cell FMA:67756 replaced with CL:0002144 4 instances of myocardium of right atrium FMA:83531 with cardiac muscle of right atriumUBERON:0003379 6 instances of Myocardium of interventricular septum FMA:83539 with cardiac muscle tissue of interventricular septum UBERON:0003383 5 instances unmapped mast cell, add mast cell CL:0000097 9 instances unmapped pericyte, add pericyte CL:0000669 Row 193 moderator band AS has telocyte: Replaced 1 instance of telocyte (interstitial like cell of cajal) heart valve cell CL:1000147 with telocyte 5 instances of lymphatic endothelial cell unmapped; add lymphatic endothelial cell CL:0002138 5 instances unmapped NK/T lymphocyte Add: immature NK T cell CL:0000914 5 instances unmapped B lymphocyte mapped to B cell CL:0000236 4 instances unmapped ILC mapped to innate lymphoid cell CL:0001065 4 instance unmapped to endocardial mapped to endocardial CL:0002350 4 instance unmapped Purkinje fiber cell mapped to Purkinje myocyte CL:0002068

anitacaron commented 2 years ago

Hi Ellen, thank you for all the edits! I updated the table above to track all your changes. Did you also update the 5 instances for the unmapped telocyte?

You comment on one instance that is not listed here.

Row 193 moderator band AS has telocyte: Replaced 1 instance of telocyte (interstitial like cell of cajal) heart valve cell CL:1000147 with telocyte

emquardokus commented 2 years ago

@anitacaron All instances of telocytes were mapped;however, the instance I refer to here was a situation where telocyte was in the wrong anatomical structure, so I replaced it with the correct heart valve cell CL:1000147.

anitacaron commented 2 years ago

Thank you, Ellen. I've updated the table above. I'll double-check in the following validation release.