ccf-validation-tools/Lung/comments/ #213
giscus[bot]
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Replies: 31 comments 26 replies
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New Terms in CL Rows 32, 59, 77, 101, 118, 153: 'vein endothelial cell of respiratory system' CL:4033008 Rows 40, 68: 'goblet cell of epithelium of lobar bronchus' CL:4033009 Rows 41, 69: 'neuroendocrine cell of epithelium of lobar bronchus' CL:4033010 |
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@aleixpuigb Rows 42, 70: should be brush cell of epithelium of segmental bronchus and brush cell of subsegmental bronchus and neither of those exist in CL---only row 29 should have : 'brush cell of epithelium of lobar bronchus' CL:4033007 |
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New Term in CL Row 144: 'secondary crest myofibroblast' CL:4033016 Row 129, 133, 136 'bronchiolar smooth muscle cell' CL:4033017 Row 167: 'lung megakaryocyte' CL:4033018 Row 27: 'perichondrial fibroblast' CL:4033025 'lung perichondrial fibroblast' CL:4033026 'myoepithelial cell of trachea gland' CL:4033021 'mucus secreting cell of trachea gland' CL:4033020 'mucus secreting cell of bronchus submucosal gland CL:4033022 'airway submucosal gland collecting duct epithelial cell' CL:4033023 'airway submucosal gland duct basal cell' CL:4033024 |
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Wondering about status of "new_cl_terms" that are not yet listed below: UBERON:0002299 alveolus of lung alveolus of lung alveolar macrophage proliferating NA NA |
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The following term has been added and will be available in the next uberon release: The following terms are in process to be added. The term names are provisional and subject to change: |
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Hi Gloria, I've noticed that in the table, the new Uberon ID was dragged and autocomplete at some point. That caused that the wrong identifier was carried to the rows below: |
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Thanks so much Aleix! It was so helpful to meet you yesterday and thank you for the speed in getting these to these stages. Have a great day.
…Sent from my iPhone
On Apr 14, 2023, at 7:02 AM, Aleix Puig ***@***.***> wrote:
The following term has been added and will be available in the next uberon release:
UBERON:8600009 subsegmental bronchus
The following terms are in process to be added. The term names are provisional and subject to change:
CL:4033038 CD4+ T cell resident memory
CL:4033039 CD8+ T cell resident memory
CL:4033040 alveolar macrophage proliferating
CL:4033041 alveolar macrophage CCL3+
CL:4033042 alveolar macrophage MT-positive
CL:4033043 Interstitial macrophage
CL:4033044 deuterosomal cell
CL:4033045 migratory dendritic cells of the lung
CL:4033046 peribronchial fibroblast
CL:4033047 peribronchial mast cell
CL:4033048 respiratory suprabasal cell
UBERON:8600010 ciliated duct for bronchial submucosal gland
UBERON:8600011 terminal ciliated duct for tracheal submucosal gland
UBERON:8600012 submucosal gland acini
UBERON:8600013 submucosal gland collecting duct
UBERON:8600014 submucosal gland ciliated duct
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Corrected the subsegmental Uberon IDs, the copy forward was even worse than you noted. Thasnk so much for catching this. |
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That is great, thank you! :) |
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Hi Gloria, I've noticed another case of autocomplete. |
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Would like to add requests for |
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Thank you for the new term, I have added it in the NTR table with the description you have provided. I am finishing some open tickets at the moment, and I think next week I will be able to continue adding terms in the ontology. |
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Hi Gloria, Thank you! |
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Thanks Aleix
I’m sorry this has happened so much! If I wanted to “copy down” sequential numbers I’d have had trouble recalling how to do it, and here I’ve clearly done it repeatedly. I’ll pay more attention. I’ve corrected that second set, thanks so much for catching,
Gloria
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On May 4, 2023, at 9:15 AM, Aleix Puig ***@***.***> wrote:
Hi Gloria,
There are some more at the bottom of the table (there are two block of tracheobronchial tree, and the second one still have the wrong ID)
[image]<https://urldefense.com/v3/__https://user-images.githubusercontent.com/94959119/236210931-718f3d34-e8dd-495d-a890-66d87d46fe68.png__;!!MkQhnT5yHH0MPvOc00c!VM-b4VNk33tgu1gvOmwiz4R2LyI-LoTHMVpCww5qZLsS8UksGjM1xKQCwDbHONchUZ3XnrNHUR7Sg1nTgI4-2Vj0LTPK_ElL3kvxuOM$>
Thank you!
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No worries, I have had that problem before as well. What I do now is copy the cell, select all cells where I want the paste, and then paste. I will run a release of the validation reports with the updated table. |
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Sorry, I missed subsegmental bronchus earlier. The correct ID is UBERON:8600009. It shouldn't affect the report, but just in case I will run after. |
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That is what I usually do and why it surprises me that these copy down errors have occurred. Thanks for catching!!
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On May 4, 2023, at 9:28 AM, Aleix Puig ***@***.***> wrote:
No worries, I have had that problem before as well. What I do now is copy the cell, select all cells where I want the paste, and then paste.
I will run a release of the validation reports with the updated table.
Thank you!
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HI Gloria, |
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New Terms in CL Note: Some term labels were changed during the review process and do not match the proposed one. They need to be corrected in the table. |
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Hi Gloria, |
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Hi Aleix, I'm conferring with authors who have reported these megakaryocytes in the lung with transcript profiles that distinguish them from bone marrow megakaryoctyes and will get back on this question. |
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Thank you Gloria! |
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Consensus is to continue to use 'lung megakaryocyte' to distinguish those found in lung tissue from bone marrow megakaryocyte. Not yet ready to change to 'lung resident megakaryocytes.' |
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Thank you very much! |
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Hi @emquardokus and @gpryhuber. |
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Hi Aleix, thanks for this notice. Is there a way to see (a list) of which new terms were added/officially released? |
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Hi Gloria, we were checking yesterday if we could see it automatically, but we could not. All the terms are in this thread and I have seen that Ellen has already integrate them in the tables. |
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@gpryhuber @aleixpuigb Here are edits I've done to the working lung draft table for HRA 6th release addressing validation report issues where it was clear; there are some remaining ---are ciliated cell types verified yet? Lung_v1.4-DRAFT: Different labels Change underscore to colon: from metadata validation report run by Bruce Herr Blank ontology ID
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@gpryhuber @aleixpuigb Here are edits I've done to the working lung draft table for HRA 6th release addressing validation report issues where it was clear for anatomical structures. It appears that this term has not yet been added: pulmonary interlobular septum FMA:84472 to Uberon yet. Lung_v1.4-DRAFT: Terms from another ontology
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Thank you for all the edits, @emquardokus.
I have revisited this and I will add the submucosal gland ciliated duct, and use these references PMID:17707699, https://doi.org/10.1152/ajplung.00068.2019. It will be part of the
Until recently I was advised to focus on terms not present in other ontologies, but recently we have started and I will add it to CL. |
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Thanks so much!
I will review.
Gloria
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On Sep 7, 2023, at 12:25 PM, emquardokus ***@***.***> wrote:
@gpryhuber<https://urldefense.com/v3/__https://github.com/gpryhuber__;!!MkQhnT5yHH0MPvOc00c!SXjG2jgmoMC29Tvk0f0mS11vIfVEnuKi0bGyWNZ_6GLF3NKRfnY6USfUigT6pIanY4SVLpP5vgN5DnL4a0h4ZajX046Y9Mcrb-DpyEk$> @aleixpuigb<https://urldefense.com/v3/__https://github.com/aleixpuigb__;!!MkQhnT5yHH0MPvOc00c!SXjG2jgmoMC29Tvk0f0mS11vIfVEnuKi0bGyWNZ_6GLF3NKRfnY6USfUigT6pIanY4SVLpP5vgN5DnL4a0h4ZajX046Y9McrnEC4rgY$> Here are edits I've done to the working lung draft table for HRA 6th release addressing validation report issues where it was clear; there are some remaining ---are ciliated cell types verified yet?
Lung_v1.4-DRAFT:
https://docs.google.com/spreadsheets/d/1StCXeg1J9YZaxRb-nnKsso3Dfv5pkH0DxF_8sz_DVMA/edit#gid=1109843030<https://urldefense.com/v3/__https://docs.google.com/spreadsheets/d/1StCXeg1J9YZaxRb-nnKsso3Dfv5pkH0DxF_8sz_DVMA/edit*gid=1109843030__;Iw!!MkQhnT5yHH0MPvOc00c!SXjG2jgmoMC29Tvk0f0mS11vIfVEnuKi0bGyWNZ_6GLF3NKRfnY6USfUigT6pIanY4SVLpP5vgN5DnL4a0h4ZajX046Y9McrzSe3Zqk$>
Different labels
Corrected to match ontology: 9-7-2023:
-[ ] Removed the trailing space after venous blood vessel in rows 116 and 117. In row 116, the term UBERON:0003920 has different name/label in the source ontology. The name/label in the ASCT+B table is venous blood vessel _ and the one in the ontology is _venous blood vessel. For reference, the given name/label by SMEs is venous blood vessel . Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
-[ ] Changed to alveolar type 2 fibroblast cell. In row 85, the term CL:4028006 has different name/label in the source ontology. The name/label in the ASCT+B table is adventitial fibroblast and the one in the ontology is alveolar type 2 fibroblast cell. For reference, the given name/label by SMEs is adventitial fibroblast. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
-[ ] Changed to bronchial submucosal gland ciliated duct In row 13, the term UBERON:8600010 has different name/label in the source ontology. The name/label in the ASCT+B table is ciliated ducts of bronchial submucosal gland and the one in the ontology is bronchial submucosal gland ciliated duct. For reference, the given name/label by SMEs is ciliated ducts of bronchial submucosal gland. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
Change underscore to colon: from metadata validation report run by Bruce Herr
WARNING: Invalid characters in data cell at column: W row: 37 where data cell: UBERON_0004242 (Code 5)
WARNING: Invalid characters in data cell at column: AA row: 49 where data cell: UBERON_0004242 (Code 5)
WARNING: Invalid characters in data cell at column: AI row: 76 where data cell: UBERON_0004517 (Code 5)
Blank ontology ID
* Added deuterosomal cell CL:4033044 In row 22, no term id was found for the name/label airway deuterosomal cell.
* Added respiratory suprabasal cell CL:4033048 In row 24, no term id was found for the name/label respiratory suprabasal cell.
* Added respiratory suprabasal cell CL:4033048 In row 39, no term id was found for the name/label respiratory suprabasal cell.
* Added deuterosomal cell CL:4033044 In row 44, no term id was found for the name/label airway deuterosomal cell.
* Added deuterosomal cell CL:4033044 In row 57, no term id was found for the name/label airway deuterosomal cell.
* Added respiratory suprabasal cell CL:4033048In row 60, no term id was found for the name/label respiratory suprabasal cell.
* Added deuterosomal cell CL:4033044 I In row 64, no term id was found for the name/label airway deuterosomal cell.
* Added CCL3-positive alveolar macrophage CL:4033041 In row 118, no term id was found for the name/label alveolar macrophage CCL3+.
* Added alveolar macrophage CL:0000583; cell state terminology not captured In row 120, no term id was found for the name/label alveolar macrophage proliferating.
* Added metallothionein-positive alveolar macrophage CL:4033042 In row 121, no term id was found for the name/label alveolar macrophage MT-positive.
* Added lung interstitial macrophage CL:4033043 In row 122, no term id was found for the name/label Interstitial macrophage.
* Added lung resident memory CD4-positive, alpha-beta T cell CL:4033038 In row 135, no term id was found for the name/label CD4+ T cell resident memory.
* Added lung resident memory CD8-positive, alpha-beta T cell CL:4033039 In row 139, no term id was found for the name/label CD8+ T cell resident memory.
* Added lung migratory dendritic cell CL:4033045 In row 143, no term id was found for the name/label migratory dendritic cell.
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Note on: "Changed to alveolar type 2 fibroblast cell. In row 85, the term CL:4028006 has different name/label in the source ontology. The name/label in the ASCT+B table is adventitial fibroblast and the one in the ontology is alveolar type 2 fibroblast cell. For reference, the given name/label by SMEs is adventitial fibroblast. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table." The lung community is working hard on the various types of fibroblasts, there is consensus that the previously requested 'alveolar type 2 fibroblast' is better named 'adventitial fibroblast' with alveolar type 2 fibroblast remaining as a synonym. |
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@aleixpuigb Please see this request to modify CL:4028006 to be 'adventitial fibroblast' with 'alveolar type 2 fibroblast' kept as synonym. based on consensus in our nomenclature discussions over several meetings and multiple experts in the field. |
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Is there any label to replace 'alveolar type 1 fibroblast' (CL:4028004)? I have tagged you in the issue to relabel some pulmonary terms: obophenotype/cell-ontology#2169. Thank you! |
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Hi Gloria, Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J, Berry GJ, Shrager JB, Metzger RJ, Kuo CS, Neff N, Weissman IL, Quake SR, Krasnow MA. A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature. 2020 Nov;587(7835):619-625. doi: 10.1038/s41586-020-2922-4. Epub 2020 Nov 18. PMID: 33208946; PMCID: PMC7704697. |
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This term was added in the last release (21/09/2023). New Term in CL Row 13, 31, 51:'airway submucosal gland duct ciliated cell' CL:4033055 |
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Lung_v1.4-DRAFT: Blank ontology ID missing parent |
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@aleixpuigb |
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I have added this term in the new term request table and I will add it to Uberon. |
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New term in last Uberon release: This term can replace Pulmonary interlobular septum FMA:84472 |
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Lung_v1.4-DRAFT As per email from Gloria on November 5, 2023, pulmonary interlobular septum i(was FMA ID) is now in Uberon with ID UBERON:8600022; removed FMA and used Uberon ID for rows 101, 102, 103. Different labels Note on: "Changed to alveolar type 2 fibroblast cell. In row 85, the term CL:4028006 has different name/label in the source ontology. The name/label in the ASCT+B table is adventitial fibroblast and the one in the ontology is alveolar type 2 fibroblast cell. For reference, the given name/label by SMEs is adventitial fibroblast. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table." The lung community is working hard on the various types of fibroblasts, there is consensus that the previously requested 'alveolar type 2 fibroblast' is better named 'adventitial fibroblast' with alveolar type 2 fibroblast remaining as a synonym. |
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The following ticket was created to change four lung terms. I am waiting feedback from @gpryhuber on 1. since there adventitial fibroblast in non alveolar location, if it would be acceptable the label 'alveolar adventitial fibroblast', and 2. if there are any other cell types that should be relabeled. If the label is ok and there aren't any other terms that need to be relabeled, I will change them. |
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New term added in Uberon: Lung: 'pulmonary venule' (UBERON:8600024) |
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The following terms have been renamed in CL:
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There are 2 new lung cell types in the last CL release: |
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Lung_v1.6_DRAFT Update mappings Different labels
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New terms needed @aleixpuigb |
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I’d like to suggest that we hold off a week or two to allow us to digest the decisions made in the recent NIH Lung Cell Nomenclature Workshop.
Gloria
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From: emquardokus ***@***.***>
Date: Thursday, November 21, 2024 at 9:07 PM
To: hubmapconsortium/ccf-validation-tools ***@***.***>
Cc: Pryhuber, Gloria ***@***.***>, Mention ***@***.***>
Subject: [EXT] Re: [hubmapconsortium/ccf-validation-tools] ccf-validation-tools/Lung/comments/ (Discussion #213)
@aleixpuigb<https://urldefense.com/v3/__https:/github.com/aleixpuigb__;!!MkQhnT5yHH0MPvOc00c!Te-rZKH97q4O3Mor9CIwUaPeCa7Ys6yR8wNc2CpW-v26mREuY8vv88sskrsP4DFMtB_hUIPDDjL_9BFw2j66-mSJGRuLqSceeB3eMOs$> Rows 42, 70: should be brush cell of epithelium of segmental bronchus and brush cell of subsegmental bronchus and neither of those exist in CL---only row 29 should have : 'brush cell of epithelium of lobar bronchus' CL:4033007
Similarly, rows now 43 and 63 should be appropriately paired with the lung region. goblet cell of segmental bronchus and goblet cell of subsegmental bronchus, neither exist.
Same for Rows 41, 69: now rows 41 and 65 should be appropriately paired with lung region. neuroendocrine cell of epithelium of segmental bronchus and neuroendocrine cell of epithelium of subsegmental bronchus; neither exists in CL.
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In general, I’d like to suggest that we hold off a week or two to allow us to digest the decisions made in the recent NIH Lung Cell Nomenclature Workshop.
Meanwhile, it is clear that this one is
incorrect in the Ontology. The “alveolar adventitial fibroblast” should be revised to just adventitial fibroblast – it is not exclusively in the alveolus and is actually predominant in the adventitial tissue around airways and vessels.
This one is not correct: FIXED The term CL:4028006 has a different name/label in the source ontology in the following 3 rows 85, 92, 99. The name/label in the ASCT+B table is alveolar type 2 fibroblast cell and the one in the ontology is alveolar adventitial fibroblast. For reference, the given name/label by SMEs is adventitial fibroblast. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
Gloria
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From: emquardokus ***@***.***>
Date: Thursday, November 21, 2024 at 9:07 PM
To: hubmapconsortium/ccf-validation-tools ***@***.***>
Cc: Pryhuber, Gloria ***@***.***>, Mention ***@***.***>
Subject: [EXT] Re: [hubmapconsortium/ccf-validation-tools] ccf-validation-tools/Lung/comments/ (Discussion #213)
Lung_v1.6_DRAFT
https://docs.google.com/spreadsheets/d/1q-G0O3kkIBa1DO06nxI_Q6xOCUNKnZL2cElRcIEpp0Y/edit?gid=1109843030#gid=1109843030<https://urldefense.com/v3/__https:/docs.google.com/spreadsheets/d/1q-G0O3kkIBa1DO06nxI_Q6xOCUNKnZL2cElRcIEpp0Y/edit?gid=1109843030*gid=1109843030__;Iw!!MkQhnT5yHH0MPvOc00c!XLL_XzUf8ToZhTu8APqcgu92TRkH2KVqykDFJZDeBamnppIC0LBgBKv5iVwVMu3N73yDjtc0MEux7e_BWBfNdiN6DQbUrMT50WNTauw$>
Update mappings
row 120 change mapping to newly added alveolar macrophage proliferating CL label: cycling alveolar macrophage CL:4033077 from previous alveolar macrophage parent CL:0000583
Different labels
1. FIXED problem where pulmonary vein UBERON:0002016 was mapped incorrectly to pulmonary artery term UBERON:0002012. The term UBERON:0002012 has a different name/label in the source ontology in the following 4 rows 112, 112, 113, 113. The name/label in the ASCT+B table is pulmonary vein and the one in the ontology is pulmonary artery. For reference, the given name/label by SMEs is pulmonary vein. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
2. FIXED UBERON label The term UBERON:8600010 has a different name/label in the source ontology in the following 4 rows 31, 31, 51, 51. The name/label in the ASCT+B table is ciliated ducts of bronchial submucosal gland and the one in the ontology is bronchial submucosal gland ciliated duct. For reference, the given name/label by SMEs is ciliated ducts of bronchial submucosal gland. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
3. FIXED The term CL:4028006 has a different name/label in the source ontology in the following 3 rows 85, 92, 99. The name/label in the ASCT+B table is alveolar type 2 fibroblast cell and the one in the ontology is alveolar adventitial fibroblast. For reference, the given name/label by SMEs is adventitial fibroblast. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
4. FIXED The term UBERON:8410043 has a different name/label in the source ontology in the following 12 rows 31, 31, 32, 32, 33, 33, 34, 34, 35, 35, 36, 36. The name/label in the ASCT+B table is bronchial submucosal gland and the one in the ontology is bronchus submucosal gland. For reference, the given name/label by SMEs is bronchial submucosal gland. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
5. FIXED The term CL:0002062 has a different name/label in the source ontology in the following 3 rows 83, 90, 97. The name/label in the ASCT+B table is type I pneumocyte and the one in the ontology is pulmonary alveolar type 1 cell. For reference, the given name/label by SMEs is alveolar type I cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
6. FIXED The term CL:0002063 has a different name/label in the source ontology in the following 3 rows 82, 89, 96. The name/label in the ASCT+B table is type II pneumocyte and the one in the ontology is pulmonary alveolar type 2 cell. For reference, the given name/label by SMEs is alveolar type II cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
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Thank you @emquardokus and @gpryhuber. We are gathering all the information to discuss (next Monday) as well, so it we have a plan on how to introduce the changes in the ontology. But I agree we need one or two weeks to digest all the information and allow time participants have more time to contribute on the MIRO board. |
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@gpryhuber and @aleixpuigb I wanted to work my way through the most recent validation report and in doing so, realized we had outstanding issues still for NTRs as well as the issue with the renaming of a cell that is now not correct “alveolar adventitial fibroblast” should be revised to just adventitial fibroblast "---glad you caught this Gloria! |
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ccf-validation-tools/Lung/comments/
https://hubmapconsortium.github.io/ccf-validation-tools/Lung/comments/
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