Validate HCA bionetwork draft PBMC heirarchy

[dosumis]

Aim here is to validate the draft PBMC hierarchy generated by @amcujba for the blood cell type reconciliation effort of the HCA

To do this we need to convert the hierarchy into a standard validation table with IDs. Validation can then be carried out using @anitacaron 's https://pypi.org/project/relation-validator/ lib. The current hierarchy has only labels (although these should align with CL labels), so an initial mapping is needed (manual or semi-automated).

Suggested division of work:

• @aleixpuigb to work with @amcujba on prep (with help from @anitacaron if needed.
• @aleixpuigb to work with @anitacaron to use (and test) relation-validator on the prepared data and share results with (and demo validation workflow to @amcujba.

[aleixpuigb]

I have generated a CT table based on the PBMC hierarchy generated by @amcujba. All cells could be mapped except two:

• progenitor (parent term innate lymphoid cell). There is an immature innate lymphoid cell, but it is not a progenitor.
• IGA.IGL (parent term plasma cell)

@amcujba, are these two cells missing in CL ontology?
@anitacaron, can you use this table for validation? I have used the same format from ASCT+B tables, but let me know if you need a different format.

[anitacaron]

Thank you, @aleixpuigb! When using the python lib relation-validator, we need a more straightforward table with the columns:

s	slabel	user_slabel	o	olabel	user_olabel
the subject term ID	the label of the term in the column s	optional label for the term given by user	the object term ID	the label of the term in the column s	optional label for the term given by user

[aleixpuigb]

Thanks! I have it in this format now. I will save it as .csv and try run it.

[aleixpuigb]

This is the output of the relation-validator:

s	slabel	user_slabel	o	olabel	user_olabel
CL:0000050	megakaryocyte-erythroid progenitor cell	megakaryocyte-erythroid progenitor cell	CL:0000556	megakaryocyte	megakaryocyte
CL:0000233	platelet	platelet	CL:0000556	megakaryocyte	megakaryocyte
CL:0000798	gamma-delta T cell	gamma-delta T cell	CL:0000789	alpha-beta T cell	alpha-beta T cell
CL:0000786	plasma cell	plasma cell	CL:0000785	mature B cell	mature B cell
CL:0000813	memory T cell	memory alpha-beta T cell (memory T cell?)	CL:0000791	mature alpha-beta T cell	mature alpha-beta T cell
CL:0000898	naive T cell	naive T cell	CL:0000791	mature alpha-beta T cell	mature alpha-beta T cell
CL:0000815	regulatory T cell	regulatory T cell	CL:0000791	mature alpha-beta T cell	mature alpha-beta T cell

These are the proposed fixes for the relations:

• megakaryocyte --> megakaryocyte-erythroid progenitor cell
  megakaryocyte 'develops from' some megakaryocyte progenitor cell, which is a child term of megakaryocyte-erythroid progenitor cell.

• megakaryocyte --> platelet
  platelet 'develops from' some megakaryocyte.

• alpha-beta T cell --> gamma-delta T cell
  gamma-delta T cell is a sibling of alpha-beta T cell.

• mature B cell --> plasma cell
  plasma cell has no relation to mature B cell.

• mature alpha-beta T cell --> memory T cell
  memory T cell is too general, it should be under the absent term mature T cell, which should go under T cell.

• mature alpha-beta T cell --> naive T cell
  naive T cell should go under mature T cell.

• mature alpha-beta T cell --> regulatory T cell
  regulatory T cell should go under mature T cell.

[amcujba]

Hi, thanks for this @aleixpuigb and @anitacaron. I can double check these changes with the immune bionetwork and get back to you. I believe David will be attending the meeting tomorrow at 2pm, so we can take it from there as well.

[aleixpuigb]

Hi @amcujba, based on the proposed changes to validate, I have generated an updated hierarchy. The green cells are the edits (cell has been moved or a term has been added). I am available if you would like to discuss it in person or in a call.

[amcujba]

Hi @aleixpuigb. Please send me your email addresses and I will invite you to our immune bionetwork meeting, where you can share the hierarchy. I can also share it with them before the meeting, if that is okay with you. Thank you.

[aleixpuigb]

Hi @amcujba, no problem at all, you can share it. My email address is [email protected]. Thanks!

[aleixpuigb]

Hi @dosumis, can this ticket be closed as completed?

[amcujba]

I have cc'd you in the email to the immune bionetwork, Aleix, apologies for the delay.

…

On Tue, Jul 18, 2023 at 3:21 PM Aleix Puig ***@***.***> wrote: Hi @dosumis <https://github.com/dosumis>, can this ticket be closed as completed? — Reply to this email directly, view it on GitHub <#1912 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUYJ4XTDVPMDB5FTQ6GUAIDXQ2LU7ANCNFSM6AAAAAAWKFVMLY> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[aleixpuigb]

Hi @amcujba, can this ticket be closed as completed? Thank you.

[aleixpuigb]

Hi @amcujba, I will close this ticket as completed. Feel free to reopen it if there's something else needed. Thank you.

[aleixpuigb]

Hi @amcujba,

I am writing to you because we are preparing a manuscript about the validation tool that we used to validate the HCA hierarchy in this ticket. The manuscript will be focused mainly on how this tool was built to validate the ASCT+B tables from HuBMAP, but it would be very beneficial if we could provide more use cases. I was wondering if you would be ok that we use the validation of the HCA hierarchy as a use case. Thank you!

[amcujba]

Hello Aleix, Could you please contact me via ***@***.***? I do not always check this email, apologies for the late reply. What would you need me to provide? more unmatching labels? thank you!

…

On Fri, Mar 1, 2024 at 3:44 PM Aleix Puig ***@***.***> wrote: Hi @amcujba <https://github.com/amcujba>, I am writing to you because we are preparing a manuscript about the validation tool that we used to validate the HCA hierarchy in this ticket. The manuscript will be focused mainly on how this tool was built to validate the ASCT+B tables from HuBMAP, but it would be very beneficial if we could provide more use cases. I was wondering if you would be ok that we use the validation of the HCA hierarchy as a use case. Thank you! — Reply to this email directly, view it on GitHub <#1912 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AUYJ4XTSV6WMST6U5CEJLBTYWCH6NAVCNFSM6AAAAAAWKFVML2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZTGMZDONZTGM> . You are receiving this because you were mentioned.Message ID: ***@***.***>