[NTR] fetal hepatobiliary progenitor cell

[paolaroncaglia]

Cc @pnejad
Stemming from a request from a Human Cell Atlas curator (HumanCellAtlas/ontology#72):

Preferred term label:
fetal hepatobiliary progenitor cell

Synonyms
exact synonym: fetal hepatobiliary hybrid progenitor cell
related or narrow synonym (as it’s an abbreviation): HHyP cell

Definition (free text, please give PubMed ID in format PMID:XXXXXX)
A progenitor cell with hepatic and biliary lineage potential, identified in mouse and human, and anatomically restricted to the ductal plate of fetal liver.
PMID:31350390

Parent cell type term (check the hierarchy here https://www.ebi.ac.uk/ols/ontologies/cl):
subclass of progenitor cell

What is the anatomical structure that the cell is a part of? Please check Uberon: https://www.ebi.ac.uk/ols/ontologies/uberon
part of UBERON:0004820 bile duct epithelium
part of UBERON:0000323 late embryo

Your nano-attribution (ORCID)
https://orcid.org/0000-0002-3163-0115

Any additional notes or concerns
subset tag: added_for_HCA

I’m unsure about axiomatising any of the markers listed in the paper. If we did add any, it should be as (‘has plasma membrane part' some [appropriate PRO ID]), but probably avoiding equivalences? @dosumis @addiehl please.

[paolaroncaglia]

Note for self and FYI @pnejad:
I'll add 'fetal hepatobiliary progenitor cell' as soon as the CL editors resolve an issue with merging CL files.
I added the question about markers for discussion at the next CL meeting. Depending on resolution, I might add axioms to the new term, but I'll aim to create the new term first and add details later if I can't do both at once.

[dosumis]

Are markers required to distinguish from other, similar cell types?

We probably don't have sufficient logic available for an equivalentClass definition if we need to define wrt developmental potential.

[paolaroncaglia]

@dosumis

Are markers required to distinguish from other, similar cell types?

Not in this case, no. I noticed some mentions of (potentially not even unique) markers in the paper, hence my question. I'll add the term without markers - better anyway as they could be of limited use in this case. Thanks!

We probably don't have sufficient logic available for an equivalentClass definition if we need to define wrt developmental potential.

[paolaroncaglia]

• Paola to look for a better anatomy term (update: I'll propose 'liver bud')
• Re. markers - they might be useful after all - how exactly are the authors discriminating these cells from others - how would one reproduce the experiment? But it's a borderline case, not sure if adding markers would be useful here.

[paolaroncaglia]

Note for self: do not close this ticket untill all items in #964 (comment) have been addressed.

Update: UBERON:8410003 ductal plate has now been created (not released yet) to be used as per PR comment above.

[paolaroncaglia]

Hi @pnejad ,
The new term is CL_0009013 (fetal hepatobiliary progenitor cell).
It will be available at the next CL release (not sure when that'll be, but I'll push for a release soon).
It will then be automatically brought into HCAO via its subset tag.

Quick (final) notes for self:

• When Uberon is next released, replace CL_0009013 (fetal hepatobiliary progenitor cell) part of bile duct with part of ductal plate => need to import UBERON:8410003 'ductal plate' first (Import UBERON:8410003 'ductal plate' in CL #1255 )
• Add taxon note as appropriate (found/present in Mammalia)

[paolaroncaglia]

Note to self - waiting for Uberon release

[paolaroncaglia]

Depends on #1255 .

[paolaroncaglia]

Note for self, this can be addressed now.