[Class hierarchy] CL:4023056 vascular leptomeningeal cell (Mmus), species specific cell?

[ANiknejad]

CL:4023056

I am wondering what is the meaning of this CL class? a species-specific CL class? while CL:4023051 ! vascular leptomeningeal cell, already exists.

[Term] id: CL:4023056 name: vascular leptomeningeal cell (Mmus) def: "A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain." [PMID:30096314] subset: BDS_subset synonym: "VLMC (Mus musculus)" EXACT [] is_a: CL:4023051 ! vascular leptomeningeal cell relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002292 PR:P11087 {xref="PMID:30096314"} ! expresses collagen alpha-1(I) chain (mouse) relationship: RO:0002292 PR:P26618 {xref="PMID:30096314"} ! expresses platelet-derived growth factor receptor alpha (mouse) relationship: RO:0002292 PR:P51885 {xref="PMID:30096314"} ! expresses lumican (mouse)

[ghost]

@ANiknejad, yes, CL:4023056 is a species-specific (for Mus musclus) class. The parent class is not restricted to a specific taxon. There are several examples of taxon-specific cell types in CL, similar to how there are general and species-specific classes of genes in GO.

If this above does not answer your question, feel free to reopen and comment on this issue.

[ANiknejad]

I am wondering how this strategy fits with the UBERON one, where the aim is to have a generic class that groups species ?

[ghost]

@ANiknejad, the species-agnostic classes in Uberon should invoke the species-agnostic CL classes in the axioms. Species-specific cell type classes are also required in CL where there are species-specific features of the cell type and/or specific use case requirements.

[ghost]

To illustrate the point above, UBERON:0005206 'choroid plexus stroma' has the axiom has part some dendritic cell, NOT 'dendritic cell, human'.

'dendritic cell, human' has a definition specific to Homo sapiens.

[ANiknejad]

But in the precise example of CL:4023056 name: vascular leptomeningeal cell (Mmus) what could be the need to create this class?

[ghost]

But in the precise example of CL:4023056 name: vascular leptomeningeal cell (Mmus) what could be the need to create this class?

After a review of the provenance of this term, it appears both the general and mouse-specific classes were created based on the conversation that follows from this comment: https://github.com/obophenotype/cell-ontology/pull/968#discussion_r611683838

[ANiknejad]

yes, but in this comment, they talk about VLMC-like, and CL:4023056 name: vascular leptomeningeal cell (Mmus) is not described as a like one, right? and none marker is reported in its definition

Create species-specific entries and add above markers to them instead

[ANiknejad]

oh sorry, I see the RO with markers!

relationship: RO:0002292 PR:P11087 {xref="PMID:30096314"} ! expresses collagen alpha-1(I) chain (mouse) relationship: RO:0002292 PR:P26618 {xref="PMID:30096314"} ! expresses platelet-derived growth factor receptor alpha (mouse) relationship: RO:0002292 PR:P51885 {xref="PMID:30096314"} ! expresses lumican (mouse)

[ghost]

yes, but in this comment, they talk about VLMC-like, and CL:4023056 name: vascular leptomeningeal cell (Mmus) is not described as a like one, right? and none marker is reported in its definition

In the comment I see "We should have species neutral terms for VLMC and ABC." Both neutral and mouse-specific classes were added in the PR noted above.

If you believe the mouse-specific class should be edited/obsoleted, you are welcome to propose changes and/or reach out to the editors involved on the PR to get more insight on their decisions for adding both.

[ghost]

oh sorry, I see the RO with markers!

relationship: RO:0002292 PR:P11087 {xref="PMID:30096314"} ! expresses collagen alpha-1(I) chain (mouse) relationship: RO:0002292 PR:P26618 {xref="PMID:30096314"} ! expresses platelet-derived growth factor receptor alpha (mouse) relationship: RO:0002292 PR:P51885 {xref="PMID:30096314"} ! expresses lumican (mouse)

@ANiknejad, if you have any other concerns, kindly add them here. If your question has been answered, kindly close the ticket. Thank you for your contributions.

[ANiknejad]

thank you for clarifications, Bradley, yes so far I close the issue