There are two CLIDs for the same term 'plasmacytoid dendritic cell'

obophenotype / cell-ontology

An ontology of cell types

https://obophenotype.github.io/cell-ontology/

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There are two CLIDs for the same term 'plasmacytoid dendritic cell' #2421

Open Tulasi08 opened 4 months ago

Tulasi08 commented 4 months ago

CL term - plasmacytoid dendritic cell

Description of typo, bug or error In the cl.obo file I had found two different CLIDs for plasmacytoid dendritic cell (CL:0001058 and CL:0000784) as both are subset of cellxgene_subset and human_reference_atlas.

Please let me if I have misunderstood anything.

Thanks and Regards, Tulasi S

addiehl commented 4 months ago

Hi Tulasi,

CL:0000784 'plasmacytoid dendritic cell' is a general term for plasmacytoid dendritic cells from any species that has this cell type.

CL:0001058 'plasmacytoid dendritic cell, human' is a specific term that applies only to human plasmacytoid dendritic cells

CL:0000784 'plasmacytoid dendritic cell' is the parent term of CL:0001058 'plasmacytoid dendritic cell, human'

The inclusion of both types in CL is warranted. Their use in annotating cellxgene data and whether they have been misapplied is not under the control of the CL developers. Note that it is not incorrect to use CL:0000784 when annotating human data, it is just less specific.

Thanks, Alex

aleixpuigb commented 4 months ago

Thank you for your reply @addiehl. Is you question answered, @Tulasi08? If so, I will close this ticket. Thank you for your contribution!

Tulasi08 commented 4 months ago

Yeah! Thanks for the clarification.

Best Tulasi S

On Tue, 9 Jul 2024 at 8:46 PM, Aleix Puig @.***> wrote:

Thank you for your reply @addiehl https://github.com/addiehl. Is you question answered, @Tulasi08 https://github.com/Tulasi08? If so, I will close this ticket. Thank you for your contribution!

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/cell-ontology/issues/2421#issuecomment-2217995103, or unsubscribe https://github.com/notifications/unsubscribe-auth/A5DLB63P6HJ4LOQLLKQRZP3ZLP5FJAVCNFSM6AAAAABKJSTCKCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMJXHE4TKMJQGM . You are receiving this because you were mentioned.Message ID: @.***>

lubianat commented 4 months ago

I think this may be closed, but I ping @jahilton for information here, as CELLxGENE indeed often contains annotations both to the species-agnostic and the human-specific cell types (which are not wrong, but somewhat inconsistent)