#191 T cell

GO-Cell-XP
open
5
2014-12-02
2012-03-22
Melanie Courtot
No

Hi, In the current CL file (March 22nd 2012) T cell is defined as "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." However I couldn't see any restriction to that effect, nor a class "T cell receptor complex"

Use case: I am trying to query the file to get something along the lines of "what type of cells is CD3 positive" which I would expect to return T cells. CD3 is part of the T cell receptor complex, so that would require that the restrictions/class above are explicitly added to the file.

Thanks,
Melanie

Discussion

  • Hi Melanie,

    It does appear that the textual definition of T cell has never been updated to match the logical definition. I believe that there was a conflict between DN2 thymocytes being immature T cells but not yet expressing the TCR complex that led to the change in the logical definition, although this is not a fully satisfying solution. We do need to fix the textual definition.

    The class "T cell receptor complex" exists in the GO, GO:0042101, and is part of the logical definition for 'mature T cell ; CL:0002419".

    [Term]
    id: CL:0002419
    name: mature T cell
    namespace: cell
    def: "A T cell that expresses a T cell receptor complex and has completed T cell selection." [GOC:tfm]
    synonym: "CD3e-positive T cell" EXACT []
    synonym: "CD3epsilon T cell" RELATED []
    synonym: "mature T-cell" EXACT []
    is_a: CL:0000084 ! T cell
    intersection_of: CL:0000084 ! T cell
    intersection_of: has_completed GO:0045058 ! T cell selection
    intersection_of: has_plasma_membrane_part GO:0042101 ! T cell receptor complex
    relationship: has_completed GO:0045058 ! T cell selection
    relationship: has_plasma_membrane_part GO:0042101 ! T cell receptor complex
    created_by: tmeehan
    creation_date: 2010-10-12T01:56:15Z

    The term stanza for GO:0042101 is part of the cl.obo file available through the OBO Foundry site, but this GO protein complex term does not logically specify CD3 or more accurately the subunits of CD3, as parts. Of course, CD3e is really the only CD3 subunit that people stain for.

    If there's a breakdown in the ability to query for CD3e-positive cell types it would be at the level of the GO not specifying protein complex components, rather than the CL. In any case, the CL does not attempt to capture all protein expression on given cell types, only that which is necessary and sufficient to define a cell type.

    So, sadly, the combination of the CL and GO are not sufficient to answer your query at this time.

    Best regards,

    Alex

     
    • assigned_to: Alexander Diehl
    • Group: --> GO-Cell-XP