[Ontology-editors] [Obo-cell-type] help wanted getting CL and GO consistent

[David Sutherland]

On Tue, 7 Oct 2008, Chris Mungall wrote:

> 
> On Oct 7, 2008, at 2:26 AM, David Sutherland wrote:
> 
> > On Mon, 2008-10-06 at 14:39 -0700, Chris Mungall wrote:
> >> We have a set of computable cross-product definitions for a subset of
> >> GO-biological process terms referencing cell types. See:
> >>
> >> 	http://wiki.geneontology.org/index.php/XP:biological_process_xp_cell
> >>
> >> Using the OBO-Edit reasoner we can find implied links in GO. The
> >> policy in GO is to redundantly assert links that can be implied by  
> >> the
> >> reasoner through xp defs.
> >>
> >> For example, CL says:
> >>
> >> * oenocyte is columnar/cuboidal epithelial cell
> >>
> >> The xp defs say:
> >>
> >> * oenocyte differentiation = cell differentiation that
> >> results_in_acquisition_of_features_of oenocyte
> >> * columnar/cuboidal epithelial cell differentiation = cell
> >> differentiation that results_in_acquisition_of_features_of columnar/
> >> cuboidal epithelial cell
> >>
> >> Given this, a reasoner will infer:
> >>
> >> * oenocyte differentiation is_a columnar/cuboidal epithelial cell
> >> differentiation
> >>
> >> This link is not present in GO
> >>
> >> There is a summary of these results here:
> >>
> >> https://sourceforge.net/tracker/index.php?func=detail&aid=1940574&group_id=36855&atid=440764
> >>
> >> - Many of these pertain to immunology; Alex suggested waiting on CL
> >> revisions based on recent immunology work. This seems reasonable -
> >> provided this is reasonably imminent. If not, I think we should just
> >> go in and make things consistent.
> >>
> >> - The non-immunology ones seem fairly straightforward cases of one
> >> ontology being right and the other being wrong.
> >>
> >> - David S : can you comment on oenocyte?
> >
> > This is wrong.  Oenocytes are *not* epithelial.  They are large cells
> > which sit in clumps under the epidermis.  Function is not well
> > characterised, but I believe there is some evidence that the adult
> > oenocytes have some function in pheromone release.
> 
> Great, we're getting somewhere!
> 
> I will move oenocyte to be an is_a child of cell for now. We can find  
> better is_a parentage for it later, the important thing for now is to  
> be not wrong.
> 
> The current structure is somewhat curious. Here is the is_a hierarchy:
> 
>       is_a CL:0000066 ! epithelial cell
>        is_a CL:0000075 ! columnar/cuboidal epithelial cell
>         is_a CL:0000463 ! epidermal cell (sensu Insecta)  
> [develops_from: epidermoblast]
>          is_a CL:0000487 ! oenocyte ***
> 
> oenocyte has no is_a sibling, so I will go ahead and obsolete CL: 
> 0000463 ! epidermal cell (sensu Insecta)
> 
Please don't!  It's a pretty fundamental cell type - and very disimilar to
vertebrate epidermal cells.

Quick stab at a short def:
columnar/cuboidal epithelial cell which secretes cuticle from its apical
side.

Can be much more difficult to pin down what cells are epidemoblasts.  Some
Neuroblasts have one or two epidermal cells at the end of their lineage
trees.  Are epidermoblasts as well as neuroblasts?

David


> This term seems to exist purely to provide developmental lineage to  
> epidermoblast. I can retain this by making a direct develops_from link  
> from oenocyte to epidermoblast -- but then we would be making a  
> stronger statement than is present in fly_anatomy, which provides no  
> developmental lineage for oenocyte, even over part_of. I will thus err  
> on the side of caution for now.
> 
There is lineage for the larval oenocytes in FBbt.  Not sure anyone has
studied where adult oenocytes come from though.

David
> This was CL previously:
> 
> 
>