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

[David Sutherland]

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.

David
> 
> I volunteer to make required changes to CL - just send me a list of  
> what needs fixed
> 
> I also volunteer to fix GO too (I can check in directly or just send  
> someone an updated file to check in). There's no reason to do this by  
> hand when it can be done with a few clicks in OE. I can also give  
> another demo of how this can be done in OE if people are interested.
> 
> Cheers
> Chris
> 
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