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

[Chris Mungall]

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?

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