Potentially incorrect inference from lacks_membrane_part

[GoogleCodeExporter]

The same problems previously pointed out regarding lacks_part apply equally to 
lacks_plasma_membrane_part.  

Here's an example of inference that a cell type does not have *any* 'KLRB1-like 
protein' in its plasma membrane, when the definition only states the lack 
specific subclass of this protein type:

Explanation for: 'Kit and Sca1-positive hematopoietic stem cell' SubClassOf 
lacks_plasma_membrane_part some 'KLRB1-like protein'

'Kit and Sca1-positive hematopoietic stem cell'
 - EquivalentTo 'hematopoietic stem cell' and (has_plasma_membrane_part some 'SLAM family member 1') 
and (has_plasma_membrane_part some 'mast/stem cell growth factor receptor') 
...
and (lacks_plasma_membrane_part some 'killer cell lectin-like receptor 
subfamily B member 1C') 
and (lacks_plasma_membrane_part some 'lymphocyte antigen 76')

 - 'killer cell lectin-like receptor subfamily B member 1C' SubClassOf 'KLRB1-like protein'

I'm not sure that there is a good solution for this, short of explicitly 
stating negation.

Original issue reported on code.google.com by dosu...@gmail.com on 4 Nov 2013 at 1:28

[paolaroncaglia]

Class Usage for lacks_plasma_membrane_part = 432. Commenting to prevent staleness.

[dosumis]

@addiehl worked with James Overton to run tests for inconsistency when these were converted to explicit negation. Some issues discovered were fixed. Alex - it would be great if we could periodically run these tests. Is the code available? Maybe we could make a ticket to fold this into the cl MakeFile extension as an optional test.