[Psidev-pi-dev] CV: regexp for default enzymes

[Martin E. <mar...@ru...>]

Hi Andreas, Angel, all,

I tried two variants for encoding regular expressions
for the default enzymes into the OBO file:
1) "xref" and 2) "has_a" relationship.

See http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo 


Excerpt from obo file (for Trypsin):


[Term]
id: PI:00251
name: Trypsin
xref_analog: regexp:(?<=[KR\])(?\!P)
is_a: PI:00045 ! cleavage agent name
relationship: has_a PI:00176 ! (?<=[KR])(?!P)

For the 1st variant, the regular expression is only a string.

For the 2nd variant, the regular expression is itself a 
term (PI:00176) and child of a "regular expression" term.


Both methods have disadvantages:
In OBOEdit the xref gives a warning, because it contains non-URI characters.

In OBOEdit the has_a relationship is not shown in the tree view, but only in 
the Parent Plugin (see screenshot attached).

@Angel, do you know a better method?

@All: Which do we prefer?

@Andreas, the obo file is yours now...


  Bye
   Martin