[Psidev-pi-dev] Issue 30 in psi-pi: Specifying the enzyme rules used in the search

[<cod...@go...>]

Issue 30: Specifying the enzyme rules used in the search
http://code.google.com/p/psi-pi/issues/detail?id=30

Comment #37 by eisenachM:
Two possible variants for encoding regular expressions
for the default enzymes into the OBO file:
1) "xref" and 2) "has_a" relationship.

[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).

Which do we prefer?




-- 
You received this message because you are listed in the owner
or CC fields of this issue, or because you starred this issue.
You may adjust your issue notification preferences at:
http://code.google.com/hosting/settings