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

[Phil J. @ E. <pj...@eb...>]

Hi Martin,

I would be inclined to go for the separate term / relationship
mechanism.  I would not worry too much about OBO-edits failings as far
as making this decision is concerned.

I would also suggest that if you are going to define a new
relationship type for this purpose, you could make it more specific,
e.g. 'has_regular_expression' instead of just 'has_a'.  When defining
the relationship (which at the end of the day is just another term in
the CV) you can also give it a definition so that the intent of the
regular expressions is unambiguous and the OBO file is self
documenting.


Cheers,

Phil.

2008/11/7 Martin Eisenacher <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
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
>
>



-- 
Phil Jones
Senior Software Engineer
InterPro Team
PANDA Group, EMBL-EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD
UK.

Work phone: +44 1223 494406 (NEW NUMBER)
Skype: philip-jones