Re: [Psidev-pi-dev] Have I ever mentioned that I don't like OBO edit?

[Jones, A. <And...@li...>]

Last week on the call we decided on manually writing the OBO file... not ideal
but it is fairly easy.

 

The only plus side of OBO is that the ProDac people seem to be willing to make
sure that the validator works with schema + mapping file + OBO CV, I suspect
this would require quite a lot more work if we switched to OWL. Also, PSI wants
to have a coordinated CV strategy for all WGs – this means OBO for all us, or
opening up an old argument again J

 

Cheers

Andy

 

 

 

 

 

From: Angel Pizarro [mailto:an...@ma...] 
Sent: 15 October 2008 15:33
To: psi...@li...
Subject: [Psidev-pi-dev] Have I ever mentioned that I don't like OBO edit?

 

So in creating CV terms for the various enzymes it is legal in the OBO format to
add any "name: value" pair to a term, but OBO-edit does not support this
feature. It will not even show the annotation if it is put manually in place. I
wanted to add a specific place for a "cleavage_rule_regx"  but this won't fly in
OBO-edit

As for using another ontology editor, such as Protoge, it seems that the java
library used to transalate OBO into OWL will apply th ecomment rule to any
shriek ("!") even if it is escaped. Trying the perl tools now to see if they are
any better, but I would like to put on the table (again) that we use some other
format and tool for our CV other than OBO and OBO edit. The situation is uch
that I am even considering writing some ontology editing tool myself. 

Any thought on this by anyoen? 
-angel