[go] representation of -> in go term names

[Suzanna Lewis]

Hi Jim,

It might (almost certainly will) cause problems for some software, but  
the consensus we reached on the go-top call the other day is that we  
would not be putting any escape characters into the OBO files. These  
would contain only the pure unadulterated text and it would be up to  
any downstream software to pre-process the text to add any escape/ 
macros as appropriate for the formatter in question. I think Mike said  
that there is one case where a sneaky escape '\' had crept in before a  
curly brace and this will be removed. Two reasons for this. One is  
that different formatting tools have different ways of recognizing  
oddball characters, and second we want to avoid those people who  
present plain text from showing the escapes as if they were a formal  
part of the name.

-S

-
On Feb 21, 2008, at 4:40 AM, Midori Harris wrote:

> Hi Jim,
>
> I can't comment on the techy aspects of your questions, such as  
> which representations of arrows are compatible with which software,  
> but I do think GO term names should choose one and use it  
> consistently. I also
> think we'll probably need to keep synonyms that use some of the  
> alternate representations.
>
> Chris - can you run a check for consistency for this?
>
> midori
>
> On Wed, 20 Feb 2008, Jim Hu wrote:
>
>> There are some go terms that use -> to represent a right arrow.  On  
>> GONUTS we have
>>
>> http://gowiki.tamu.edu/wiki/index.php/Category:GO:0033942_%21_4-alpha-D-%28%281-4%29-alpha-D-glucano%29trehalose_trehalohydrolase_activity
>>
>> the same term on AMIGO:
>>
>> http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&show_associations=direct&search_constraint=terms&depth=0&query=GO:0033942
>>
>> For wiki compatibility, we convert curly brackets to parentheses.   
>> I converted the -> to a -, but I'm not sure whether that is  
>> appropriate.
>>
>> Mike Cherry and I discussed this a tiny bit off list.  Mike wrote  
>> (off-topic discussion of iPhones redacted):
>>> 4-alpha-D-((1->4)-alpha-D-glucano)trehalose trehalohydrolase
>>> I find the -> at several places, although some use 1,4 instead of  
>>> 1->4. Also GO has the { escaped by not the }.  It seems that no  
>>> one is removing the \, this include MGI and QuickGO web sites.
>>> I think this is a good thing to bring up to the GO list.  There  
>>> are lots of synonyms that have '->'.
>>
>> I'm not sure whether 1,4 and 1->4 mean the same thing.  The ->  
>> causes problems for mediawiki when it's in a page title, as we use  
>> term names as pages on GONUTS.  It seems to work ok in AMIGO.  Is  
>> this a good standard way to represent right arrows?  Will the '>'  
>> cause problems for othe software besides mediawiki?
>>
>> Jim
>>
>> =====================================
>> Jim Hu
>> Associate Professor
>> Dept. of Biochemistry and Biophysics
>> 2128 TAMU
>> Texas A&M Univ.
>> College Station, TX 77843-2128
>> 979-862-4054
>>
>>
>