[go] representation of -> in go term names

[Jim Hu]

Ideally, this would be represented by a real right arrow, though,  
instead of a dash and a greater than.  But if someone is trying to  
search for 1->4, they will probably type it that way.

JH

On Feb 21, 2008, at 1:29 PM, Harold Drabkin wrote:

> It is being used in place of the right pointing arrow (not a dash).
> From IUPAC: Carbohydrate Nomenclature (1992, 2nd edition)
>
> "Between the name of one glycosyl radical and the next
> are placed two locants which indicate the respective positions
> involved in this glycosidic union; these locants are
> separated by an arrow (pointing from the locant corresponding
> to the glycosyl carbon atom to the locant corresponding
> to the hydroxylic carbon atom involved) and are enclosed in
> parentheses."
>
> I have included an example. The arrow comes FROM the carbon that  
> carries the glycosyl "O";
>
> We really need the arrow or you lose info.
>
> hjd
>
> Judith Blake wrote:
>> I agree,
>> my first take is that this is a convention thing, an alternative to  
>> using a dash...
>>
>> judy
>>
>> 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
>>>>
>>>>
>
> <Picture 3.png>

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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