[go] representation of -> in go term names

[Colin Batchelor]

Forgot to say: some names have double-headed arrows, which have a
different meaning, instead, which is why we don't just use dashes.

http://www.chem.qmul.ac.uk/iupac/2carb/38.html

Colin.

> -----Original Message-----
> From: Colin Batchelor
> Sent: 21 February 2008 17:10
> To: Judith Blake; Midori Harris
> Cc: Jim Hu; GO mailing list
> Subject: RE: [go] representation of -> in go term names
> 
> Hello,
> 
> It's a carbohydrate nomenclature thing, and it really is an arrow.
> IntEnz uses a character entity for this.  I've asked one of our
natural
> products people and he said that generally authors used arrows, but
fell
> back on dashes if they didn't know how.
> 
> So a - would be OK, I suppose.
> 
> Best wishes,
> Colin.
> --
> Dr Colin Batchelor MChem MRSC, Production Systems Analyst
> Informatics Department,
> Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
> batchelorc at rsc.org t: +44 1223 432280
> 
> > -----Original Message-----
> > From: Judith Blake [mailto:jblake at informatics.jax.org]
> > Sent: 21 February 2008 15:45
> > To: Midori Harris
> > Cc: Jim Hu; GO mailing list
> > Subject: Re: [go] representation of -> in go term names
> >
> > 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
> =t
> > erms&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
> > >>
> > >>
> 
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