[go] representation of -> in go term names

Thu Feb 21 12:31:02 PST 2008

Has the addition to Amigo of a special-symbol selection field that some edit and search interfaces have.  For instance, http://en.wikipedia.org/w/index.php?title=Wikipedia:Sandbox <http://en.wikipedia.org/w/index.php?title=Wikipedia:Sandbox&action=edit> &action=edit .  One could use Unicode of HTML character entity references (the entity reference is used in wikimedia based things like Wikipedia) for arrow encoding in the data itself; see http://www.alanwood.net/unicode/arrows.html.

Regards,

Courtland

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-----Original Message-----
From: owner-go at genome.stanford.edu [mailto:owner-go at genome.stanford.edu]On Behalf Of Jim Hu
Sent: Thursday, February 21, 2008 3:17 PM
To: hjd at informatics.jax.org
Cc: Judith Blake; Midori Harris; GO mailing list
Subject: Re: [go] representation of -> in go term names

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 <http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&show_associations=direct&search_constraint=terms&depth=0&query=GO:0033942> &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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