Re: Proposed format for PPS hyperglossary

Kurt Giles (
Sat, 10 Feb 1996 14:52:38 +0200

On Feb 9, 9:17pm, Darren Fast wrote:
> Subject: Proposed format for PPS hyperglossary
> Hi there, I have been following the discussion on the list and am somewhat
> overwhelmed by the technology.

You're not the only one :-)

> But despite this, I would propose as a
> starting point, the following outline for the glossary.

Excellent, this is just what I came in today to do.

> The basis for the
> divisions are in the broad categories that I as a biochemist think about
> proteins.

Here's what I think the list should be based on Darren's original list and
taking into account Peter's comments. I guess it doesn't matter too much since
we should be able to move things around.

-hydrogen bond

Genetic code

Protein Biosynthesis
-post-translational modifications
--amino acid modification
--lipid attachment

Protein structure
-primary structure
--amino acids
--torsion angles
-secondary structure
--alpha helix
--3-10 helix
--beta sheets
-tertiary structure
--classification systems ****I think it would be a lot of unnessesary work
---SCOP ****to list all examples here, if links could just
---Enzyme commission ****be put into e.g. SCOP
-quaternary structure

One important point is how basic do we start? (the PPS95 glossary contains
terms like 'acid') This could produce a very large list of terms for
'Terminology' and it might therefore be better to have sub-headings of
terminology within each section or 'concept' i.e. Genetic code, Protein
Biosynthesis and Protein structure. Terminology applicable to more than one of
these concepts could easliy also be linked to from another.
It's probably best to base it almost solely on protein structure to start with
then add additional concepts if and when we need them.

Here's how I envisage the structure of each entry:

[three to four lines max.]

Related words
[intra and inter VHG links, i.e. at least a list of the sub-directories or
terms leading from the 'concept']

Related information
[other WWW links]


                              Dr. Kurt Giles                     
  Department of Structural Biology   |  e-mail:
  Weizmann Institute of Science      |     vox: +972-8-9343759
  76100 Rehovot, Israel              |     fax: +972-8-9344159
           ** **