Re: definitions - starting with amino acids

peter Murray-rust (
Wed, 5 Jun 1996 15:06:45 +0100 (BST)

On Wed, 29 May 1996, Kurt Giles wrote:

> Firstly a couple of general points.
> For those of you that haven't bookmarked them yet, the definitions are at:
> These will be constantly updated as decisions are made on term definitions.


> I've tried to edit the definitions so that the term being defined is not
> included in the definition. Many definitions were of the format:
> [term]
> [term] is.......
> There may still be a couple left, so please point them out if you see them.

This sort of thing takes a lot of time - so if you find yourself doing a
good deal of fiddly re-organisation keep you spirits up!

> Where the term is an acronym, should the full name be used as the term (even
> when the acronym is in common usage - SCOP is a good example)?

This is an excellent illustration of the importance of curation. the most
important thing is to have a consistenmt style. In that case I think the
acronym is really the only thing that most people want to know. 'DNA' is
on the borderline. I prefer 'Interleukin-2' to IL-2 (for a glossary).

Abbreviations are also a problem here - but just go ahead and build your
own policy :-)

> The definitions of the individual amino acids are probably one of the most
> important to get sorted out first.
> If a molecular formula is going to be shown, is it really necessary in the
> definition to state that it has, for example, a polar side chain. Some level of

IMO definitely NO. This is a glossary - 'what *is* X?' - not an
encyclopedia entry. Perfectly OK to hyperlink it to 'physical properties
of AA...'

For example I want to know what PCA is, what its formula is - perhaps when
I might encounter it (e.g. 'a modified AA with the formula (I) sometimes
found at the N-terminus of proteins (? as a result of?).

But to show that even Homer nods, compare the entries in Medline for
'Mice' and 'Horses'.

> --------------------------------------------------------------------------

Peter Murray-Rust, Glaxo Research & Dev. (; (BioMOO: PeterMR)
Birkbeck College,, CBMT/Daresbury,