#27 special chars in IntEnz and ChEBI

[Kirill Degtyarenko]

<I have posted the same bit of text on IntEnz forum>

http://www.ebi.ac.uk/intenz/encoding.html

This is much shorter list than the one we use in ChEBI.
In particular, I has no <stereo>, <element>, <protein>
and some other tags which we do use in ChEBI as well as
IntEnz. Since our aim is to have all the tags in IntEnz
names exactly as in ChEBI, I think we should use the
same list for the both databases, even though it is
unlikely that we will ever use all ChEBI tags in IntEnz
(but you never know)

</I have posted the same bit of text on IntEnz forum>

Which reminds me that in ChEBI <protein> does not
behave like it does in IntEnz. Viz.
<protein>protein</protein> should be visualized as
[protein]

[pmatos]

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This IntEnz encoding is not upto date and I think its not
worth keeping up to date for the public as nobody uses it
except curators. BTW the ChEBI set is not upto date either:
http://www.ebi.ac.uk/chebi/pages/html/help.html#specialCharacters

Another note the ChEBI and IntEnz encoding have diverged
slightly. Changes were made when the IntEnz flat-file
writing was created. This means that in a handful of cases
the translation of some tags into ASCII for IntEnz and ChEBI
are slightly different. This does not affect the function
and definition of the tags - it just affects the display of
the ASCII format.

The most up to date set can be found in the ChEBI curator
tool. I would suggest that for each tag - a defintion is
created and where it should/should not be used.