[Biodevelopers] XML Standardization?

[Patrick McConnell]

Can schema's easily represent parsed character data like DTD's can?  That
is, can you have this:

<annotation>This gene, <accession>ABC123</accession>, is a precursor to
<accession>DEF456</accession>, which is a <keyword>G-Protein
regulator</keyword>.</annotation>

represented by a schema?

My feeling is that DTD's are better at representing this sort of
document-style XML.  Am I wrong here?

-Patrick





Alex Milowski <alex at milowski.com>@bioinformatics.org on 01/13/2003 12:40:29
PM

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Subject:    Re: [Biodevelopers] XML Standardization?


On Friday, January 10, 2003, at 02:03 PM, Joe Landman wrote:

>   There are Ontologies projects which are trying to keep naming
> consistent across organisms.  The information needed in each
> sub-discipline is subtly different.  There are overall efforts within
> specific groups such as MicroArrays (MGED) and others.  However the
> vocabularies to help define the data structures properly needs to
> follow
> from a common set of agreed upon terms (hence the ontologies issues).
>

So, what about type libraries?  With the advent of XML Schema
(something I had
some involvement in), it would seem that common schema type libraries
across common
areas would be very helpful.

Most of the efforts that I see out there use DTDs.   That seems rather
restricting
for the complexity of data being described.

Basically, naming efforts, while a good thing, aren't enough.

This still doesn't address the coordination issues.  There are
organizations like
OASIS (see http://www.oasis-open.org) which have the structure to allow
standardization
of vocabularies.  Although, while I'm a fan of standardized
vocabularies, that needs to
come after some success with using them.  That is, you can't
standardize a vocabulary
until you have one that has some evidence of functioning.

Alex Milowski                FAX: (707) 598-7649
  alex at milowski.com

"The excellence of grammar as a guide is proportional to the paucity of
the
inflexions, i.e. to the degree of analysis effected by the language
considered."

Bertrand Russell in a footnote of Principles of Mathematics


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