(GEN) Schema independence
G.Hagedorn at BBA.DE
Mon Nov 29 18:09:49 CET 1999
> > * I propose to have 3 XML Namespaces for our different XML
> > vocabularies:
> > o biological descriptions (generalities)
> > o botany
> > o zoology
> I'm sure you don't mean to leave out Mycology, Bryology, etc.
Exactly (says a mycologist). Also, what about at least 20 different
name spaces for protists, 50 or so for bacteria. Viruses, mycoplasms,
Biological diversity is well beyond our current grasp. We should
admit that we do NOT understand it in any way sufficiently. Even what
we understand is obscured by terminoly inadequacies or concurrent,
but not entirely synonymous terminology. From my own experience, I
think that unifying character definition even among fairly closely
related groups of a small group of the fungi can be a challenging
Richard Pankhurst could probably step in here and explain why it is
so difficult to even draw up a core consensus character set for all
higher plants (an effort he is concerned with for several years now).
The tendency in this discussion to assume that things like leaf,
petiole, veins etc. should be directly coded into the standard
worries me. The examples are fine for the purpose of discussion, but
I hope that most people agree that the schema independence of DELTA
(and principally also NEXUS, although NEXUS leaves most of the
definition to free text in a published article) is a big achievement,
and I would not like to sacrifice it.
This does not mean that we should not try to unify character schemas,
but it definitely should be a separate task. We need a general
standard, and an applied standard that acutally uses a defined
So, I believe we need:
o Character schema definition language, expressed in XML-DTD or
- Researchers working on weird stuff like Tardigrada should not be
required to wait until somebody creates a schema for them, but
must go ahead and develop their own schema.
- DELTA is, in part, such a language.
o Character schema (an applied character definition, that acutally
defines names, type, constraints, etc. for a set of characters),
expressed in the new Character schema definition language.
- The character definition of a DELTA data set is such a schema.
- The thing to achieve would be, to express this in such a way
that it becomes a usable XML Namespace definition, while still
linking into the Character schema definition language! I could
then be directly used by XML tools, but it would be developed
with added value by the more relevant additional definition in
the Character schema definition language!
o An application to express item descriptions using these tools.
- Example: DELTA ITEM DESCRIPTION.
Thus I envision something like:
+ Character definition language,
adding special metainformation to:
+ Standard XML Namespace definition,
which, however, can be used independently
Both together form a character schema of a new standard, which would
be used in item descriptions. The item descriptions themselves have
+ A markup language to mark existing (or computer generated) free
+ A data language, to exactly define the data used, including
knowledge management support
See also the separate post "Markup of text descriptions Vs.
structured data (GEN)"
Inst. for Plant Virology, Microbiology, and Biosafety
Federal Research Center for Agriculture and Forestry (BBA)
Gregor Hagedorn Net: G.Hagedorn at bba.de
Koenigin-Luise-Str. 19 Tel: +49-30-8304-2220
14195 Berlin, Germany Fax: +49-30-8304-2203
Often wrong but never in doubt!
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