Name for the standard

Kevin Thiele kevin.thiele at BIGPOND.COM
Wed Sep 17 16:07:21 CEST 2003

Well, in practice (though perhaps not in philosophy) there isn't actually
any great difference between describing a specimen and "describing" a
taxon - in the former case we're describing a real thing (we don't actually
use describe the characters of the object, rather we use characters to
describe), in the latter case we're describing a 'platonic ideal' - an
idealised 'object'. In the same way we describe a triangle as being a three
sided figure and we describe the angles as equalling 180 degrees, but what
we're actually describing is a platonic triangle, not any real one.

The platonic taxon can be handled in exactly the same way as a real object -
we can say that a real specimen has leaves 10-15 cm long, and the taxon to
which it belongs has leaves 8-18 cm long - easy.

In Lucid we are implementing a system for coding specimens, and specimens
merely become twigs on the taxon tree. We don't even seem to find that we
need to specify that this node of the tree is a specimen and that node is a

Note also that, for efficiency, different features are described at
different levels of the tree. Thus, whether the ovary is superior or
inferior is often most efficiently coded at family level, whether the leaves
are opposite or alternate may best be coded at genus level, what colour the
flowers are at species level, and how long the seeds are may be best at
specimen level. Ultimately, you're right, all coded features 'inherit' to
the ends of the tree (the specimens) but it would be inefficient to code, or
to store, the data there.

SDD still needs to visit specimen coding, but I think when we do we'll find
that it's trivial.

As to the scope of SDD, you're right that it should be possible in principle
to use it to describe the morphology of a widget, a soil, a nematode, or
perhaps even an asteroid. In practice, though, I doubt that it will be
useful for us to specifically scope SDD beyond the taxonomic domain -
probably the hardest domain to deal with anyway, so the ultimate challenge.

I quite like SDBO. Is there a courier service from Lisbon to Hawaii?

Cheers - k

----- Original Message -----
From: "Richard Pyle" <deepreef at BISHOPMUSEUM.ORG>
Sent: Wednesday, September 17, 2003 2:32 PM
Subject: Re: Name for the standard

> > you are right, in part.  Although the SDD activity is undertaken by
> > taxonomists, it extends beyond the core of taxonomy and nomenclature to
> > delineation and description of the objects themselves (taxa mostly, to a
> > lesser extent specimens).
> This is the part I'm having trouble understanding.  What is being
> "Described" are characters....correct?  While it is true that researchers
> have traditionally used character descriptions as a "short-hand" attempt
> delineate taxonomic concepts; the bottom line is that characters are
> intrinsically part of actual living, breathing (respirating) physical
> beings -- not the concepts (represented by names) that are intended to
> circumscribe a set of individual organisms deemed to belong to a common
> taxon.  When a taxonomist describes a character in the context of a taxon
> concept, what is really being asserted is that the character as described
> shared by the primary type specimen of the name used to represent the
> concept, as well as the primary type specimens of any/all names deemed to
> synonymous, as well as a wide swath of other individual organisms, a tiny
> fraction of which have been collected and curated in Museums; the vast
> majority of which live out their lives in their natural environment. In my
> mind, characters belong to individual organisms -- to associate them
> directly with taxon concepts (by way of the implied existence of
> organisms that share the character) is merely a short-hand convenience.
> Maybe this is getting off track, but my basic point is that if "SDD" is to
> be qualified in any way, I think it should be qualified in terms of
> biology, or biological objects; not necessarily taxonomy.
> > we we may be getting into the philosophical realm here...
> Dear God, no!.... :-)
> > Our Rainforest
> > Key project actually scored recorded individual specimens for each
> > taxon...  most DELTA and LUCID implementations amalgamate and
> > abstract this
> > to the level of taxon or taxon concept and score at this level...
> >
> > of course, SDD should ideally handle both approaches...
> I agree...but in my optimized view of the data management world, I'd like
> see characters linked with taxa via implied (if not real) specimens, even
> no specific physical specimen can be cited.  But if this is getting too
> philosophical for the issue at hand, I'll gladly step back to my previous
> status of quiet observer, so as not to clutter the list with tangential
> issues.
> > >Ultimately, this is about a Standard for Structured Data to Describe
> > >Biological Objects -- isn't it?
> >
> > I think that is what we are talking about...  you could leave out
> > 'structured data' too and it will still make sense...
> (Standard for Description of Biological Objects)
> (Description of Biological Objects Markup Language)
> (Biological Object Description Markup Language)
> None very sexy, though...
> Aloha,
> Rich

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