Characters and States and GUIDs and descriptive data
J.Kennedy at NAPIER.AC.UK
Wed Jan 25 17:48:20 CET 2006
This isn't strictly GUID stuff but we did some work on looking at
character descriptions of plants and tried to find a mechanism that
would help tie down the definitions of descriptions so that we might be
able to compare taxon concepts based on character descriptions and
looked at using id to refer to these to aid comparison in databases.
Currently descriptions tend towards natural language with the same term
being used in many different contexts to mean different things so rather
than stay with that approach we wanted to tie the taxonomists down to
some agreed terminology - but of course this was not something they
wanted as it didn't give them enough freedom. So we proposed a
We tried to avoid using characters (in the traditional taxonomic sense)
as a character could be too many different things and had a simple model
that a description would be of a structure (which could be a part of
some super structure(s) and all of which were defined) each structure
had properties (e.g. length, colour etc) and one could assign values to
these properties which for qualitative properties were all from a list
of defined terms.
What we tried to do was get a set of terms that could be defined in a
general sense (and could have a GUID) and then when combined i.e.
structure id + property id + value id this would have a different
meaning for different instance combinations.
So we could search on the character (if you like) or on any part of the
Ok this is hard to describe here and the model is a bit more complicated
than I've described, but if you're interested you could look at one of
our papers. Unfortunately we haven't done any more work recently, but I
still think there is an idea in there....
Paterson, T., Kennedy, J., Pullan, M., Cannon, A., Armstrong, K.,
Watson, M., Raguenaud, C., McDonald, S. and Russell, G. (2004). A
Universal Character Model and Ontology of Defined Terms for Taxonomic
Description. In E.Rahm, Lecture Notes in Bioinformatics: Proceedings of
Data Integration in the Life Sciences (DILS) Leipzig 2004 LNBI 2994
63-78. : Springer Verlag.
Paterson, T. and Kennedy, J. (2004). Approaches to Storing and Querying
Structural Information in Botanical Specimen Descriptions (c) BNCOD21
http://www.macs.hw.ac.uk/BNCOD21. In L.M. MacKinnon, A.G. Burger, P.W.
Trinder (Eds), 21st Annual British National Conference on Databases
(BNCOD21) (pp. 80-91). Edinburgh: Heriot-Watt University.
Pullan, M., Armstrong, K., Paterson, T., Cannon, A. and Kennedy, J.
(2005). The Prometheus Description Model: An examination of the
taxonomic description building process and its representation. Taxon,
> -----Original Message-----
> From: Taxonomic Databases Working Group GUID Project [mailto:TDWG-
> GUID at LISTSERV.NHM.KU.EDU] On Behalf Of Dag Terje Endresen
> Sent: 25 January 2006 17:04
> To: TDWG-GUID at LISTSERV.NHM.KU.EDU
> Subject: Re: Characters and States and GUIDs and descriptive data
> Thanks for the interesting discussion on descriptive data! This is of
> high relevance to the germplasm genebanks as well.
> Assigning a GUID to phenotype (character) would allow a statement like
> disease resistance measured on specimen GUID_#s1 according to the
> measurement method described and defined by GUID_#p1 (which could for
> example be percent of leaf covered by fungus or similar). Food crop
> phenotypes are often measured according to measurement standards
> defined and published by IPGRI or UPOV. I think persistent actionable
> GUIDs for the characters would be of great value and that we would
> see plant breeders and scientists collecting public phenotype data if
> the measured values (states) from different datasets are made more
> readily interoperable. Assigning GUIDs are however not the complete
> solution. The context of the measurement (like for example climate,
> humidity) would make the scored values incomparable without
> on this modifier. I think this is addressed by SDD. Comparing
> states from different datasets and different context are much more
> challenging than uniquely identifying characters and states. But it
> would be one nice step in a useful direction.
> Dag Terje
> Quoting Roger Hyam <roger at tdwg.org>:
> Hi Robert,
> I think you restated the question well. I am afraid I have the
> just now but not the answer ;)
> To me it seems to make more sense for a user to string concepts
> to make a meaning rather than defining every possible contextual
> meaning. So if a central thesaurus defined flower and colour they
> be strung together as a series of assertions in a descriptive
> In N3:
> mytaxa:rose myterms:has _:att .
> _:att rdf:type myterms:flower .
> _:att myterms:is myterms:red .
> There would still be room for specific complex predicates and objects
> be defined centrally but in general this appears to allow for greater
> flexibility in an open system. It might not suite all tastes though.
> Robert Huber wrote:
> > Thank you Roger!
> > I heard about DELTA and SDD seems to be very interesting! So when we
> are thinking about GUIDs in this context I assume you would assign a
> GUID on the 'contextual meaning of terms'? E.g. what open means when
> you describe a open umbilicus?
> > A GUID would then direct the user to a document/ db entry which
> explains that ? Or would the GUID be assigned to a complete SDD
> > best regards,
> > Robert
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