[tdwg-tnc] LSIDs and taxon concepts
Eamonn O Tuama
eotuama at gbif.org
Mon Oct 8 16:25:57 CEST 2007
I'd like you to comment on the issue of validation. In RDF, with its Open
World assumption, we loose the ability to validate. So how easy is it to
take RDF output and, if an application requires it, re-format it so that it
can be validated against an XML Schema, i.e., take your example below and
link it to an XML Schema. I understand that there are multiple ways in RDF
to express the same thing, so would that create problems for a schema if the
RDF was coming from different data providers. Or do we have control of that
because of the LSID vocabularies?
From: tdwg-tnc-bounces at lists.tdwg.org
[mailto:tdwg-tnc-bounces at lists.tdwg.org] On Behalf Of Roger Hyam
Sent: 05 October 2007 16:51
To: Richard Pyle
Cc: tdwg-tnc at lists.tdwg.org
Subject: Re: [tdwg-tnc] LSIDs and taxon concepts
Paul, Rich et al.
I'll try and answer all the questions in a single mail and also keep
Taxon Concept Schema (TCS) is an XML Schema that was standardized by
TDWG in 2005 but TCS also uses as short hand for distinguishing
between Taxon Names and Taxon Concepts.
The fundamental thing that TCS does (both the schema and the way of
modeling) is separate TaxonNames (or nomenclatural acts) from
TaxonConcepts (actual delimited or implied taxa that one would
identify something to).
In order to issue LSIDs for TaxonNames or TaxonConcepts it is
necessary to represent them in RDF rather than XML Schema. RDF is far
more modular by nature than XML Schema and so two vocabularies were
put together to represent TaxonNames and TaxonConcepts (rather than
one schema) but unless you are issuing pure nomenclatural data you
will usually use both.
The TaxonName vocabulary is being used by IPNI, Index Fungorum and
soon ZooBank. It is also being used by GBIF and anyone else who uses
the TaxonConcept or TaxonOccurrence because it is embedded within
these vocabularies. In fact it could be used anywhere some one wants
to break apart a name string.
The TaxonOccurrence vocabulary is being issued by the CATE project
(don't have the reference to hand) and Species2k/Catalogue of life
are going to use it for their checklist and of course by others who
issue TaxonOccurrence data.
I'll show and example of the embedding as it makes things clearer.
This is abbreviated for clarity. Suppose we want to express an
occurrence of a taxon (perhaps as a specimen)
<dc:title>Hyam.R.D. 284927 - Rhododendron ponticum L.</dc:title>
<.... other stuff ...>
<tcom:publishedIn>Some monograph by
So we have a TaxonOccurrence (really like a DarwinCore record but
with embedding). In order to express the identification of this
specimen in more detail than just a string we include a TaxonConcept
and a TaxonName. Neither the concept nor the name have identities
(they are both anonymous) but they are both objects of that type.
They could be replaced by references to external instances. There are
also properties to allow the supplier to "cop-out" of embedding
referencing anything and simply include a string if that is all they
have in their database.
So in issuing a TaxonOccurrence record I use both TaxonConcept and
TaxonName vocabularies. I am not using TCS in the sense of the XML
Schema but I am using in the sense of the notions involved.
This is where we are headed with integrated standards and semantic
I hope this helps.
BTW I hope it answers Rich's question as it is possible to add
reference info in the TaxonConcept to say where it was published
using the common properties defined in:
All the best,
On 5 Oct 2007, at 13:58, Richard Pyle wrote:
> Hi Paul and others,
> This leads me to a couple of questions about serving TCS data. For
> strictly speaking, ZooBank will be return metadata in accordance
> with the
> (http://wiki.tdwg.org/twiki/bin/view/TAG/TaxonNameLsidVoc), which
> is based
> on TCS, but is not TCS per se (ZooBank is concerned with taxon
> names, not
> concepts). There is also the TaxonConceptLsidVoc
> (http://wiki.tdwg.org/twiki/bin/view/TAG/TaxonConceptLsidVoc), which
> together with the TaxonNameLsidVoc and other more genral ontologies,
> collectively represent the same information as a TCS XML document.
> I guess
> that one of the things I'm not clear on is whether RDF returned for
> an LSID
> counts as "TCS", or does TCS specifically mean a document structured
> according to the TCS XML Schema?
> Also, what are we really serving when we say we're serving TCS
> Name-only data is part of TCS, but I wouldn't think of it as TCS
> per se. I
> think you need it in the cntext of an "accordingTo" instance. (By
> the way
> -- Roger -- I'd always thought of "accordingTo" as referring to a
> PublicationCitation, not an Actor or Team. A topic of discussion for
> another day...
> But my point is, I've got hundreds of thousands of database records
> [Name accordingTo Publication], which each represent a pointer to a
> concept (that is, "concept" sensu Kennedy, not sensu Pyle). And
> for many of
> these, I also have information on synonymies within the Publication
> taxon concepts defined at the resolution of names, which means at the
> implied resolution of type specimens). What I don't have, however, is
> robust sets of "taxon concept" records that go into more specific
> regarding the definition of the concept itself (in terms of non-type
> specimens and/or character data, for example). Also, I don't have
> much in
> the way of third-party RelationshipAssertions to define how these
> concepts map to each other.
> This leads to the question I've been meaning to ask, which is "How
> information do I need before I call it a TCS document?" I would
> say raw
> names data alone don't cut it -- you would need at least an
> before you could call it a concept/TCS document. But if all I have
> as an
> accordingTo (with no additional specimens or characters or
> RelationshipAssertions), do I still call it TCS?
> Sorry if I'm over-thinking this...
>> -----Original Message-----
>> From: tdwg-tnc-bounces at lists.tdwg.org
>> [mailto:tdwg-tnc-bounces at lists.tdwg.org] On Behalf Of Paul Allen
>> Sent: Friday, October 05, 2007 2:11 AM
>> To: tdwg-tnc at lists.tdwg.org
>> Subject: [tdwg-tnc] LSIDs and taxon concepts
>> Hi all,
>> I'm new to this list and hope that the following are
>> appropriate questions.
>> In Bratislava, I wasn't keeping detailed enough notes on
>> projects and their current and future plans wrt TCS.
>> What sites are currently publishing TCS-formatted data or
>> will be within the year? I know that zoobank.org will be
>> publishing TCS data in the near future. Is GBIF? ITIS? Species2000?
>> What sites are publishing real "taxon concept" data (in TCS
>> format or not)?
>> Conversely, what sites are simply publishing "nominal taxon
>> concepts" as opposed to detailed authoritative taxon concepts?
>> Is this the kind of thing for which we should generate a
>> survey to send to sites (i.e. their plans for publishing TCS)
>> or distrubute to TDWG members?
>> Paul Allen, Assistant Director
>> Information Science pea1 at cornell.edu
>> Cornell Lab of Ornithology (800) 843-BIRD
>> 159 Sapsucker Woods Road (607) 254-2480 (direct)
>> Ithaca, NY 14850 (607) 254-2415 (fax)
>> tdwg-tnc mailing list
>> tdwg-tnc at lists.tdwg.org
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