Hi Roger,
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?
Éamonn
-----Original Message----- From: tdwg-tnc-bounces@lists.tdwg.org [mailto:tdwg-tnc-bounces@lists.tdwg.org] On Behalf Of Roger Hyam Sent: 05 October 2007 16:51 To: Richard Pyle Cc: tdwg-tnc@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 it short.
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.
http://rs.tdwg.org/ontology/voc/TaxonName
http://rs.tdwg.org/ontology/voc/TaxonConcept
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)
<to:TaxonOccurrence rdf:about="urn:lsid:example.com:specimens:1234"> dc:titleHyam.R.D. 284927 - Rhododendron ponticum L.</dc:title> to:collectorRoger Hyam</to:collector> <.... other stuff ...> to:identifiedTo to:Identification to:expertNameChris Browning</to:expertName> to:taxonNameRhododendron ponticum L.</to:taxonName> <to:taxon > tc:TaxonConcept tc:hasName tn:TaxonName tn:genusPartRhododendron</tn:genusPart> tn:specificEpithetponticum</tn:specificEpithet > tn:authorshipL.</tn:authorship > tn:TaxonName </tc:hasName> tc:accordingToStringBrown and Smith 1995</tc:accordingToString> tcom:publishedInSome monograph by some guys</tcom:publishedIn> tcom:microReferencepage 32</tcom:microReference> <tcom:publishedInCitation rdf:reference="http:// some.uri.to.some.citation.for.the.pub"/> </tc:TaxonConcept> </to:taxon> </to:Identification> </to:identifiedTo> </to:TaxonOccurrence>
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 approaches.
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:
http://rs.tdwg.org/ontology/voc/Common
All the best,
Roger
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 example, strictly speaking, ZooBank will be return metadata in accordance with the "TaxonNameLsidVoc" (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 documents? 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 for [Name accordingTo Publication], which each represent a pointer to a taxon concept (that is, "concept" sensu Kennedy, not sensu Pyle). And for many of these, I also have information on synonymies within the Publication (i.e., 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 detail 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 alternate concepts map to each other.
This leads to the question I've been meaning to ask, which is "How much 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 "accordingTo" 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...
Aloha, Rich
-----Original Message----- From: tdwg-tnc-bounces@lists.tdwg.org [mailto:tdwg-tnc-bounces@lists.tdwg.org] On Behalf Of Paul Allen Sent: Friday, October 05, 2007 2:11 AM To: tdwg-tnc@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?
Thanks, Paul
Paul Allen, Assistant Director Information Science pea1@cornell.edu Cornell Lab of Ornithology (800) 843-BIRD 159 Sapsucker Woods Road (607) 254-2480 (direct) Ithaca, NY 14850 (607) 254-2415 (fax)
http://www.birds.cornell.edu/ http://bna.birds.cornell.edu/ http://www.ebird.org/ http://bird.atlasing.org/
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