[tdwg-tag] Embedding specimen (and other) annotations in NeXML

"Markus Döring (GBIF)" mdoering at gbif.org
Mon Feb 23 22:58:57 CET 2009

all ontology work within TDWG so far should be classified as  
experimental in my opinion. As you have pointed out, none of this work  
has gone through a proper standards process (with the exception of NCD  
maybe), but was driven by immediate needs for LSID resolution.

Also there is a large overlap between the xml schema based TDWG  
standards such as ABCD, TCS, DWC, NCD and SDD. Plus pretty much all of  
them use different schema design patterns, so it wouldn't be trivial  
to integrate them into one. Some standards like TCS actually have  
placeholders (TCS even has a PlaceholderType complex type) to refer to  
specimens or publications, as it was not considered the job of TCS to  
define those. But then again one needed to express the relationship to  
those objects at a time when the those standards were not yet  
finalised or used different, incompatible design patterns.

To me the only way out would be to step back and try to reconcile all  
those standards into a single ontology with an corresponding xml schema.
The new DarwinCore terms dont exactly try to do that, but at least  
they represent a consistent way of representing the basics of our  
domain, in particular specimen, names  & taxonomies. Please keep in  
mind when looking at the DwC terms that the development had the  
flexibility and simplicity of Dublin Core in mind rather than a true  
RDF ontology. It therefore also tries to be technology independent in  
its core, but provides guidelines for the different implementation/ 
serialisation technologies like XML, (X)HTML, RDF or tab delimited  
text files that make use of the same term definitions.

I am really glad that you pointed out all these problems, as I think  
we still have serious work in front of us.


On Feb 23, 2009, at 21:51, Matt Jones wrote:

> This thread has prompted me to ask some naive questions about the
> process under which the vocabularies are formed.  Maybe I'm the only
> one who is confused about the vocabularies, their status, and the
> process of forming new terms, but it seems maybe I'm not alone.  And
> clarification on some of these points will help me with our direction
> on the development of the Observation Ontology under the OSR group,
> which I think will fit right in with Stan's point about fitting some
> of the concepts into a broader Observation framework.
> For me there is a lot of confusion over the TDWG vocabularies, partly
> because they capture concepts that are present in existing TDWG
> standards, but are generally incomplete.  For example, the TCS
> standard provides the field 'Specimens/Specimen', which I think is
> relevant to Hilmar's question.  However, the listed TDWG vocabulary
> for TCS is the TaxonConcept vocabulary
> (http://rs.tdwg.org/ontology/voc/TaxonConcept), which does not provide
> a class for the TCS 'Specimen' concept.  In addition, the ABCD TDWG
> standard  also seem to have  a way for specimens to be represented,
> but they are generalized as 'Unit's with a 'RecordBasis' of
> 'PreservedSpecimen'. So there are at least two official TDWG
> 'standards' for representing Specimen information, in addition to
> whatever DwC does.  It seems to me that the best thing to do would be
> to finish the LSID vocabularies for TCS and ABCD so that they
> completely represent the concepts in TCS and ABCD, then get that
> approved as a valid way to represent these TDWG standards. In the
> process, one could try to resolve the differences in modeling
> approaches employed by the different standards, such as mapping the
> Specimen concept in TCS to its corresponding concept in DwC and ABCD.
> This would help avoid multiple TDWG standards defining overlapping
> versions of these concepts, and let people use the vocabularies in
> place of the XML schema versions of these standards.
> What is the process for approval of the LSID vocabularies?  They seem
> to be bypassing the normal TDWG standards track.  Some of the
> vocabularies have a status of 'Available' (like TaxonConcept,  even
> though it is incomplete), while others are marked as 'Developmental'.
> The page on OntologyGovernance
> (http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntologyGovernance)
> states:
> "Relationship Between TDWG Standards and the Ontology --
> Concepts are standardized by being included in TDWG Standards. Once
> they have been mentioned in a standard the Ontology Manager has the
> responsibility of maintaining their URIs and descriptions as per the
> standard. Concepts must be promoted to the live branch before the
> standard enters the standards process. "
> So it seems that the OntologyManager replaces the standards process
> for the purpose of the vocabularies. Is this correct?  And does the
> OntologyManager make sure that concepts like 'Specimen' that are
> defined in TCS make it into the corresponding LSID vocabulary before
> it is classified as 'Available'?  And how does the OntologyManager
> decide which concept and representation for 'Specimen' to use -- the
> one from TCS or the one from ABCD? Does 'Available' have the same
> weight as a published TDWG standard, and if so, shouldn't these
> vocabularies be listed on the Standards page as well?  Finally, does
> the existence of a concept such as 'Specimen' in TCS have any bearing
> on the development of new standards such as DwC that may want to
> define the concept differently, or more completely?
> Matt
> On Mon, Feb 23, 2009 at 11:22 AM, Blum, Stan <sblum at calacademy.org>  
> wrote:
>> Given that this ontology work has to be formally correct in a  
>> several ways,
>> I'd like to suggest (strongly) that the
>> name of "TaxonOccurrence" concept
>> be changed to
>> "OrganismOccurrence".
>> One of the properties of OrganismOccurrence would be the
>> TaxonomicIdentification.
>> If this has a parent "thing", it should be something like the
>> ObservationMeasurement thing that Simon Cox (or other larger  
>> ontologies)
>> described at least year's meeting.
>> -Stan
>> -----Original Message-----
>> From: tdwg-tag-bounces at lists.tdwg.org
>> [mailto:tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Kevin Richards
>> Sent: Monday, February 23, 2009 11:26 AM
>> To: Hilmar Lapp; Technical Architecture Group mailing list;  
>> rogerhyam Hyam
>> Cc: Enrico Pontelli; Rutger A. Vos; Arlin Stoltzfus; Brandon Chisham;
>> nexml-discuss at lists.sourceforge.net
>> Subject: Re: [tdwg-tag] Embedding specimen (and other) annotations  
>> in NeXML
>> Was this particular question answered?
>> "2) Is there a TDWG vocabulary (in RDF or OWL) that has a relation  
>> for
>> referring to a specimen record, or are you aware of another one that
>> has this?"
>> Is the Occurrence RDF vocab at
>> http://rs.tdwg.org/ontology/voc/TaxonOccurrence what you are  
>> looking for?
>> I'm not sure I fully understood what you are after, but have a look  
>> and see
>> if it matches your requirements.
>> Kevin
>> -----Original Message-----
>> From: tdwg-tag-bounces at lists.tdwg.org
>> [mailto:tdwg-tag-bounces at lists.tdwg.org] On Behalf Of Hilmar Lapp
>> Sent: Monday, 23 February 2009 11:04 a.m.
>> To: Technical Architecture Group mailing list; rogerhyam Hyam
>> Cc: Enrico Pontelli; Rutger A. Vos; Arlin Stoltzfus;
>> nexml-discuss at lists.sourceforge.net; Brandon Chisham
>> Subject: [tdwg-tag] Embedding specimen (and other) annotations in  
>> NeXML
>> Hi Roger and everyone else involved in DwC and the core ontology,
>> in preparation for the upcoming hackathon [1] here we've worked our
>> way through a number of use-cases for attaching metadata to data
>> elements in NeXML [2] in a way that is semantically defined. The
>> results are here:
>> http://evoinfo.nescent.org/Database_Interop_Hackathon/ 
>> Metadata_Support
>> If you can take a critical look specifically at the section on
>> 'Specimens within collections' (http://tinyurl.com/djdby3) that'd be
>> great.
>> Specific questions related to that:
>> 1) Is this using DarwinCore in a correct and/or sanctioned way?
>> 2) Is there a TDWG vocabulary (in RDF or OWL) that has a relation for
>> referring to a specimen record, or are you aware of another one that
>> has this?
>> 3) I could only find the XML schema for DarwinCore. Are there any
>> plans for (or did I miss the existence of) a corresponding ontology
>> defined in OWL or RDF, similar Dublin Core (which has a RDF ontology
>> at http://purl.org/dc/elements/1.1 and DCterms ontology at
>> http://purl.org/dc/terms)
>> .
>> 4) It wasn't immediately clear how one would use the TDWG core
>> ontology for doing the same thing in RDF (or OWL) - is this ontology
>> supposed to be used yet, and are there usage examples, or does  
>> someone
>> have a recommendation for how one would write the same example using
>> the core ontology?
>> I know it's a rather tiny subset of DwC that we're using here but
>> that's only a start and one use-case.
>> Of course, any other feedback to or suggestions for this or any of  
>> the
>> other stuff on that page is welcome too!
>> Cheers,
>>       -hilmar
>> [1] http://evoinfo.nescent.org/Database_Interop_Hackathon
>> [2] http://nexml.org
>> --
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:- hlapp at duke dot edu :
>> ===========================================================
>> _______________________________________________
>> tdwg-tag mailing list
>> tdwg-tag at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>> Please consider the environment before printing this email
>> Warning:  This electronic message together with any attachments is
>> confidential. If you receive it in error: (i) you must not read, use,
>> disclose, copy or retain it; (ii) please contact the sender  
>> immediately by
>> reply email and then delete the emails.
>> The views expressed in this email may not be those of Landcare  
>> Research New
>> Zealand Limited. http://www.landcareresearch.co.nz
>> _______________________________________________
>> tdwg-tag mailing list
>> tdwg-tag at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>> _______________________________________________
>> tdwg-tag mailing list
>> tdwg-tag at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
> -- 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Matthew B. Jones
> Director of Informatics Research and Development
> National Center for Ecological Analysis and Synthesis (NCEAS)
> UC Santa Barbara
> jones at nceas.ucsb.edu                       Ph: 1-907-523-1960
> http://www.nceas.ucsb.edu/ecoinfo
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> _______________________________________________
> tdwg-tag mailing list
> tdwg-tag at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-tag

More information about the tdwg-tag mailing list