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

Matt Jones jones at nceas.ucsb.edu
Mon Feb 23 21:51:07 CET 2009


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 :
> ===========================================================
>
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



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