[tdwg-tag] darwin core terms inside tdwg ontology

[Jerry Cooper]

Here's my 2-cents worth...

An example of important taxon concept content missing from DwC and its extensions (unless I missed it - which is very possible) ...

The identification history of a specimen is a vital audit trail of information. It is the history of taxon concepts within the context of a single specimen. A harvested knowledge of that history across specimens allows you to make important inferences about taxonomic stability. For example if the taxon concept has wandered over a spread of names which are heterotypic in origin then its' telling you that you are dealing with a taxonomically fuzzy entity. If you are a biosecurity officer deciding whether a new organisms should be released into the environemnt or allowed across the border then that is a vital piece of information. It's a 'kind of' taxon concept within organism occurrence.

It's in ABCD of course.

So let's add a other extension to DwC. But then what difference between DwC + extensions and ABCD within the context of specimens? One  important difference I see is that ABCD is scary to end users because it humungous.

IMHO DwC should be a bunch of simple core metadata  concepts for simple observations/occurrences (not appropriate for surveys!) that facilitates resource discovery. If you wish to 'get data' within this context then one approach is to wrap the package into  ' metadata + data extensions' . And one way of ensuring the data wrapped by the 'data extensions' are integrable across domains is build them from concepts defined within an overarching agreed standard ontology. Likewise I see the observation/occurrence metadata concepts as the potential entry points to the semantic  RDF triple-trails also defined by the same ontology.

That's the way I look at it, which is probably too simplistic.

And like Paul I'd be intrigued to see DwC deal with some of the tortuous nomenclatural data complexities we recently had to untangle in IndexFungorum to port it into Rich Pyle's 'all codes of life' Global Name Usage Bank (GNUB) data structure. It was distantly removed from anything currently in DwC.

Jerry

From: David Remsen [mailto:dremsen at mbl.edu]
Sent: Tuesday, 28 April 2009 1:47 a.m.
To: Kevin Richards
Cc: David Remsen; Blum, Stan; Technical Architecture Group mailing list; exec at tdwg.org
Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology

Kevin,   Can you tell me what the limitations are on being able to exchange taxonomic information with the DwC terms?  As far as I can tell, you can exchange fairly complex taxonomic information short of concept-to-concept relations and I find the DwC-with-extensions approach we are using to exchanging information tied to taxa (not instances of taxa) to be a nice and practical compromise between complexity and practicality.   My understanding is that the IPT can output TCS/RDF for those who want it.   I am personally very happy to see the DwC taxon terms added.  Finally I can provide format specifications that biologists can understand.

David Remsen


On Apr 25, 2009, at 9:52 AM, Kevin Richards wrote:


I see the ontology as a model of ALL (hopefully, eventually all) the data in our domain of biodiversity informatics.
I would love to see it as a standard (at the least it might give it a bit more clout).
I agree that the ontology is useful to tie other TDWG schemas together, using it as a core/master model.  I would be happy to see it used for ALL tasks within TDWG, but I understand the usefulnes of the more specific schemas/standards - horses for courses.

If I understand Stan here, I agree with him about the dubious use of DwC for representing Taxon Concepts/Names.  As far as I know, it was really intended as a transfer standard for observation records??  It contains very limited taxon information!  It really is not a overly difficult job to use a more suitable schema/ontology.  I think the popularity of Darwin Core is due to its simplicity - and I wonder if what Roger is proposing will help with this - ie an XML implementation of the ontology as well as an RDF version.  This will allow people to create very simple XML documents with reasonably simple/flat data, eg an xml document of TaxonName entities, with perhaps 6 or 7 or so key fields - even simpler than DwC.   :-)

Kevin

________________________________
From: tdwg-tag-bounces at lists.tdwg.org<mailto:tdwg-tag-bounces at lists.tdwg.org> [tdwg-tag-bounces at lists.tdwg.org<mailto:tdwg-tag-bounces at lists.tdwg.org>] On Behalf Of Blum, Stan [sblum at calacademy.org<mailto:sblum at calacademy.org>]
Sent: Saturday, 25 April 2009 6:12 a.m.
To: Technical Architecture Group mailing list; exec at tdwg.org<mailto:exec at tdwg.org>
Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology
From: tdwg-tag-bounces at lists.tdwg.org<mailto:tdwg-tag-bounces at lists.tdwg.org> on behalf of John R. WIECZOREK
Sent: Fri 2009-04-24 8:58 AM
To: Roger Hyam
Cc: Technical Architecture Group mailing list
Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology
Anything I should do on the DwC side in anticipation of harmony?

http://rs.tdwg.org/dwc/terms/index.htm#theterms
===========================================================
John,

At some point, all or (most) of the DarwinCore terms need to be added to the TDWG ontology.

But having said that, I also need to say that I'm uncomfortable with:

1) The current state of the TDWG ontology (primarily the naming conventions; lets just use terms names), and our understanding of the role it plays in TDWG and how it will be managed (entry of terms, integration of terms into the conceptual [is-a / has-a] relationships to other terms); and

2) the fact that the new DarwinCore straddles or overlaps the roles of an ontology and an application schema.

I understood the past TAG roadmaps to indicate that we were adopting an approach in which the TDWG Ontology would be a repository for data concepts that are present in (or implied by) TDWG standards; and that real data transmission would be accomplished with application schemas.  The ontology itself would not be a standard, but would be a tool that helps integrate standards.  I thought our standards would be created to function as application schemas or components of application schemas (as in the DwC and its extensions).  I am now pretty confused.  I'd like to hear the rationale for combining taxonomic name/concept with organism occurrence.  I haven't gone over all the existing docs, so apologies if I've missed that, but I think it's confusing that a (new) DarwinCore record could be either a taxonomic name or an organism occurrence, or maybe something else.  Maybe I'm too attached to object orientation and just don't GET the semantic web, but it feels to me like we are stepping into squishy ground.

Also, I the the DCMI maintenance procedures are also more appropriately applied to the ontology than a TDWG standard.  The existing process for ratifying TDWG standards and the procedure in the DwC seem to be pretty explicitly in conflict; one can change the other cannot (without becoming another thing).

Is anyone else having these same trepidations?  I don't think I've been as much of a Rip Van Winkle as Jim Croft, but I clearly missed some important shifts.

-Stan




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