[tdwg-tag] darwin core terms inside tdwg ontology

Tue Apr 28 02:56:29 CEST 2009

I think there maybe a difference in how people thing about species
identifiers:
1) Some, mainly conservationists, ecologists, medical entomologists etc.
want a stable identifier that they can use to connect their data and
publications
    to.

2) Others, often taxonomists, want an identifier that conveys information
about  the different ways that a species may connect to the phylogenetic
tree.

Another way of thinking about this is that the taxonomic hypothesis for a
given species is subordinate and ephemeral compared to the species itself.

The people in group 1 do not think of the species description as the
species, they think of it as a human attempt to describe and delimit a
species.

One of the problems I had with the current system is that records tagged by
name and uBio LSID will see *Aedes triseriatus* and *Ochlerotatus
triseriatus*
as different things when people in group 1 see them as the same thing with
two different taxonomic hypotheses.

Here is a page that explains my thinking: http://about.geospecies.org/

Here is the RDF showing my current way of representing this species concept:
http://species.geospecies.org/specs/Ochlerotatus_triseriatus.rdf

(Safari will download the RDF, FireFox will display it)

I link to both of the uBio LSID's because I want to tie to the different
information that is about the same species but linked via different LSIDs

Here is the species page
http://species.geospecies.org/specs/Ochlerotatus_triseriatus

Here is the URI for that concept:

http://species.geospecies.org/spec_concept_uuid/84b8badd-b899-40ea-8f89-f39f3048c270/

I don't think that I have all the answers, I just needed something that
worked like twdg/uBio for the people in group 1.

The way I think about it is to first create a species concept and then point
all the potential taxonomic hypotheses at it. These different hypotheses
could
have different weights depending on current opinion.

Later you can shore up the species concept by combining morphological,
genetic and population genetic data into a more robust, and hopefully more
stable,
understanding of that species.

Just my two cents :-)

- Pete

P.S. I had some trouble finding the current ontology information. I now know
that the DarwinCore ontology is on GoogleCode at:
http://darwincore.googlecode.com/svn/trunk/index.htm

Where is the latest TDWG ontology? Is it here:
http://wiki.tdwg.org/twiki/bin/view/TAG/TDWGOntology

On Mon, Apr 27, 2009 at 8:46 AM, David Remsen <dremsen at mbl.edu> wrote:

> 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 [tdwg-tag-bounces at lists.tdwg.org]
> On Behalf Of Blum, Stan [sblum at calacademy.org]
> *Sent:* Saturday, 25 April 2009 6:12 a.m.
> *To:* Technical Architecture Group mailing list; exec at tdwg.org
> *Subject:* Re: [tdwg-tag] darwin core terms inside tdwg ontology
>
> *From:* 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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-- 
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
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