[tdwg-tag] darwin core terms inside tdwg ontology
Dave Vieglais
vieglais at ku.edu
Tue Apr 28 05:58:47 CEST 2009
Using Darwin Core to describe a complete specimen or observation (or
any biologically relevant) record is perhaps analogous to using the
Dublin Core to describe a book. Sure you get some valuable
information, but the content can be vastly different and depending on
the end use, far less satisfying.
Hence, it has always been my position to consider DwC as the
biological equivalent of DC (which was the original intent - I never
imagined it would still be argued a decade later). That is, it
provides metadata about some biological thing. Very helpful for
discovering relevant information, and in some situations sufficiently
rich to act as a surrogate for the actual data (e.g. putting dots on a
map, or transmitting small sets of facts), and indeed, some of the
terms are sufficiently concise that they can be used as data. In
other situations though, far more complete information is required,
and that is the role of more complex and perhaps conceptually
complete, though more specialized data representations.
Ideally, one would consider a mixed model, choosing sufficiently
concise definitions drawn from an array of appropriate vocabularies
and ontologies, and structured according to agreed rules and
constraints to accurately capture and convey the desired intent.
Dave V.
On Apr 27, 2009, at 18:27 , Kevin Richards wrote:
> Again, it depends on what the data will be used for, ie how
> structured does it have to be, to be useful.
>
> Your minimum fields (?) (and mappings based on DwC athttp://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreDraftStandard)
> :
>
> name - dwc:ScientificName
> nomenclatorLSID - dwc:GlobalUniqueIdentifier
> status - ?? curatorialExt:TypeStatus ?
> who - dwc:AuthorYearOfScientificName (not componentised) ?
> when - dwc:AuthorYearOfScientificName (not componentised) ?
> where - ?? dwc:ScientificName ??
>
> Does this look ok??
>
> Kevin
>
>
> From: Paul Kirk [mailto:p.kirk at cabi.org]
> Sent: Tuesday, 28 April 2009 10:21 a.m.
> To: Kevin Richards; David Remsen
> Cc: Technical Architecture Group mailing list; exec at tdwg.org
> Subject: RE: [tdwg-tag] darwin core terms inside tdwg ontology
>
> I guess I should take a look at the DwC+Ext to see if it has all the
> appropriate 'containers and pointer' to handle complex botanical
> taxonomic synonymy. But is the DwC+Ext designed to handle taxonomy
> or nomenclature (or both)? >From your comments it appears that it's
> both. But if it's just the former doesn't it need just the minimum I
> noted below - with the proviso that 'status' would be either
> accepted (no more needed) OR synonym (with the accepted name and
> nomenclatorLSID appended)?
>
> Paul
>
> From: Kevin Richards [mailto:RichardsK at landcareresearch.co.nz]
> Sent: Mon 27/04/2009 22:54
> To: David Remsen; Paul Kirk
> Cc: Technical Architecture Group mailing list; exec at tdwg.org
> Subject: RE: [tdwg-tag] darwin core terms inside tdwg ontology
> Sorry, I'm not a taxonomic expert, I just feel uncomfortable using
> an observation schema for a taxonomic job. But if you have examples
> of representing complex taxonomies using DwC, then good oh. It
> will probably be fine if you have basic taxon name strings and a
> simple hierarchy, but issues may come up when you have for example,
> some names with authors and year and some without, etc, and working
> out if they are the same name … and as Paul says homonyms,
> misapplications, etc, etc - depends on what you want to do with the
> data. As I said probably "horses for courses".
>
> Why not use the TDWG ontology? That contains more structure
>
> Kevin
>
>
> From: tdwg-tag-bounces at lists.tdwg.org [mailto:tdwg-tag-bounces at lists.tdwg.org
> ] On Behalf Of David Remsen
> Sent: Tuesday, 28 April 2009 9:05 a.m.
> To: Paul Kirk
> Cc: Kevin Richards; Technical Architecture Group mailing list; exec at tdwg.org
> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology
>
> Paul - I'll post some examples as soon as I can (I'm in a GBIF
> Science Committee meeting the next two days) that illustrate how we
> can use the DwC terms to create simple schemas for representing rich
> taxonomic data. Markus and I have modelled complex zoological and
> botanical taxonomies using it for testing the GBIF IPT and it
> works. I'll get these examples served in the next day or so. It
> includes some Euro+Med Plants data and a Smithsonian taxonomic
> bulletin on Cetacean taxonomy (zoological + botanical examples).
> It covers all of the components of taxonomic opinion to which you
> refer and more. It can represent all that I know are contained in
> Index Fungorum and Species Fungorum unless you are hiding a lot
> more, which you may well be. The only thing it doesn't do well are
> the explicit concept-to-concept assertions enabled by TCS but I have
> other strategies for achieving that. There are some homonym cases
> as well which I'm not sure we do well but which Markus thinks we can
> so I need to dig in there a bit.
>
> If you have some sample taxonomic or nomenclatural data that you
> think will break it I would be happy to take it for a ride within
> the DwC-with-extensions approach that is employed within the IPT and
> see if it can't be effectively addressed. I don't mind being wrong
> about it so long so as I or someone else can provide some clues as
> where to go from here.
>
> DR.
>
> On Apr 27, 2009, at 4:20 PM, Paul Kirk wrote:
>
> I tend to agree with David ... but only to a point.
>
> Are we not discussing the equivalent here of database
> normalization ... where two diametrically opposite opinions hold -
> fully normalized and it don't work (performance issue) or fully de-
> normalized and it don't work (integrity issues - accepting that a
> well designed UI can protect database content (and integrity) from
> the user)? Here we have DwC-with-extensions on the one hand and
> something like TCS/CDM? on the other. By taxonomic information I
> assume we mean that a taxonomic opinion on a name has been expressed
> (usually by a person). If so, the requirements are fairly basic -
> name with nomenclatorLSID, status, who, when and where. It gets
> complex, and it's what I do not think DwC supports, when everything
> in a complex taxonomic opinion (homotypic names, heterotypic names,
> misapplications, pro-parte synonyms etc) is placed in one 'object' -
> the equivalent of recursive joins to go back to a database analogy.
>
> In haste,
>
> Paul
>
> From: tdwg-tag-bounces at lists.tdwg.org [mailto:tdwg-tag-bounces at lists.tdwg.org
> ] On Behalf Of David Remsen
> Sent: 27 April 2009 14:47
> To: Kevin Richards
> Cc: 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 [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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