[tdwg-content] Expressing some relationships in DwC?

Wed Oct 26 12:48:37 CEST 2011

We already have MANY ways to present bad data content, so this is just
continuing an existing reality.  At several conversations at TDWG (BiSciCol,
RDF), came up the issue of how strongly to impose ontological rules to
provided content.  Having a robust ontology that met the needs of most use
cases would be wonderful, of course.  But failing that, an alternative is to
let early-adopter content providers provide what they want (or think is
right to provide), and then analyze this content to find where such
illogical/impossible/circular/etc. content emerges.

At one of the RDF sessions, the example was shown of:

http://fu.bar hasIdentification rabbit

I presume this means a literal "rabbit" (a text string) -- which is entirely
reasonable to expect some providers to provide.  But others would provide
something like:

http://fu.bar hasIdentification http://nameprovider.org/1234

...where the latter resolves to some metadata-rich object that includes
among many of its properties the text-string "rabbit".  But yet other
providers may represent something like this:

http://fu.bar hasIdentification
http://someorganization.org/identification/5678

...where the latter resolves to some metadata-rich object along the lines of
the DwC Identification class, which includes among its properties a link to
a particular instance along the lines of the DwC Taxon class, which itself
has many properties, among which is the text literal "rabbit".

In any case, that people will expose irrational data is not, in itself, a
reason to shy away from exploring more robust data exchange mechanisms in
the context of TDWG standards.

Aloha,
Rich

> -----Original Message-----
> From: Bob Morris [mailto:morris.bob at gmail.com]
> Sent: Wednesday, October 26, 2011 11:33 AM
> To: Markus Döring (GBIF)
> Cc: Richard Pyle; tdwg-content at lists.tdwg.org
> Subject: Re: [tdwg-content] Expressing some relationships in DwC?
>
> To your list of drawbacks, I would add one that has previously surfaced in
this
> list: when there are multiple uses in the same record, the usage patterns
> may require advance agreement about how to disambiguate them.  For
> example, what is to be made of a set of assertions that two different name
> URI's are both asserted to be that of an "accepted" name? Is that the two
> URI's reference the same thing?
> Is it that the record set contains an inconsistency? Is that the issue
must be
> resolved by URI resolution , thereby introducing a requirement for
> resolvability) . These decisions may be very specific to the relation, and
may
> make mapping  between different community's relations quite complex.
>
> On Wed, Oct 26, 2011 at 6:14 AM, "Markus Döring (GBIF)"
> <mdoering at gbif.org> wrote:
> > Well sure, valid is overloaded just as accepted is which we nevertheless
use
> for the "accepted" taxonomic relation.
> > Leaving aside what the actual term name is, validNameUsage,
> correctNameUsage, amendedNameUsage or sth else - it seems to fix the
> problem, doesn't it?
> >
> > "DwCa 2.0" would be a drastic change which feels like reinventing the
> > relational wheel. It might be better to go with sth existing in that
> > case, e.g. Google Dataset Publishing Language:
> > http://code.google.com/apis/publicdata/
> >
> > Using the generic relationship extension is good, but also has serious
> drawbacks. Immediately these come to my mind:
> >  - it is much harder to publish and consume data in this format. Without
> publishing tools you will be lost.
> >  - the controlled vocabulary for the relationship type must be *very*
> controlled. Especially we need to avoid overloading which will easily
happen
> very quickly, see valid or accepted.
> > - all linked resources must have unique ids across all classes, pretty
much
> globally unique ids. Nice to have, but hard for publishers.
> >
> > Markus
> >
> >
> > On 26.10.2011, at 00:58, Richard Pyle wrote:
> >
> >> Hmmm.... watch out for that tricky word "valid".  It means different
> >> things to botanists & zoologists. The term "accepted" is generally
> >> seen as a more code-neutral term to mean "valid" (sensu zoology) or
> "correct"/"accepted"
> >> (sensu botany).  But if you mean "valid" in the botanical sense
> >> (="validly published", or "available" sensu zoology).  I'm not
> >> entirely sure which sense of "valid" is meant in this context.
> >>
> >>
> >> More fundamentally, however, I'd like to report that a number of
> >> folks at TDWG seemed to have converged on the same idea that,
> >> perhaps, we should be using resourceRelationship more frequently
> >> (perhaps a *LOT* more frequently).  A lot of these terms that
> >> effectively represent the functional equivalent to "foreign keys"
> >> might be better packaged in the more open-ended structure of
> >> resourceRelationship.  In fact, at one of the sessions at TDWG (I
> >> believe it was at the AudubonCore break-out session), we discussed
> >> the idea of DwCA "2.0", which would essentially define n-number of
> >> "Cores", and then package the relationships among them via a set of
> >> resourceRelationship records.  This idea emerged from a discussion
> >> about how people have been trying to "force" many-to-many sorts of
> >> data into the one-to-many DwCA format.  The beauty of using a more
> >> generic resourceRelationship set for this function is that it allows
> >> one-to-one, one-to-many, and many-to-many relationships all in one
> >> structure.  It may seem klunky now, but if we used it as a general
method
> to describe all relationships between instances of DwC "classes", it would
> become pretty straightforward, I think.
> >>
> >> Something to think about, anyway...
> >>
> >> Aloha,
> >> Rich
> >>
> >>> -----Original Message-----
> >>> From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-
> >>> bounces at lists.tdwg.org] On Behalf Of Tony.Rees at csiro.au
> >>> Sent: Tuesday, October 25, 2011 4:34 PM
> >>> To: mdoering at gbif.org
> >>> Cc: tdwg-content at lists.tdwg.org
> >>> Subject: Re: [tdwg-content] Expressing some relationships in DwC?
> >>>
> >>> Hi Markus,
> >>>
> >>> You wrote:
> >>>
> >>>> I begin to wonder if a new term dwc:validNameUsageID would solve
> >>>> this issue gracefully and remove the need for a relationship
extension.
> >>>
> >>> Yes, I believe this would cover both the cases I need, I think, when
> >>> accompanied by nomenclatural status = misspelling / nomenclatural
> >>> status = nomen nudum... - comments, anyone?
> >>>
> >>> Cheers - Tony
> >>>
> >>> ________________________________________
> >>> From: "Markus Döring (GBIF)" [mdoering at gbif.org]
> >>> Sent: Wednesday, 26 October 2011 1:43 AM
> >>> To: Rees, Tony (CMAR, Hobart)
> >>> Cc: tdwg-content at lists.tdwg.org
> >>> Subject: Re: [tdwg-content] Expressing some relationships in DwC?
> >>>
> >>> Hi Tony,
> >>> thanks for these practical questions. See inline for answers.
> >>> Markus
> >>>
> >>>> I have a few nomenclatural relationships between name that I would
> >>>> like
> >> to
> >>> express using DwC, and would like to know the preferred way to do
> >>> this if any. The relationships are as follows:
> >>>>
> >>>> (1) Point a nomen novum to the basionym it replaces. From reading
> >>>> there
> >>> was formerly a concept basionym/basionymID, apparently this is now
> >>> replaced with originalNameUsage/originalNameUsageID. So one
> quesiton
> >>> is, is this sufficient to infer this is a basionym, when accompanied
> >>> by noneclaturalStatus = 'nomen novum'?
> >>> yes, that is exactly right. As far as I understand the term basionym
> >>> is
> >> more of
> >>> a botanical term and was not used as the final dwc term therefore.
> >>>
> >>>> (2) Point an orthographic variant to the name which it is a variant
> >>>> of
> >>> (whether or not the latter is now the accepted name). In other
> >>> words, if name A is a variant of name B which is now a synonym of
> >>> name C, I capture the A=>C relationship with a synonym assertion,
> >>> but I want a way to capteure the A=>B relationship too.
> >>> This is only possible with an extension I am afraid. For example the
> >> generic
> >>> dwc relationship one:
> >>> http://rs.gbif.org/extension/dwc/resource_relation.xml
> >>>
> >>>> (3) Point a nomen nudum to a validly published instance that comes
> >>>> later
> >>> (or do the same in reverse, i.e. this name was preceded by xxx as a
> >>> nomen nudum). Again, this should be independent of whether the
> >>> validly published name is an accepted name or now a synonym of
> something else.
> >>> same problem as above.
> >>> I begin to wonder if a new term dwc:validNameUsageID would solve
> >>> this issue gracefully and remove the need for a relationship
extension.
> >>>
> >>>
> >>>> Advice appreciated,
> >>>>
> >>>> Regards - Tony Rees
> >>>> _______________________________________________
> >>>> tdwg-content mailing list
> >>>> tdwg-content at lists.tdwg.org
> >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>> _______________________________________________
> >>> tdwg-content mailing list
> >>> tdwg-content at lists.tdwg.org
> >>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
> >>
> >>
> >>
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>
> --
> Robert A. Morris
>
> Emeritus Professor  of Computer Science
> UMASS-Boston
> 100 Morrissey Blvd
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> IT Staff
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> Department of Organismal and Evolutionary Biology Harvard University
>
>
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This message is only intended for the addressee named above.  Its contents may be privileged or otherwise protected.  Any unauthorized use, disclosure or copying of this message or its contents is prohibited.  If you have received this message by mistake, please notify us immediately by reply mail or by collect telephone call.  Any personal opinions expressed in this message do not necessarily represent the views of the Bishop Museum.