name provider index?

[Matt Yoder]

Hi All-

Is there somewhere that GUIDs are being assigned/indexed for taxon
name providers? If not do you think we could propose to develop a
prototype index, or should we just build an in-house index and not
worry about the issue? I'm thinking along the lines of provenance here
and it might be key to some of my thinking re the proposal.

M

[Gaurav Vaidya]

Hi Matt,

One of the things Rob and I thought I might do at my NESCent stay next semester is to catalogue all the name providers the big name providers use information from (e.g. the name "Pachycondyla dubia" is in GBIF Nub from Catalogue of Life from ITIS from the Hymenoptera Name Server). That might be a useful part of a taxon name provider database! In some cases, such as EOL, it's pretty easy to get a list of all the name providers it uses directly (see http://eol.org/api/provider_hierarchies/1.0).

cheers,
Gaurav

[Matt Yoder]

Excellent- the more I think about it the more key this is going to be
to our efforts. CoL has a complete list of providers that will likely
let you go a long way as well. We need to make it adaptable for
anyone to "create a namespace" as well (literally anyone, including
applications, GUIDs are cheap an unlimited). The trick is that we
will assume any one provider will only have one set of relationships
among STRINGS (not concepts). Thus we can build an foundation that
has a hope in hell of being cross linked via linkages defined int he
ontologies our group will adapt/produce.

M

[Cody Hinchliff]

I wonder if the assumption of providers having one set of relationships each for their name strings would end getting violated? I don't have the familiarity with the name provider data to be sure, but I know that cycles in the taxonomy is a problem we have run into with our chimera... Could have been an artifact of how it was constructed though.

--

[Cody Hinchliff]

Or maybe that wouldn't violate the assumption anyway...

[Matt Yoder]

I don't think it will violate the assumption.

[David Patterson]

You could also use the 22 million names in GNI, and the GN parser is
pretty good. Also Zoobank is keeping track of new people.

But a very good idea to do this

Botanists have a standard list of names providers, Brummitt at Kew was
important in assembling this.

Paddy

> --
>
>



--
___________________________________
David J Patterson

Senior Scientist, Marine Biological Laboratory
7 MBL Street, Woods Hole, MASS 02543, USA.

Research Professor
School of Life Sciences, Arizona State University
Tempe, AZ 85287-4501

Professor (MBL) Ecology and Evolutionary Biology
Brown University, Providence, Rhode Island

Life Sciences Lead, Data Conservancy dataconservancy.org

globalnames.org

[Matt Yoder]

This just came across tdwg-rdf, food for thought.

[1]Halpin et al., "When owl:sameAs isn’t the Same: An Analysis of
Identity in Linked Data?",
ISWC2010, http://iswc2010.semanticweb.org/pdf/261.pdf

M

> --
>
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[Robert Guralnick]

  The timing is good if you want to actually assign an opaque GUID such as a DOI or ARK to data elements that form part of records in the triplestore.   I am involved in the BiSciCol project and two key pieces of software is a Triplifier Simplifier that processes Darwin Core archives into triples and assigns guids to the associated outputs.  We have developed software that does all these steps.  The GetMyGuid service basically assigns DOIs to datasets (and dataset level metadata) and ARKs to elements of the triples.  Most of you know about DOIs; ARKs are similar and borne out of the museum and library world.  Happy to explain more.

Best, Rob

On Wed, Nov 28, 2012 at 6:27 PM, Gaurav Vaidya <gau...@ggvaidya.com> wrote:

--

[Gaurav Vaidya]

Hi everybody,

On 28 Nov, 2012, at 9:56 PM, Matt Yoder <diap...@gmail.com> wrote:
> This just came across tdwg-rdf, food for thought.
>
> [1]Halpin et al., "When owl:sameAs isn’t the Same: An Analysis of
> Identity in Linked Data?",
> ISWC2010, http://iswc2010.semanticweb.org/pdf/261.pdf

In looking for papers talking about circumscribing organisms, I found this paper about building an ontology to describe multiple/changing circumscriptions by linking them to references: http://link.springer.com/chapter/10.1007%2F978-3-642-21064-8_18

Here's a description of the ontology they built: http://schema.onki.fi/taxmeon/ -- and they've got datasets to play around with or download at http://onki.fi/en/browser/

Looks interesting!

cheers,
Gaurav