Re: [Treebase-devel] [dryad-dev] Re: Dryad API, advice on cyberinfastructure

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Hi Hilmar, William, List,

Isn't Dryad already using dc:identifier to reference TreeBASE (i.e. this
example <http://datadryad.org/handle/10255/dryad.4939?show=full>)?
I'm sometimes puzzled in how to parse the returns when very different
content is all included as dc:relation
i.e. this example<http://www.datadryad.org/oai/request?verb=GetRecord&identifier=oai:datadryad.org:10255/dryad.1619&metadataPrefix=oai_dc>,
dc:relation is sometimes a handle, sometimes a doi, a journal title, or a
number I don't recognize.
Is there anything more clever than a bunch of grep rules for distinguishing
between these?

Is there a way to get the URL of the actual data file (i.e. some csv file)
through the dryad API?  So far I can only return the website that contains
the data file.

Thanks much.
Carl

On Thu, May 12, 2011 at 2:34 PM, Hilmar Lapp <hl...@ne...> wrote:
> The mutual cross-referencing at the level of data package and TB study
makes
> sense. Please don't use the Dryad handles or handle URIs - the use of
> handles within Dryad is legacy and being phased out (except perhaps for
> individual files, which are not relevant here).
> If we use isPartOf for both references, then that suggests that the Dryad
> package and the TB study are semantically equivalent objects, which I
think
> they are cleary not. I would think that Dryas would reference the TB study
> through a dcterms:hasPart property if TB references the Dryad package
> through dcterms:isPartOf. Or again the simpler dc.relation.
>
> -hilmar
> Sent with a tap.
> On May 12, 2011, at 10:04 AM, William Piel <wil...@ya...> wrote:
>
>
> Is there a consensus, then, that TreeBASE should express the corresponding
> Dryad DOIs, prefixed with http://dx.doi.org/, using dcterms:isPartOf  via
> both OAI and PhyloWS ?
> Or, for that matter, express the handle that Dryad labels
dc:identifier.uri
> (e.g. http://hdl.handle.net/10255/dryad.15417).
> Meanwhile Dryad should express the corresponding TreeBASE URI also
> using dcterms:isPartOf ?
> A slight wrinkle is to make sure we are mutually cross-referencing the
> proper "level" of object.
> Dryad issues "Data Package" identifiers, which I guess is synonymous with
a
> TreeBASE URI to a "study".  These two identifiers point to the same
package:
> dc:identifier: doi: 10.5061/dryad.tf48r
> dc:identifier.uri: http://hdl.handle.net/10255/dryad.15415
> But in addition, Dryad issues identifiers for particular data sets. These
> two identifiers point to the same data set within the above package:
> dc:identifier: doi: 10.5061/dryad.tf48r/2
> dc:identifier.uri: http://hdl.handle.net/10255/dryad.15417
> There is no one-to-one equivalency between these data set identifiers and
> TreeBASE's URIs, because TreeBASE's URIs point to matrix objects and tree
> objects, which are all extracted from the same or different data set(s).
> Hence I think that for both TreeBASE and Dryad, the cross-referencing of
> identifiers should be at the level of "package" and "study" respectively.
> bp
>
> On May 12, 2011, at 9:32 AM, Greenberg, Jane wrote:
>
> All -- I am not sure I've followed this conversation all the way, but
> Hilmar's interpretation of dcterms:isPartOf (or simple/unqualified DC
> w/dc:relation) makes  good sense to me; and will help w/interoperabilty.
>
> W.r.t. PRISM, the Drayd 3.0 ap (application profile) has moved away from
> PRISM to BIBO, see: http://bibliontology.com/specification.  There seems
to
> be increased interest in and discussion of this scheme on various metadata
> lists.  I am a tad wary about the overall upkeep (latest version,
etc.)....
> but it is Sematic Web compatible, rdf, etc...
>
> Hope this helps.
>
> ~ jane
>
> -----Original Message-----
> From: dry...@go... [mailto:dry...@go...] On
> Behalf Of Hilmar Lapp
> Sent: Thursday, May 12, 2011 9:06 AM
> To: Rutger Vos
> Cc: William Piel; Tre...@li...; Vision, Todd J;
> DaveVieglais; Ryan Scherle; Dryad Developers
> Subject: [dryad-dev] Re: [Treebase-devel] Dryad API, advice on
> cyberinfastructure
>
> Or perhaps simply dc:relation, or dcterms:isPartOf [1], which is actually
a
> refinement of the former?
>
> I agree though that the relationship ought to be general enough that a DC
or
> dcterms property will probably best facilitate use, and I also wouldn't
> kludge this - these become de-factor standards sooner than you want, and
> then you're stuck with them.
>
> -hilmar
>
> [1] http://dublincore.org/documents/dcmi-terms/#terms-isPartOf
>
> Sent with a tap.
>
> On May 12, 2011, at 8:41 AM, Rutger Vos <R....@re...> wrote:
>
> On the other hand, I'd rather not do a schema change. But we have a
>
> field called "URL", which we could pre-populate with
>
> "http://dx.doi.org/10.5061/dryad.8661". This field is usually used
>
> for publications that don't have a doi, and instead have a particular
>
> url -- and it's rarely used.  So one kluge (short of a schema change)
>
> is to pre-populate the url field with
>
> "http://dx.doi.org/10.5061/dryad.8661" and then expose that under the
>
> "prism:url" element.  What would be a good element to use other than
> "prism:url" or "prism:doi"?
>
> Citation.url is a string so we can put whatever we like there in order
>
> to store it. As for the element to store it under, maybe:
>
> - dcterms:source, defined as "A related resource from which the
>
> described resource is derived. The described resource may be derived
>
> from the related resource in whole or in part. Recommended best
>
> practice is to identify the related resource by means of a string
>
> conforming to a formal identification system." (or a subclass thereof,
>
> e.g. tb.source.study.dryad)
>
> - dcterms:isReferencedBy, defined as "A related resource that
>
> references, cites, or otherwise points to the described resource.", or
>
> dcterms:references, depending on how you would qualify the
>
> relationship between the two. Or prism:isReferencedBy
>
> - dcterms:identifier, defined as "An unambiguous reference to the
>
> resource within a given context."
>
> (or a subclass thereof, e.g. tb.identifier.study.dryad)
>
> - prism:isVersionOf, defined as "The described resource is a version,
>
> edition, or adaptation of the referenced resource."
>
> To me, dcterms:source sounds like a sensible candidate.
>
>
>
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-- 
Carl Boettiger
UC Davis
http://www.carlboettiger.info/