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

[Hilmar L. <hl...@ne...>]

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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