Re: Fwd: Nature Publishing Group Linked Data Platform

Hi Tony,

Last time I asked the NCBI help desk they preferred the use of "
http://www.ncbi.nlm.nih.gov/pubmed/15618302" instead of going via pubmed.org
.
Let us know which you settle on and I will add owl:sameAs links from the
uniprot.org RDF as well.

Regards,
Jerven

On Thu, Apr 19, 2012 at 2:27 PM, Hammond, Tony <t.hammond@nature.com> wrote:

> Hi Michel:
>
> Just wanted to respond to your earlier post [1] about NPG's Linked Data
> Platform. (And apologies for not responding sooner - I only came across
> this
> now.)
>
> > unfortunately, after a cursory look ( hope i'm wrong) - i don't think the
> > data links into anything on the semantic web... (mesh terms are literals,
> > pmids are in NPG's namespace with no links to identifiers.org, etc)
>
> I've listed below (at end of message) a given NPG :Record object which has
> these features:
>
>    1. Is typed and identified in the npg: namespace
>
>    2. Has links to a PubMed record:
>
>    a) Uses one form of URI used by the owner:
>
>    <http://pubmed.org/20436485>
>
>    b) Uses a second form of URI which is not dereferenceable but is a
> "standard" name (covered by RFC - and IANA):
>
>    <info:pmid/20436485>
>
>    3. Has MeSH descriptor/qualifier terms in text form (as used by PubMed)
>
> Some comments:
>
>    1. The object is from a data package used within our realm - and so is
> consistently represented as such. (All our objects have npg: types
> alongside
> other types as appropriate.)
>
>    2. As far as I am aware this data does not have canonical RDF
> representations from the ontology owner - NLM.  We have used a URI form
> that
> is used by PubMed although it is not clear if that is intended as an
> address
> rather than a name:
>
>    <http://pubmed.org/20436485>
>
> We could have selected this form - with similar caveats:
>
>    <http://www.ncbi.nlm.nih.gov/pubmed/20436485>
>
> We thought the first form was more acceptable but are ready to be
> corrected.
>
>    3. We have used an explicit name form URI:
>
>    <info:pmid/20436485>
>
>    This is not an HTTP URI - and hence will be frowned on by Liked Data
> purists. But is is a valid RDF URI and as such functions as a unique
> linking
> point - albeit without offering any additional information. (One step up
> from a blank node, and two steps down from an HTTP named node.)
>
>    4. So, should we also have added one of these forms below? And if so,
> which is to be preferred? And are there others?
>
>    <http://identifiers.org/pubmed/20436485>
>    <http://bio2rdf.org/pubmed:20436485>
>    <http://purl.org/commons/record/pmid/20436485>
>
>    5. As for MESH terms we would be willing to take some guidance. Both
> Bio2RDF (and the earlier Neurocommons work) provided URIs for descriptors
> and  qualifiers:
>
>    <http://bio2rdf.org/mesh:D005602>
>    <http://bio2rdf.org/mesh:D005602Q000208>
>    <http://purl.org/commons/record/mesh/D005602>
>
>    Again, which to pick?
>
>    6. It is a pity though that the ontology owner has not (to my knowledge)
> provided some guidance for how their ontology may be used within an RDF
> context.
>
> We are still learning and looking to improve the stability and reach of the
> triples we're making available and eager to get any helpful feedback.
>
> Cheers,
>
> Tony
>
>
> [1]
> http://lists.w3.org/Archives/Public/public-semweb-lifesci/2012Apr/0023.html
>
> ==
> @prefix dc:       <http://purl.org/dc/elements/1.1/> .
> @prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
>
> <http://ns.nature.com/records/pmid-20436485>
>      a       <http://ns.nature.com/terms/Record> ;
>      <http://www.w3.org/2000/01/rdf-schema#label>
>              "20436485" ;
>      dc:identifier <http://pubmed.org/20436485> , <info:pmid/20436485> ;
>      dc:subject "Terminal Repeat Sequences" , "Lymphoma/genetics" , ... .
> ==
>
>
>
>
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-- 
Jerven Bolleman
me@jerven.eu