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Re: Fwd: Nature Publishing Group Linked Data Platform

From: Hammond, Tony <t.hammond@nature.com>
Date: Thu, 19 Apr 2012 13:27:05 +0100
To: <public-semweb-lifesci@w3.org>
Message-ID: <CBB5C329.396CA%t.hammond@nature.com>
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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Received on Thursday, 19 April 2012 12:27:41 GMT

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