Re: [Ops-ttf] Fwd: DrugBank not available?

Hi Alasdair,
  Our library does have support for source data versions, but we currently
specify this with the "version" predicate from biositemaps

http://www.ncbcs.org/biositemaps/formatDescription.html

I don't have any preference, but i would perhaps encourage us to
consolidate provenance information with the prov-o effort.

moreover, http://purl.org/pav/version does't answer - and I would like to
see an RDF representation.

I added versioning, where possible, to Bio2RDF Release 3.

https://github.com/bio2rdf/bio2rdf-scripts/issues/milestones

m.


On Wed, Dec 12, 2012 at 6:12 AM, Alasdair J G Gray <A.Gray@cs.man.ac.uk>wrote:

> Thanks for the link. Great to see you using VoID to describe the data.
>
> I'd argue for having a triple capturing the explicit version number of the
> DrugBank dataset using a triple like the following. My reason is that we
> encountered a lot of problems in Open PHACTS tracing what versions of
> datasets were being used when the only information we had to go on was the
> conversion date.
>
> <http://bio2rdf.org/bio2rdf_dataset:drugbank> <http://purl.org/pav/version> "3.0" .
>
>
> I note that you describe both the RDF version of DrugBank and the original
> DrugBank data as a void:Dataset. My understanding of the class definition
> is that the dataset should be captured in RDF [1]. For this reason, in our
> Open PHACTS work we would tend to use the dctype:Dataset class to define
> the original DrugBank data [2].
>
> Alasdair
>
> [1] http://vocab.deri.ie/void#Dataset
> [2]
> http://dublincore.org/documents/2012/06/14/dcmi-terms/?v=dcmitype#Dataset
>
> On 12 Dec 2012, at 10:40, Michel Dumontier <michel.dumontier@gmail.com>
> wrote:
>
> Hi,
>   The parser works on the v3 XML files. We don't currently specify the
> source dataset at that level of detail - here's the link to the provenance:
>
> http://download.bio2rdf.org/release/2/drugbank/bio2rdf-drugbank-20121008.nt
>
> m.
>
> On Wed, Dec 12, 2012 at 4:53 AM, Alasdair J G Gray <A.Gray@cs.man.ac.uk>wrote:
>
>> Is there a metadata description of the data set capturing this kind of
>> information?
>>
>
>
>
> --
> Michel Dumontier
> Associate Professor of Bioinformatics, Carleton University
> Chair, W3C Semantic Web for Health Care and the Life Sciences Interest
> Group
> http://dumontierlab.com
>
>
> Dr Alasdair J G Gray
> Research Associate
> Alasdair.Gray@manchester.ac.uk
> +44 161 275 0145
>
> http://www.cs.man.ac.uk/~graya/
>
> Please consider the environment before printing this email.
>
>


-- 
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com