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Re: [BioRDF] Comments from Christoph Grabmuller on BioRDF microarray provenance

From: Helen Parkinson <parkinson@ebi.ac.uk>
Date: Mon, 08 Nov 2010 15:50:27 +0000
Message-ID: <4CD81C43.8000802@ebi.ac.uk>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
CC: HCLS <public-semweb-lifesci@w3.org>, Christoph Grabmueller <grabmuel@ebi.ac.uk>
Hi a few comments on the EFO parts of this.


> Generally I like the data model, seems intuitive to me. Btw in the
> graph at http://biordfmicroarray.googlecode.com/hg/sparql_endpoint.html
> the edge 'experimentSet dct:isPartOf    microarray_experiment' is
> missing.
> What I have so far is a simplified subset of this model, I don't see
> any conflicts. The main difference is that I'm using the EFO directly,
> and then link to DO (only possible after 'fixing' the EFO myself); and
> I'm not using gene name strings but official uniprot URIs
> (http://purl.uniprot.org/uniprot/P30089).
EFO only uses namespaces from a subset of ontologies, mostly those which 
are either OBO foundry approved,
or in the process of this, or where is a lack of orthogonal ontologies. 
For disease we have many terms from many different sources, and so we 
cross reference rather than use namespaces as there is no single 
authoritative source (in our opinion). We have replaced namespaces 
programmatically in the past, so we could provide this code if this is 
of interest, or we could consider a release with DO terms namespace if 
this is of general use, though this probably would not be our production 
> Regards,
> Christoph

Helen Parkinson, PhD
Team Leader
Functional Genomics Group

EBI 01223 494672
Skype: helen.parkinson.ebi
Received on Monday, 8 November 2010 15:51:07 UTC

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