Hi a few comments on the EFO parts of this.
best
Helen
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
release.
Regards,
Christoph
--
Helen Parkinson, PhD
Team Leader
Functional Genomics Group
EBI
EBI 01223 494672
Skype: helen.parkinson.ebi
