uot;
; "Ravi Shankar"
Sent: Wednesday, November 10, 2010 4:21 AM
Subject: Re: [BioRDF] Comments from Christoph Grabmuller on BioRDF
microarray provenance
Interesting question and one we've been discussing in other contexts. HGNC
is only valid for human genes of course, and not
On Tue, Nov 9, 2010 at 4:45 PM, mdmiller wrote:
> this i've seen as more a de facto best practice than anything for
> identifying a sequence (but i'm not sure what you mean by a standard input
> format).
I meant: what are valid and/or (minimally) required ways to refer to a
gene? Is it enough to
Interesting question and one we've been discussing in other contexts.
HGNC is only valid for human genes of course, and not all species have
this type of sign off on ids. I would use an Ensembl id, from there you
can get other id cross references
best
Helen
On 10/11/2010 10:24, Christoph Gra
> The DO is a OBO Foundry candidate, and there is an official OWL
> release [1], so wouldn't that be the authoritative source for URIs? Of
> course it's easy to replace the definition_citations, but wouldn't it
> be much nicer if the user can just download two 'officially' released
> OWL files and
o explore this idea and its
ramifications.
this leaves to others more knowledgeable the actual identification work of
genes and proteins and their relationship.
cheers,
michael
- Original Message -
From: "Christoph Grabmuller"
To: "mdmiller"
Cc: "M. Sc
On Mon, Nov 8, 2010 at 4:02 PM, mdmiller wrote:
> 2) Many 'things' are represented as strings (e.g. genes), which makes
> it often impossible to run a federated query against another endpoint.
> Gene names might somewhat consistent for HUGO, but what about other
> species? Also, just the simple va
On Mon, Nov 8, 2010 at 3:50 PM, Helen Parkinson wrote:
> 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 source
hi all,
my comments in line,
cheers,
michael
- Original Message -
From: "M. Scott Marshall"
To: "HCLS"
Cc: "Christoph Grabmueller"
Sent: Monday, November 08, 2010 7:41 AM
Subject: [BioRDF] Comments from Christoph Grabmuller on BioRDF microar
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:isPartOfmicroarray_experiment' is
missing.
What I have so far is a si
[Forwarding Christoph's comments on the BioRDF Provenance article
draft for discussion. Cheers, Scott]
Hello Scott,
I finally had a look at the provenance draft, a few points:
1) Why is provenance so important? Is the lab where the data came from
so significant? Or should I understand provenance
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