input half way through that I hadn't coded for
c) make sure that I had some understanding of all the data
Jeremy J Carroll
Principal Architect
Syapse, Inc.
On Apr 3, 2013, at 1:20 PM, Michael Miller
wrote:
> hi jeremy,
>
> sorry i missed your talk this morning, it was early o
n
allele since not all alleles have a base sequence, e.g. a deletion of only some
approximate length
Jeremy J Carroll
Principal Architect
Syapse, Inc.
the header declarations gives you enough
to understand the content, and I imagine that there is in practice sufficiently
little variation for that to be automatable ...
Jeremy J Carroll
Principal Architect
Syapse, Inc.
On Apr 1, 2013, at 4:24 PM, Michael Miller
wrote:
> hi jeremy,
>
sequences - Reese at al
> [5] http://www.sequenceontology.org/resources/gvf.html
> [6] ftp://ftp.ensembl.org/pub/current_variation/gvf/homo_sapiens/
>
> On Apr 1, 2013, at 10:59 AM, Jeremy J Carroll wrote:
>
>> Hi Kingsley,
>>
>> I wasn't going to but since you
Hi Kingsley,
I wasn't going to but since you ask:
http://www.slideshare.net/JeremyJCarroll/vcf-and-rdf
or
http://lists.w3.org/Archives/Public/www-archive/2013Apr/att-0002/W3C-JJC-LifeSci.pdf
Jeremy J Carroll
Principal Architect
Syapse, Inc.
On Apr 1, 2013, at 10:13 AM, Kingsley I
mapping 1000 genomes into RDF
I will circulate slides shortly
Jeremy J Carroll
Principal Architect
Syapse, Inc.
989, at a presentation in Saarbrücken, Germany. My title was [Graph]
"unification considered harmful". Given the date and location it was the least
well chosen title I have ever used.
Jeremy J Carroll
Principal Architect
Syapse, Inc.
uch an opening up, that the owners of the knowledge (the
scientists and the clinicians) are imprisoned by the owners of the knowledge
format (the bioinformaticians) … of course, to some extent that is inevitable.
Jeremy J Carroll
Principal Architect
Syapse, Inc.
s the impact of a genetic variant at a given location? This is a hot
> field of study within genetic/bioinformatic research, and solutions to this
> problem will be critical for clinical personalized medicine programs.
>
> Bob
>
>
> From: public-semweb-lifesci-requ...@listhu
21, 2013 at 7:56 PM, Peter Ansell wrote:
> On 22 March 2013 12:05, Alan Ruttenberg wrote:
> > On Wed, Mar 20, 2013 at 3:15 PM, Jeremy J Carroll wrote:
> >>
> >> To me, that seems to lead us back to the earlier discussion (rathole?)
> >> about owl:sameAs
> &
Jerven suggests:
"instead of saying chrM it would have been solved by
using
http://my.lab.org/confidential/patientXXYYZZ/genome/sampleXX/ChrM/assemblyTTv43/VariantCalls5";
rather than continuing the philosophical/theological threads ….
I am interested in this practical question.
chrM as an ad
Is this issue wholly addressed by having a URI for the reference? Or is there
some subtlety that I am missing here?
i.e. I would expect a minor version of a reference genome to have a different
URI from a different minor version of the same major version of the reference
genome …. am I naive?
t; variant called, mapped assembly) instead of what you are discussing in
> english (a patients chromosome) you will end up fine. If you do this
> you don't need anything as exotic as frames etc...
>
> Regards,
> Jerven
>
> On Wed, Mar 20, 2013 at 9:23 PM, Graham Klyn
Pat Hayes wrote:
"[RDF] is intended for recording data, and most data is pretty mundane stuff
about which there is not a lot of factual disagreement."
One of the things I am learning about genetic sequencing is this process, which
is meant to tell you about the patient's DNA, is in fact somewha
I confess to having lost interest in this overly long thread, but then thought
maybe one observation might help clarify the disagreement of sorts between Pat
and David.
The dispute seems to be expressed ontologically: what is the interpretation of
a URI?
But the practical examples seem to be
question and discussion, but i am
> clueless as to what "horses for courses" compliant means.
>
> Joanne
>
> Sent from my iPhone
>
> On Mar 15, 2013, at 5:11 PM, Jeremy J Carroll wrote:
>
>>
>> On Mar 15, 2013, at 2:06 PM, Kingsley Idehen wrote:
>>
>>> "horses for courses" compliant
>>
>> wonderful!
While it doesn't seem to be the convention in this group, now that I have
graduated from lurking to participating, I thought I should say why I am here.
I have a new job with a genomics company in Silicon Valley, and my remit is to
work out how best to represent both scientific knowledge about
On Mar 15, 2013, at 2:06 PM, Kingsley Idehen wrote:
> "horses for courses" compliant
wonderful!
cit, and doesn't need new predicates, though it does
> require some level of coordination.
>
> Best,
> Alan
>
> On Fri, Mar 15, 2013 at 2:55 PM, Umutcan ŞİMŞEK wrote:
> That made it clear, thanks again. I'm sure it will be helpful for other
> developers either in t
I did not find this a rookie question at all.
This seems to get to the heart of some of the real difficult issues in Semantic
Web.
My perspective is different from yours, and a resource description that I
author is a description of the resource from my perspective; a resource
description that
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