hi jeremy,
unfortunately, it isn't just the metadata that can be different between
different producers.
for a project i'm working on, similar in scope to 1000 genomes, variants
at the same location for different subjects are collapsed into one VCF
record and there is a list of possible alleles, o
This looks really helpful ….
I suspect that the key questions remain about how to effectively use the data
FALDO seems at first glance to be fairly simplistic compared with the model
implicit in VCF.
Maybe FALDO is actually more useful, concentrating on the important stuff ...
thanks
Jeremy
On 2013-04-01, at 3:40 PM, Chris Mungall wrote:
> VCF is convertible to GVF[4,5] which is a subset of GFF3 with additional
> recommended metadata. It's supported by Ensembl, gbGap and others, and the
> 1000genomes data is available in GVF[6].
>
> As GFF3 is convertible to RDF/OWL that uses FAL
Apologies if this has been covered already I haven't been following the whole
discussion.
Genome variant data is just a subset of genome data. My understanding is that
the semweb BioHackathon group looked at a variety of different kinds of genomic
data and came up with FALDO[1]. This model loo
On 4/1/13 1:59 PM, Jeremy J Carroll wrote:
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
I return the favor:
1.
http://kingsley.idehen.net/about
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 Idehen wro
On 4/1/13 1:05 PM, Jeremy J Carroll wrote:
Hi
I am hoping to present the work I am currently doing on VCF and RDF at the
Clinical Pharamcogenomics TF telecom on Wednesday.
My presentation should cover:
- business background, Syapse Discovery
- some background on VCF as a knowledge representat
Hi
I am hoping to present the work I am currently doing on VCF and RDF at the
Clinical Pharamcogenomics TF telecom on Wednesday.
My presentation should cover:
- business background, Syapse Discovery
- some background on VCF as a knowledge representation format
- and some initial results on ma
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