RE: VCF and RDF, at Clinical Pharmacogenomics TF, Wed Apr 3rd

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, one per collapsed variant.
i'm not working directly with the VCF but there is also an annotation
field to tell whether the variant is in a coding region, an exon or an
intron, or outside a coding region, whether the change makes a difference
in the amino acid, plus that all depends on which isoforms are possible.
even tho it is reasonably documented, there still are gotcha's.

the one thing i have found tho, is that one can base one's mapping on the
source of the document.  two vcf's from the same provider will likely be
parsable by the same code.  so i usually do what most would do, use a base
class to handle most of the parsing then have a derived class per provider
and try to drive everything through a configuration file.

cheers,
michael

Michael Miller
Software Engineer
Institute for Systems Biology

> -----Original Message-----
> From: Jeremy J Carroll [mailto:jjc@syapse.com]
> Sent: Monday, April 01, 2013 2:02 PM
> To: Chris Mungall
> Cc: Kingsley Idehen; HCLS hcls
> Subject: Re: VCF and RDF, at Clinical Pharmacogenomics TF, Wed Apr 3rd
>
>
> 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 J Carroll
> Principal Architect
> Syapse, Inc.
>
>
>
> On Apr 1, 2013, at 12:40 PM, Chris Mungall <cjmungall@lbl.gov> wrote:
>
> >
> > 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 looks pretty good
> to me, and importantly there is a converter from GFF3[2,3]. Of all the
> commonly used genome feature formats out there, GFF3 is by far the best
at
> encouraging provision of relevant metadata using standard
> ontologies/terminologies.
> >
> > 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 FALDO and SO, it follows
that
> GVF is too (though the converter may need tweaking to take advantage of
> the additional GVF metadata).
> >
> > I just wanted to make sure you were aware of all this previous work
> before reinventing anything.
> >
> > [1] https://github.com/JervenBolleman/FALDO
> > [2] http://www.sequenceontology.org/gff3.shtml
> > [3] https://code.google.com/p/gff3-to-owl/
> > [4] http://www.ncbi.nlm.nih.gov/pubmed/20796305 - A standard variation
> file format for human genome 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 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
> <kidehen@openlinksw.com> wrote:
> >>
> >>> 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 representation format
> >>>> - and some initial results on mapping 1000 genomes into RDF
> >>>>
> >>>> I will circulate slides shortly
> >>>>
> >>>>
> >>>> Jeremy J Carroll
> >>>> Principal Architect
> >>>> Syapse, Inc.
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>
> >>> Hopefully you'll publish to Slideshare?
> >>>
> >>> --
> >>>
> >>> Regards,
> >>>
> >>> Kingsley Idehen
> >>> Founder & CEO
> >>> OpenLink Software
> >>> Company Web: http://www.openlinksw.com
> >>> Personal Weblog: http://www.openlinksw.com/blog/~kidehen
> >>> Twitter/Identi.ca handle: @kidehen
> >>> Google+ Profile:
> https://plus.google.com/112399767740508618350/about
> >>> LinkedIn Profile: http://www.linkedin.com/in/kidehen
> >>>
> >>>
> >>>
> >>>
> >>>
> >>
> >>
> >
>

Received on Monday, 1 April 2013 23:31:49 UTC