Re: Ontology for Somatic Mutations?

     Hello,

  Thanks for all the links, has been very helpful!

     Take care
     Oliver


On Fri, Jul 26, 2013 at 7:17 AM, Phillip Lord
<phillip.lord@newcastle.ac.uk>wrote:

>
> In what sense? See if we can generate the description of the karyotype
> from a genome sequence? Or at least compare the two?
>
> I agree that this would be interesting. At the moment, the problem that
> we have is the ISCN string is computationally relatively intractable. In
> most cases, though, the ISCN is all we have: there is no sequence, and
> no biological material.
>
> Phil
>
>
> Karen Eilbeck <keilbeck@genetics.utah.edu> writes:
>
> > Hi Phil
> > Nice model of ISCN. We currently allow ISCN strings to be annotated in
> GVF to
> > describe a genome structure. It may be interesting to validate against
> whole
> > genome sequence.
> > --K
> >
> > On Jul 23, 2013, at 5:24 AM, Phillip Lord wrote:
> >
> >
> > To the extent that it helps to answer our use case, co-ordination might
> > be useful; our work on the karyotype is reasonably tightly scoped, and I
> > wish to maintain this.
> >
> > Phil
> >
> >
> > Melissa Haendel <haendel@ohsu.edu<mailto:haendel@ohsu.edu>> writes:
> > Hi all, It would be great if we could coordinate these efforts - The
> > genotype work we are doing that Chris Baker mentioned earlier on this
> > thread (see
> >
> http://www.unbsj.ca/sase/csas/data/ws/icbo2013/papers/ec/icbo2013_submission_60.pdf
> > )
> > is already being integrated into the sequence ontology.
> >
> > Cheers,
> > Melissa
> >
> > On Jul 22, 2013, at 10:22 AM, Suzanna Lewis <suzi@berkeleybop.org
> <mailto:suzi@berkeleybop.org><mailto:suzi@berkeleybop.org>> wrote:
> >
> > Check out the  Sequence Ontology. It is well-established in the genomics
> community.
> > http://sequenceontology.org/
> >
> > On Jul 22, 2013, at 4:53 PM, Phillip Lord
> > <phillip.lord@newcastle.ac.uk<mailto:phillip.lord@newcastle.ac.uk
> ><mailto:phillip.lord@newcastle.ac.uk>>
> > wrote:
> >
> >
> > We are working on a karyotype ontology which describes chromosome
> abnormalities.
> >
> > The first paper is available here which also includes links to the
> ontology.
> >
> > http://arxiv.org/abs/1305.3758
> >
> >
> >
> >
> > Oliver Ruebenacker <curoli@gmail.com<mailto:curoli@gmail.com><mailto:
> curoli@gmail.com>> writes:
> >
> >    Hello,
> >
> > Does any one know of an ontology for somatic mutations (including SNPs,
> > chromosomal abnormalities, etc.)?
> >
> >    Take care
> >    Oliver
> >
> > --
> > Phillip Lord,                           Phone: +44 (0) 191 222 7827
> > Lecturer in Bioinformatics, Email:
> > phillip.lord@newcastle.ac.uk<mailto:phillip.lord@newcastle.ac.uk
> ><mailto:phillip.lord@newcastle.ac.uk>
> > School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> > Room 914 Claremont Tower,               skype: russet_apples
> > Newcastle University,                   twitter: phillord
> > NE1 7RU
> >
> >
> >
> > Dr. Melissa Haendel
> >
> > Assistant Professor
> > Ontology Development Group, OHSU Library
> > http://www.ohsu.edu/library/
> > Department of Medical Informatics and Epidemiology
> > Oregon Health & Science University
> > haendel@ohsu.edu<mailto:haendel@ohsu.edu><mailto:haendel@ohsu.edu>
> > skype: melissa.haendel
> > 503-407-5970
> >
> >
> >
> >
> > --
> > Phillip Lord,                           Phone: +44 (0) 191 222 7827
> > Lecturer in Bioinformatics,             Email:
> phillip.lord@newcastle.ac.uk<mailto:phillip.lord@newcastle.ac.uk>
> > School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> > Room 914 Claremont Tower,               skype: russet_apples
> > Newcastle University,                   twitter: phillord
> > NE1 7RU
> >
> > Karen Eilbeck
> > Associate Professor
> > Department of Biomedical Informatics, University of Utah
> >
>
> --
> Phillip Lord,                           Phone: +44 (0) 191 222 7827
> Lecturer in Bioinformatics,             Email:
> phillip.lord@newcastle.ac.uk
> School of Computing Science,
> http://homepages.cs.ncl.ac.uk/phillip.lord
> Room 914 Claremont Tower,               skype: russet_apples
> Newcastle University,                   twitter: phillord
> NE1 7RU
>



-- 
Oliver Ruebenacker
IT Project Lead at PanGenX (http://www.pangenx.com)
Be always grateful, but never satisfied.