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Re: Ontology for Somatic Mutations?

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Fri, 26 Jul 2013 12:17:18 +0100
To: Karen Eilbeck <keilbeck@genetics.utah.edu>
Cc: Melissa Haendel <haendel@ohsu.edu>, Suzanna Lewis <suzi@berkeleybop.org>, Oliver Ruebenacker <curoli@gmail.com>, SO developers <song-devel@lists.sourceforge.net>, public-semweb-lifesci <public-semweb-lifesci@w3.org>, "jennifer.warrender\@newcastle.ac.uk" <jennifer.warrender@newcastle.ac.uk>, "monarchinitiative-dev\@monarchinitiative.org" <monarchinitiative-dev@monarchinitiative.org>
Message-ID: <87ehallge9.fsf@zerg32.ncl.ac.uk>

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                                 
Received on Friday, 26 July 2013 11:17:46 UTC

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