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Re: Ontology for Somatic Mutations?

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Tue, 23 Jul 2013 12:24:03 +0100
To: Melissa Haendel <haendel@ohsu.edu>
Cc: Suzanna Lewis <suzi@berkeleybop.org>, Oliver Ruebenacker <curoli@gmail.com>, Karen Eilbeck <keilbeck@genetics.utah.edu>, 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: <87d2q934fg.fsf@zerg32.ncl.ac.uk>

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> 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>> 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>> 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>> 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>
> 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>
> skype: melissa.haendel
> 503-407-5970
>
>
>

-- 
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 Tuesday, 23 July 2013 11:24:31 UTC

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