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Re: Minimum information about a mutation

From: Chris Baker <denguehost@gmail.com>
Date: Wed, 25 May 2011 13:07:30 -0300
Message-ID: <BANLkTimrNqzhftPPF7VTOEjHUr3NzpFdHw@mail.gmail.com>
To: Jim McCusker <james.mccusker@yale.edu>
Cc: w3c semweb HCLS <public-semweb-lifesci@w3.org>
Hi Jim,

I do not know of a MIAME-like standard for protein mutation impacts.

There are some revisions to the sequence ontology being developed
Toward a Richer Representation of Sequence Variation in the Sequence
Ontology, Michael Bada and Karen Eilbeck
http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-645/Paper6.pdf

In a rush here are some leads I came up with.

Amino Acid Ontology - Comprehensive but no mutations
http://www.co-ode.org/ontologies/amino-acid/2009/02/16/

Human Genome Variation Society Nomenclature
http://www.hgvs.org/mutnomen/

Improving sequence variant descriptions in mutation databases and
literature using the Mutalyzer sequence variation nomenclature
checker.
http://www.ncbi.nlm.nih.gov/pubmed/18000842
http://www.mutalyzer.nl/2.0/

We outline small task specific mutation impact ontology in screent
shots attached and below:

Algorithms and semantic infrastructure for mutation impact extraction
and grounding
http://www.biomedcentral.com/content/pdf/1471-2164-11-s4-s24.pdf

Deploying mutation impact text-mining software with the SADI Semantic
Web Services framework
http://www.biomedcentral.com/qc/1471-2105/12/S4/S6

See also:

TOWARDS A SYSTEMATIC EVALUATION OF PROTEIN MUTATION EXTRACTION SYSTEMS
http://www.worldscinet.com/jbcb/05/0506/S0219720007003193.html


On Wed, May 25, 2011 at 12:29 PM, Jim McCusker <james.mccusker@yale.edu> wrote:
>
> Does anyone know of a MIAME-like standard for what should be included
> in a dataset of amino acid-level mutations?
>
> Thanks,
> Jim
> --
> Jim McCusker
> Programmer Analyst
> Krauthammer Lab, Pathology Informatics
> Yale School of Medicine
> james.mccusker@yale.edu | (203) 785-6330
> http://krauthammerlab.med.yale.edu
>
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mccusj@cs.rpi.edu
> http://tw.rpi.edu
>



--
Christopher J. O. Baker Ph. D.
Associate Professor
Dept. Computer Science and Applied Statistics
University of New Brunswick, Canada
http://ca.linkedin.com/in/christopherjobaker


Received on Wednesday, 25 May 2011 16:07:59 GMT

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