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RE: Minimum information about a mutation

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 25 May 2011 09:38:37 -0700
Message-ID: <bb7058591bc148e50a1e2ba1a091c0c4@mail.gmail.com>
To: Chris Baker <denguehost@gmail.com>, Jim McCusker <james.mccusker@yale.edu>
Cc: w3c semweb HCLS <public-semweb-lifesci@w3.org>
hi chris,

excellent answer.

hi jim,

i think one aspect of MIAMI-like specifications is that the technology
that was used to discover the mutation and the protocols and raw datasets
involved is a major focus so other researchers can evaluate the evidence
for the mutation and perhaps reproduce the experiment (altho in your case
this may involve a specific sample(s)).  that may fit in with some
standard that chris has pointed out.

cheers,
michael

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
> lifesci-request@w3.org] On Behalf Of Chris Baker
> Sent: Wednesday, May 25, 2011 9:08 AM
> To: Jim McCusker
> Cc: w3c semweb HCLS
> Subject: Re: Minimum information about a mutation
>
> 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 16:39:02 GMT

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