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Re: Minimum information about a mutation

From: Jim McCusker <james.mccusker@yale.edu>
Date: Wed, 25 May 2011 12:47:00 -0400
Message-ID: <BANLkTinvFdWGY0DTiHUcNEtObzUVt7a8Tg@mail.gmail.com>
To: Michael Miller <Michael.Miller@systemsbiology.org>
Cc: Chris Baker <denguehost@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
For more context, we are seeing supplementary data like in:

http://www.nature.com/nature/journal/v463/n7278/suppinfo/nature08658.html
(Supplementary Table 4)

and in:

http://www.nature.com/ng/journal/v43/n5/full/ng.810.html#/supplementary-information
(Supplementary Table 2)

The main difference is that they are expressing SNVs but mentioning
the AA change, while we want to list the AA changes and mention the
nucleotide differences that go in to it.

Jim

On Wed, May 25, 2011 at 12:38 PM, Michael Miller
<Michael.Miller@systemsbiology.org> wrote:
> 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
>



-- 
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
Received on Wednesday, 25 May 2011 16:47:48 GMT

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