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Re: Minimum information about a mutation

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Mon, 30 May 2011 16:18:24 +0200
Message-ID: <BANLkTinyFverhKzw20FexdAA=zRcuiFMbw@mail.gmail.com>
To: Jim McCusker <james.mccusker@yale.edu>
Cc: Michael Miller <Michael.Miller@systemsbiology.org>, Chris Baker <denguehost@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, Erik van Mulligen <mulligen@gmail.com>, Peter Taschner <P.E.M.Taschner@lumc.nl>
Hi Jim,

We've been talking about this in the TM calls. Maybe you could join us.

I think that Chris had it pegged:
http://www.hgvs.org/mutnomen/recs.html

Note specific recommendations such as to use a Locus Reference Genomic
sequence (LRG).
There are also some discussions on the HGVS web site.

There is a recent article (May 2011) in Human Mutation from Taschner
and den Dunnen:
http://onlinelibrary.wiley.com/doi/10.1002/humu.21427/abstract
which properly explains 'nesting' - something I was trying in vain to
describe to colleagues on a TM call after a conversation with Peter
Taschner about modeling SNPs.

Cheers,
Scott

On Wed, May 25, 2011 at 6:47 PM, Jim McCusker <james.mccusker@yale.edu> wrote:
> 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
>
>



-- 
M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
http://staff.science.uva.nl/~marshall
Received on Monday, 30 May 2011 14:18:53 GMT

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