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RE: Minimum information about a mutation

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Thu, 26 May 2011 08:37:55 -0700
Message-ID: <b0f003b5dd38754adec93af2de58631c@mail.gmail.com>
To: Jim McCusker <james.mccusker@yale.edu>
Cc: Chris Baker <denguehost@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
hi jim,

i don't think this is what MIAMI-like standards are needed for--are you
actually just looking for a nomenclature to describe this?  or do you need
a metric to evaluate the underlying papers?

cheers,
michael

> -----Original Message-----
> From: Jim McCusker [mailto:james.mccusker@yale.edu]
> Sent: Wednesday, May 25, 2011 9:47 AM
> To: Michael Miller
> Cc: Chris Baker; w3c semweb HCLS
> Subject: Re: Minimum information about a mutation
>
> For more context, we are seeing supplementary data like in:
>
> http://www.nature.com/nature/journal/v463/n7278/suppinfo/nature08658.ht
> ml
> (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 Thursday, 26 May 2011 15:38:24 GMT

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