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RE: Minimum information about a mutation

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Thu, 26 May 2011 09:15:29 -0700
Message-ID: <25a2769e99b21bb871d6045f7fd368c0@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,

you're not giving us much to go on, the actual step by step use case would
be great.

> What is needed for people to trust these observations?

a description of how the observation was made, whatever technology was
behind it (looking through a microscope, performing a qPCR assay, mass
spec on metabolomics, looking at someone else's results and performing an
analysis, ...), what was the environment when the observation was made,
any parameters to the observation that may effect the conclusion of the
observation, who made the observation, when was the observation made, ...

michael


> -----Original Message-----
> From: Jim McCusker [mailto:james.mccusker@yale.edu]
> Sent: Thursday, May 26, 2011 8:45 AM
> To: Michael Miller
> Cc: Chris Baker; w3c semweb HCLS
> Subject: Re: Minimum information about a mutation
>
> I'm looking for an agreed upon way to describe observation of
> particular functional (AA change) mutations in specific specimens.
> What is needed for people to trust these observations?
>
> Jim
>
> On Thu, May 26, 2011 at 11:37 AM, Michael Miller
> <Michael.Miller@systemsbiology.org> wrote:
> > 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
> >
>
>
>
> --
> 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 16:15:49 GMT

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