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RE: Minimum information about a mutation

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Thu, 26 May 2011 09:33:01 -0700
Message-ID: <3dbf8faf413df66b6ff3409f07a0f7f4@mail.gmail.com>
To: "Joanne Luciano (gmail)" <jluciano@gmail.com>
Cc: Jim McCusker <james.mccusker@yale.edu>, Chris Baker <denguehost@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
hi joanne,

+1!

cheers,
michael

> -----Original Message-----
> From: Joanne Luciano (gmail) [mailto:jluciano@gmail.com]
> Sent: Thursday, May 26, 2011 9:31 AM
> To: Michael Miller
> Cc: Jim McCusker; Chris Baker; w3c semweb HCLS
> Subject: Re: Minimum information about a mutation
>
> sounds like provenance to me.
>
> joanne
>
> On May 26, 2011, at 12:15 PM, Michael Miller wrote:
>
> > 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 16:33:27 GMT

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