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Re: Minimum information about a mutation

From: Chris Baker <denguehost@gmail.com>
Date: Tue, 5 Jul 2011 11:37:47 -0300
Message-ID: <CALDyQEW3Ex8T1r9LvReT8qHGf9d=F1Qu_+WS8HAdQfLAJSrmwA@mail.gmail.com>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
Cc: Jim McCusker <james.mccusker@yale.edu>, Michael Miller <Michael.Miller@systemsbiology.org>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, Erik van Mulligen <mulligen@gmail.com>, Peter Taschner <P.E.M.Taschner@lumc.nl>
Hi - Following on from the earlier thread
I am pleased to let you know that the supplement “Proceedings of the
European Conference on Computational Biology (ECCB) 2010 Workshop:
Annotation, interpretation and management of mutation (AIMM)” has been
published today. The full content of the supplement can be found at
http://www.biomedcentral.com/1471-2105/12?issue=S4.

Characterization of pathogenic germline mutations in human Protein Kinases
Jose MG Izarzugaza, Lisa EM Hopcroft, Anja Baresic, Christine A Orengo,
Andrew CR Martin, Alfonso Valencia
BMC Bioinformatics 2011, 12(Suppl 4):S1 (5 July 2011)
http://www.biomedcentral.com/1471-2105/12/S4/S1

Genome-wide prediction of splice-modifying SNPs in human genes using a new
analysis pipeline called AASsites
Kirsten Faber, Karl-Heinz Glatting, Phillip J Mueller, Angela Risch, Agnes
Hotz-Wagenblatt
BMC Bioinformatics 2011, 12(Suppl 4):S2 (5 July 2011)
http://www.biomedcentral.com/1471-2105/12/S4/S2

Improving the prediction of disease-related variants using protein
three-dimensional structure
Emidio Capriotti, Russ B Altman
BMC Bioinformatics 2011, 12(Suppl 4):S3 (5 July 2011)
http://www.biomedcentral.com/1471-2105/12/S4/S3

Challenges in the association of human single nucleotide polymorphism
mentions with unique database identifiers
Philippe E Thomas, Roman Klinger, Laura I Furlong, Martin Hofmann-Apitius,
Christoph M Friedrich
BMC Bioinformatics 2011, 12(Suppl 4):S4 (5 July 2011)
http://www.biomedcentral.com/1471-2105/12/S4/S4

A formalized description of the standard human variant nomenclature in
Extended Backus-Naur Form
Jeroen F J Laros, André Blavier, Johan T den Dunnen, Peter E M Taschner
BMC Bioinformatics 2011, 12(Suppl 4):S5 (5 July 2011)
http://www.biomedcentral.com/1471-2105/12/S4/S5

Deploying mutation impact text-mining software with the SADI Semantic Web
Services framework
Alexandre Riazanov, Jonas Bergman Laurila, Christopher JO Baker
BMC Bioinformatics 2011, 12(Suppl 4):S6 (5 July 2011)
http://www.biomedcentral.com/1471-2105/12/S4/S6

Chris


On Mon, May 30, 2011 at 11:18 AM, M. Scott Marshall <
mscottmarshall@gmail.com> wrote:

> 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
>



-- 
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
Received on Tuesday, 5 July 2011 14:38:16 GMT

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