- From: M. Scott Marshall <mscottmarshall@gmail.com>
- Date: Mon, 30 May 2011 16:18:24 +0200
- 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 UTC