Re: Minimum information about a mutation

On May 26, 2011, at 11:44 AM, Jim McCusker wrote:

> 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?

provenance?

> 
> 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 15:55:50 UTC