W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2011

Re: Minimum information about a mutation

From: Joanne Luciano (gmail) <jluciano@gmail.com>
Date: Thu, 26 May 2011 12:30:35 -0400
Cc: Jim McCusker <james.mccusker@yale.edu>, Chris Baker <denguehost@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
Message-Id: <5091684C-59C7-4053-83F2-0C8A221A04A0@gmail.com>
To: Michael Miller <Michael.Miller@systemsbiology.org>
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 16:31:06 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:01:01 GMT