- From: Joanne Luciano (gmail) <jluciano@gmail.com>
- Date: Thu, 26 May 2011 12:30:35 -0400
- To: Michael Miller <Michael.Miller@systemsbiology.org>
- Cc: Jim McCusker <james.mccusker@yale.edu>, Chris Baker <denguehost@gmail.com>, w3c semweb HCLS <public-semweb-lifesci@w3.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 UTC