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Re: [ontolog-forum] Genetic discovery using ontology mapping ofobservati

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Barry Smith <phismith@xxxxxxxxxxx>
Date: Sun, 12 May 2013 09:03:38 -0400
Message-id: <CAN_82STyG1wswhF34Za13OQ-8ZKKDoHrbgnDCh9qA1eKgOmFeQ@xxxxxxxxxxxxxx>
On Sat, May 11, 2013 at 11:11 PM, Rich Cooper
<rich@xxxxxxxxxxxxxxxxxxxxxx> wrote:
> Thanks Barry,
>
> Looking over their website, I see it has a lot of
> tools and other freebies.  That makes it useful
> for academic purposes.  Why do you say you
> consider it successful?    (01)


More than 4800 publications on PubMed
http://www.ncbi.nlm.nih.gov/pubmed/?term=%22Gene+Ontology%22
suggest that clinical and drug researchers are using GO in their
research on disease. There are now a number of standard methods, the
main one being what is called  'gene enrichment analysis'
BS    (02)


Has it resulted in new
> insights on genetic X environmental X diagnosis
> mappings?  Or is it solely for use with genetic
> mappings and the various alleles that are known as
> of now?
>
> It looks worth while studying for a while, and I
> will give it some time for that purpose - thanks,
>
> -Rich
>
> Sincerely,
> Rich Cooper
> EnglishLogicKernel.com
> Rich AT EnglishLogicKernel DOT com
> 9 4 9 \ 5 2 5 - 5 7 1 2
>
> -----Original Message-----
> From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx
> [mailto:ontolog-forum-bounces@xxxxxxxxxxxxxxxx] On
> Behalf Of Barry Smith
> Sent: Saturday, May 11, 2013 1:48 PM
> To: [ontolog-forum]
> Subject: Re: [ontolog-forum] Genetic discovery
> using ontology mapping ofobservations
>
> Rich
> If there is one example of a success story in the
> ontology field it is
> the Gene Ontology, and the various ontologies
> created to work in
> tandem therewith in the study of disease. See
>
> http://geneontology.org
> http://www.obofoundry.org/
>
> Barry
>
> On Sat, May 11, 2013 at 4:47 AM, Rich Cooper
> <rich@xxxxxxxxxxxxxxxxxxxxxx> wrote:
>> There is a genetic relationship with many
> diseases
>> which is unknown just yet.  However, new
>> relationships are popping up all the time.  For
>> example, there is a relationship newly
> discovered
>> between Fibromyalgia and a specific gene region
> :
>>
>>
> http://medicalxpress.com/news/2013-05-strong-genet
>> ic-component-fibromyalgia.html
>>
>> Quoting from that article:
>>
>>         A genome-wide linkage scan has
> identified
>> the chromosome 17p11.2-q11.2 region as the
>> susceptibility locus for fibromyalgia, according
>> to research published in the April issue of
>> Arthritis & Rheumatism.
>>
>>
>> Likewise, neurological diseases such as
> Alzheimers
>> and Amyotropic Lateral Sclerosis (ALS, i.e. Lou
>> Gehrig's Disease, aka Motor Neurone Disease) are
>> on the rise in highly developed countries like
> the
>> US and the UK. ALS is believed to be caused by
>> reaction to a specific virus, which must have
> some
>> genetic embedding.  Alzheimers has a tangling of
>> neurons which could (or not) be genetically
>> related:
>>
>>
> http://medicalxpress.com/news/2013-05-brain-diseas
>> es-affecting-people-earlier.html
>>
>> Quoting from that article:
>>
>>         There is no one factor rather the likely
>> interaction between all these environmental
>> triggers, reflecting changes in other
> conditions.
>> For example, whilst cancer deaths are down
>> substantially, cancer incidence continues to
> rise;
>> levels of asthma are un-precedented; the fall in
>> male sperm counts - the rise of auto-immune
>> diseases - all point to life-style and
>> environmental influences.
>>
>> Could a genetic ontology be useful for mapping
> the
>> disease biochemistry and environmental exposures
>> to genetic profiles?  Perhaps such an ontology
>> could be constructed automatically, step by
> step,
>> through identifying subjects with known genetic
>> spectrum and known environmental exposures
> versus
>> diagnosed conditions.
>>
>> Forgetting about the NL relationship, the names
> of
>> genes and proteins they code for might be more
>> construable than more linguistically based
>> ontologies.  We have had a lot of difficulty on
>> this list when trying to map linguistic
>> relationships to ontologies.
>>
>> In both these articles, there are directly
>> measurable protein levels and genetic codes
> which
>> are NOT linguistic, and which might make better
>> fodder for evidence based ontological discovery
>> for that very reason.
>>
>> Comments?
>>
>> -Rich
>>
>> Sincerely,
>> Rich Cooper
>> EnglishLogicKernel.com
>> Rich AT EnglishLogicKernel DOT com
>> 9 4 9 \ 5 2 5 - 5 7 1 2
>>
>>
>>
>>
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