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[ontolog-forum] Genetic discovery using ontology mapping of observations

To: "'[ontolog-forum] '" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Rich Cooper" <rich@xxxxxxxxxxxxxxxxxxxxxx>
Date: Sat, 11 May 2013 01:47:45 -0700
Message-id: <FEC4420C734B475F87356CA19121C903@Gateway>
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 :    (01)

ic-component-fibromyalgia.html    (02)

Quoting from that article:    (03)

        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.    (04)

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:    (05)

es-affecting-people-earlier.html    (06)

Quoting from that article:    (07)

        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.     (08)

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.      (09)

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.      (010)

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.      (011)

Comments?    (012)

-Rich    (013)

Rich Cooper
Rich AT EnglishLogicKernel DOT com
9 4 9 \ 5 2 5 - 5 7 1 2    (014)

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