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Observations about facts in genomics

From: Jeremy J Carroll <jjc@syapse.com>
Date: Wed, 20 Mar 2013 09:04:50 -0700
Message-Id: <B753A456-0420-4E34-A79C-6DAF7B284479@syapse.com>
Cc: Pat Hayes <phayes@ihmc.us>
To: w3c semweb HCLS <public-semweb-lifesci@w3.org>
Pat Hayes wrote:

"[RDF] is intended for recording data, and most data is pretty mundane stuff about which there is not a lot of factual disagreement."

One of the things I am learning about genetic sequencing is this process, which is meant to tell you about the patient's DNA, is in fact somewhat problematic, resulting in facts which are disputable.

So, a data file that I am trying to get my head around at the moment contains a line like:

chrM	942	rs28579222	A	G	.	.	ASP;HD;OTHERKG;RSPOS=942;SAO=0;SF=0;SSR=0;VC=SNV;VP=050000000005000402000100;WGT=1;dbSNPBuildID=125

So far, I have understood the first five fields, as saying that in a particular position in the DNA (the 942nd base in the mitochondrial DNA, aka rs28579222), when one might have expected to see an A a sample had a G.
But that last part "a sample had a G" is in fact open to doubt  There is a complex piece of chemistry, physics and computing that guesses that there is a G in that position. It is possible to see some of the less processed data that fed into that guess, and to see levels of confidence that the different algorithms had with the results; but it is not a slam dunk by any means. So, some more skeptical people want to be able to see the 'raw read data' prior to the decision that this is a G. Usually one would expect to see some of the raw read data agree with the G, and some disagree.

Since this assertion (that this position is a G) is made with a few million similar assertions, all of which have some element of doubt - it would be highly surprising if every single call were correct: yet within the logic of RDF we probably end up asserting the truth of the whole graph  which leads us onto the dangerous path of ex contradictione quadlibet
Received on Wednesday, 20 March 2013 16:05:21 UTC

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