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Re: Observations about facts in genomics

From: Joachim Baran <joachim.baran@gmail.com>
Date: Wed, 20 Mar 2013 18:19:14 -0400
Message-ID: <CAObSwHXd9NnkSegzjj_3av98RZ1hOGshRAkqhFpgtw_2F-4O=Q@mail.gmail.com>
To: Jerven Bolleman <me@jerven.eu>
Cc: Graham Klyne <graham.klyne@zoo.ox.ac.uk>, Jeremy J Carroll <jjc@syapse.com>, w3c semweb HCLS <public-semweb-lifesci@w3.org>, Pat Hayes <phayes@ihmc.us>
Hello,

On 20 March 2013 18:09, Jerven Bolleman <me@jerven.eu> wrote:

> So instead of chromosome M you are really talking about assembly X of
> a set of reads R mapped via some (variant calling) processes to
> reference chromosome C that is also really an assembly of a different
> set of reads.

  Just to add to Jerven's comment: even when referring to a reference
assembly, it is best to add "Which version?".

  Even when talking about reference genome assemblies, you have multiple
versions (including "patches"). Additionally, when interpreting the
genomes, you will also get different results from various institutes (genes
from UCSC are not the same as Ensembl).

  I think my point here is that chromosomes (or anything, really), has
provenance that needs to be explicitly denoted.

Best,
Joachim
Received on Wednesday, 20 March 2013 22:19:40 UTC

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