[BBF Standards] Standards Digest, Vol 4, Issue 6

[J. Christopher Anderson]

This is a great start in discussing core elements of documentation
standards.  I hope we can continue this momentum and get a formal
description of a standard in a published form and start building some
software tools that read and write in these file formats.

I want to recap some of the basic principles that were discussed:

*Seamless transfer of information between individuals and the community*.
The files will be used to handle theoretical sequences, measured data, and
track samples at the level of individuals, labs, and the community.  We need
the flexibility at the lab level to have diverse tools able to access these
files and keep the files private. However, the files must also be easily
uploadable to public registries in a manner that does not cause conflicts
with other people's files.

*Keep it simple (for now)*.  We do not yet know the full scope of
information that people will need to share, but there is core information
that we all recognize as essential.  This initial version of the standard
should encapsulate core information.

*Separate **theoretical and experimental **files*.  Specific DNA samples
need a distinct file type that maps to theoretical sequences.  This
experimental file type is where sample tracking information, sample quality,
and observed data is stored.  The experimental file has tags that map it to
theoretical files.  These theoretical files contain information about the
sequence and theoretical properties of the sequence.  When using a tool that
accesses these files, the entry for "b0015" would pull up information from
both the theoretical part and experimental files mapping to this part.  The
need for separate files is that 1) experimental samples sometimes need to be
re-mapped to a different theoretical file, and 2) we need to be able to
sample track physical DNAs that exist within individual labs

For popular parts, there may be 100 distinct examples of experimental files
all mapping to a single theoretical file.  For example, every individual
using Biobricks probably has a tube labeled pSB1A2-r0040.  It is inevitable
that some of these samples will get tube-switched, mutate, or cease to
exist.  Having separate files allows us to re-map the experimental data to
their actual theoretical files upon discovery of errors.  They also lets us
manage the collection of physical DNAs that exist within our personal and
lab collections.

*What goes in what file*.  The essential question we should ask in
determining whether a piece of information belongs in the theoretical file
or the experimental file is whether that information would change if the
physical DNA no longer mapped to the theoretical sequence.  So, for example,
the description of a DNA as being a coding sequence for GFP would not change
if a physical DNA turned out to have the GFP gene deleted.  So, information
that reflects homology of the DNA to known sequences belongs in the
theoretical file.  In contrast, information such as "it turns the cells
green" belongs in the experimental file--if the DNA turned out to be
inconsistant with the theoretical sequence, it would not change the fact
that the cells are green, it simply reflects information about a distinct
theoretical sequence.

-Chris

On Sun, Apr 27, 2008 at 11:22 AM, <standards-request at biobricks.org> wrote:

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> Today's Topics:
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>   1. Notes from Saturday Afternoon Workshop Discussion on White
>      Board (Michal Galdzicki)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Sun, 27 Apr 2008 11:22:09 -0700
> From: "Michal Galdzicki" <mgaldzic at u.washington.edu>
> Subject: [BBF Standards] Notes from Saturday Afternoon Workshop
>        Discussion      on White Board
> To: Standards at biobricks.org
> Message-ID:
>        <e1e3fca60804271122sfc11b03o793afdffb9ff5140 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
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> Attached is a pdf of a data model, which was discussed as a group.
> Please make comments and discuss.
> mike galdzicki
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