[BBF Standards] Registry exchange format

[Timothy Ham]

Hi,
My name is Tim, and I am working on a part registry for the recently
formed Joint Bioenergy Institute (JBEI) here in Berkeley. I have read
many posts on this list with interest.

I was wondering what the progress is on the data exchange format for
iGEM 2008. I couldn't find anything on openwetware nor the igem web
site, and I have not heard anything back from Randy. And reading what
Raik has wrote on exchange formats leaves me wondering if it's easier
to just agree on some really minimal exchange fields.

As a biologist, what's really important to me is the "desired piece of
DNA", irregardless of packaging format. The packaging is really
helpful, but sometimes not.

So here is how I'm doing it at JBEI:

-A Part is a "unique piece of DNA" containing a "desired sequence of
DNA", the Sequence.
-The packaging format has a defined prefix and suffix nucleotide sequence.
-The Sequence may overlap with the packaging format, if necessary, in
which case the overlap must be specified. The Sequence remains the
same.
-The Sequence is sha-1 hashed for identification. Allows quick check
of duplicates or alterations.
-A "Part Number" is assigned to a Part. So a Sequence, and the same
Sequence in two packaging formats may get three total "part numbers".
-Composite Part is nothing but a new Part with a new Sequence with
regions annotated as being from other Parts.

-Exchange is done via xml.
-The db accepts, stores, and retrieves foreign tags. This allows
accepting customizations from other registries. If registry A adds a
new field for storing model information, semantics, ontology or
whatever, and sends this xml file to registry B that's not ready to
handle it, registry B still hold and export that information
unmolested. Proper namespace is required for foreign tags.
-uuids get attached to "part numbers" for global identification.

Is this minimal enough to agree on?

Some other nice fields we have:
Creator, Aliases, References, keywords, summary notes, attached files.
A draft jbei xml format is mostly complete, and I will post it here in
a few days.

Exchange of parts information should be easy as sending people e-mail.
As such, I would like to coordinate with others as much as possible.

Tim