[BBF Standards] Registry exchange format

[Timothy Ham]

Hi Raik,
Thanks for your reply.

I have looked at brickit's data model (the nice pic on the website),
and it looks great. But because we (JBEI)  are also dealing with
adopting legacy systems (all the old constructs are not in biobricks,
and will not be for a very long time), so some of your assumptions in
the tables do not apply. For example, a host strain may have a
selection marker on the genome.
I will study the source code you pointed out more carefully.

As for overlapping Sequence with packaging format, I remember a debate
some time ago where someone thought having it overlap had some neat
advantages. I didn't want to exclude those people from storing their
stuff in biobrick format. Or having the machine confused when the the
desired sequence overlaps with the packaging.

I think URI is a great idea. UUID is actually for internal tracking.
If used in exchanges, it will prevent version collisions. Users should
never see UUIDs.

I have to disagree with you on composite parts. Sadly, biological
contsructs are mutable. So when I sequence a composite part, and find
that it's different from the original parts, but it's good enough for
me, where do I record it? It is often the case that what you have is
slightly different from what you think you have. That is the basis of
my emphasis on unique dna=part.

As for sample tracking, that is a very location specific thing so I
don't understand the relevance of it in an exchange format.

Oh, I really don't know much about the advantages of RDF vs xml. Maybe
you can educate me.

Tim







On Fri, Apr 11, 2008 at 11:05 AM, Raik Gruenberg <raik.gruenberg at crg.es> wrote:
> Hi Tim,
>
>  great to get a signal from your new institute!
>