setob parser uses Sequence Ontology to bolt on sequence feature info to pobol?

[Mackenzie Cowell]

What up pobol,

The University of Washington iGEM team wrote parser (in python) that
transforms MIT registry entries into Pobol (rdf/owl). Most of you
probably heard a little about it at SB4.0. It is called setob:
http://2008.igem.org/Team:University_of_Washington/SeToB.

They are implementing a simple drag'n'drop circuit design tool (flash)
on top of their collection of pobol-ized parts. As I understand it,
they are trying to give their tool some notion of the functional
properties of the parts in the design, such as "This gene produces
SwissProID:P03023 (LacI repressor)" and "This Promoter is repressed by
SwissProID:P03023". (Side Note: the MIT registry actually does have
structured functional information for Protein Coding Genes in the form
of SwissPro IDs for the protein produced. I presume swisspro provides
some kind of machine readable information about the proteins, maybe in
Gene Ontology (GO) format? http://partsregistry.org/wiki/index.php/Part_Type:Coding)

Since Pobol doesn't support any functional information at all right
now, I thought it was interesting to see how the Seattle team was
dealing with the problem. They have turned to http://sequenceontology.org/,
which I know nothing about.

Short excerpt from the setob blog: "Furthermore, I am seeing into how
to store the feature and subparts information. Looking at Sequence
Ontology (SO), they seem to have a lot of information. I liked their
in depth "concepts" and "abstracts" (part_of, and so forth), however
all I need for now is basic information to quantify whether a part is
first of all a promoter, and then further what does it get repressed
by. Similar for say a gene, and what mRNA does it transcribes (and the
what protein does the mRNA translates into)."

So I think it would be really interesting if Paramjit could describe a
little more about what setob is going to do (hope I got it basically
correct) and how the team is supplementing Pobol with the Sequence
Ontology project.

See you at the iGEM Jamboree,
Mac