[BioSQL-l] database extensions

[Angel Pizarro]

Hello,

Relatively new to biosql, but I was wondering about a few aspects of the
schema/project.

First, about the ontology tables, what is the preferred way to map
ontology annotations to bioentries? via a seqfeature? Currently I just
added a new table to map GO associations with the evidence code from
GOA.  Not optimal as there may be multiple lines of evidence for an
association, as in the godatabase schema.

Second, are primary keys up for discussion any time soon? I realize that
a lot of external projects rely on this schema, so it has to remain
stable, but the inconsistent use of UID, compound keys or even lack of a
key really put a hindrance on the use of off-the-shelf ORMs.

Third, how does one go about submitting proposals for schema extensions?
I am wanting to extend the schema with a few modules, mainly ripped out
of either  GUS and/or chado, as well as adding a module for proteomics data.

Fourth, is the current practice for representation of biological
pathways and interactions to use the bioentryrelationship table?

Many thanks.

-- 
Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004
E: angel at mail.med.upenn.edu