mart-dev, I¹m just starting to use BioMart 0.5, my aim is to build new marts from various bio-schemas and see if I can contribute to the documentation. My first target schema is Biosql (biosql.org), I¹m using their latest schema from their CVS and have created my database in Postgres and loaded it with a small number of sequence records, ~2000. I don¹t know if you know Biosql, it¹s a small-ish schema dealing with sequence, sequence annotation, and taxonomy. There is a central bioentry table with identifiers and descriptive information on sequences.
My question: I¹m on page 17 of the manual (nice manual, by the way) which describes how to use MartBuilder. I¹ve created an SQL script from my Biosql database that should make a new mart but I¹m a bit puzzled shouldn¹t this script contain data? That¹s what page 17 seems to be saying. The SQL script I¹ve created has create and alter and drop statements but not much more. I¹m also having trouble executing this script but let¹s take this one step at a time... Thanks again, Brian O.
