Hi all, I am very new to BioMart and my goal is to use it to build marts on a Chado instance for the Sybil package (sybil.sf.net). My goal is to build a fairly comprehensive and easy to use search builder using extjs with BioMart driving the search data sets and filters. I'm just starting out but I have already run into a bit of a snag.
I am trying to connect Martbuilder 0.7 to a Postgres 8.1 Chado instance. All the tables seem to get pulled down properly but non of the foreign key relationships or unique key constraints. The keyguessing mechanism works alright except there are several instances where a table has a type_id column that needs to be linked to a cvterm_id column and these are lost and kind of integral to the schema. I am wondering if anyone is currently using BioMart with a Chado instance and if so how. I have also noticed that even doing the 'give me the first 10 rows' causes an OutOfMemory exception. The database I am trying to connect to has 7,607,708 rows in feature and I am wondering if this is a bit bigger than BioMart was designed for. I noticed some warnings about Java 1.6 which happens to be the version I am using so this may explain the memory problem. Any help and/or Chado BioMart experiences would be greatly appreciated. Thanks, Dave
