[Bioperl-l] pipeline

Imre Vastrik vastrik@ebi.ac.uk
Tue, 12 Mar 2002 09:58:35 +0000

Elia Stupka wrote:
> I have a novel idea, but I am not sure what people think about it. Can we
> make units of schema+adaptors reusable modules? i.e. put the sql in my
> compara schema, and then in a meta table register that those tables are
> under the control of the bioperl-db adaptors.

I know I won't make many friends with this suggestion but what about
revamping the whole "schema" (and I don't mean the table.sql file here)
so that all the object<->relational mapping would be done automagically?
I have the impression that quite a lot of (API)programmers' time goes to
(re)writing basic "store_object" and "fetch_object_by_attribute"
methods. Provided that there is a formal way of representing the schema
(i.e. what attributes an object has, what's the attribute type,
cardinality, etc) there should be a way of creating the relational
schema and basic store/fetch methods automatically. There are surely
more appropriate tools for creating the formal schema but I've just
"abused" an ontology and knowledgebase development tool called
Protege-2000 and all I can really say is that it works for me.


P.S. Happy to provide more information if somebody cares.