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> ... I don't want to take GO:000006 into account (two parents in which
> I am intested in). That menas, whenever I ask for children of two nodes,
> I want a DISTINCT SET of children.
To start with, you can avoid the Java and do this in SQL:
SELECT child FROM gograph WHERE parent='GO:0000002' OR parent='GO:0000005'
EXCEPT
(SELECT child FROM gograph WHERE parent='GO:0000002'
INTERSECT
SELECT child FROM gograph WHERE parent='GO:0000005');
And yes, I would certainly start by normalizing things a little bit:
CREATE SEQUENCE goid_seq;
CREATE TABLE goID ( idname TEXT, id INTEGER NOT NULL DEFAULT nextval('goid_seq')
);
INSERT INTO goid(idname) SELECT DISTINCT parent FROM gograph;
INSERT INTO goid(idname)
SELECT DISTINCT child FROM gograph WHERE NOT EXISTS (SELECT 1 FROM goID WHERE idname = child);
CREATE TABLE gomap ( parent INTEGER, child INTEGER
);
INSERT INTO gomap SELECT
(SELECT id FROM goid WHERE idname=parent),
(SELECT id FROM goid WHERE idname=child)
FROM gograph
As far as the binaryInteraction table, a little more information is needed:
how are each of these tables being populated? Why the distinct? Is it because
there may be duplicate rows in the table? The reason I as is that it might be
better to ue triggers to compute some of the information as it comes in,
depending on which tables are changes and how often.
- --
Greg Sabino Mullane greg@turnstep.com
PGP Key: 0x14964AC8 200307151035
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