'part_of' relationships for all ontologies.

Involved tweaks to relation_type loading to invert some relation types
(e.g. 'has_part' => 'part_of') and to allow for sharing relation types
between ontologies.

SO also only has a "default-namespace" defined in the header, but no
"namespace" in the definitions of the terms, so use this.

Fixed a bug in the code that figures out if a file has been processed
before or not.

Use the translations of the _canonical_ transcripts of the source and target genes as the source of GO terms to project, rather than simply the longest translation in each, which was a bit arbitrary and didn't alway work.

Also make the print option for GO term projection a bit more verbose - aids debugging.

Fetching a GO term and then displaying its ancestors recursively using
the information fetched from _fetch_ancestor_chart().

ontology term.

Fetching a GO term and then using it to get genes.

term.

Edited to remove syntax complaint - ERROR 1064 (42000) at line 10: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near ''is_constitutive' BOOLEAN NOT NULL DEFAULT 0' at line 1.

need to be cleaned manually or by using the -t (truncate) option to the
script.

FOR <user>".  Now it does.  This stopped the stable ID mapping from
running correctly for a while.

exon table.