Modify OBO parser/loader to allow for SO ontology to be loaded.

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.