removed source RefSeq_dna::gasterosteus_aculeatus
it is a duplicate of RefSeq_dna::vertebrate-other

removed ciona sources for JGI version
it is a bad assembly which should not be referred to

when fetching children/parents/descendants/ancestors of a given term, will return only relations of the same ontology
if ontology is specified, will return relations for that ontology

added fetch_all_roots method
returns all the root terms of the database
if ontology is specified, returns all the roots for a given ontology
a root is a term which has no parents within its ontology

a term is root if it has no parents within the ontology it is from

added ontology_id row to closure and relation table
a same relation can exist in two ontologies

when loading OBO files, add is_root flag to terms which are root within the OBO file loaded and part of the ontology
add ontology information to relation and closure tables
a relation's ontology is the ontology from which the relation was loaded from
for example, a GO to GO relation is an EFO relation if it was loaded from the EFO obo file

Adding more types than just haplotype to the haplotype field and uncommented compara since it was no wonder why the code was so fast

Added undef return values in the event of not finding an accession for fetch_by_dbID and fetch_by_accession.

updated ontology database, is now ensembl_ontology_71
changed RefSeq::otherfeatures to RefSeq_import::otherfeatures

Patched out a pair of CVS keywords that interfere with Git compatibility for benefit of Anacode. This in no way implies endorsement of Git for Ensembl.

added missing RefSeq sources for olive baboon

will parse refseq_import gene models and generate direct mappings to ensembl transcripts and translations,
based on overlapping coordinates

added sources RefSeq, RefSeq_mRNA and RefSeq_peptide for xrefs from refseq import in otherfeatures database
run for human and mouse

was initially added to table.sql, but not to patch_69_70_b.sql
checks if primary key exists and only adds it if it is missing

Extended support for different SQL backends through specific return values. See Michael Gray's efforts.

silly lsf has become very picky, so memory requirements need to be at the end of the block, and separated by a comma, not a colon
rusage[mem=1500:tmp=128] becomes rusage[tmp=128, mem=1500]

See JIRA ticket ENSCORESW-349

also save and restore operon_transcript_gene table
entries in the operon_transcript_gene table are not cleaned up