Have changed the link for the SO.obo file from http://downloads.sourceforge.net/project/song/Sequence%20Ontology/so_2_5/so.obo2.5 to http://www.sequenceontology.org/resources/obo_files/current_release.obo. This will allow us to get the most up to date version.

 to http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinobo/efo.obo.
We are now getting the EFO.obo file from the head.

SHIP IT! EFO now loads in without complaints from OBOParser. Also now handles duplication relations being inserted.

Added a truth test to see if the $term->{synonyms} reference was there. I'm assuming if it's there then it'll be an array

Switched to Test::More and done_testing(). This should stop tests from failing due to poor test count specification.

Make the verbose doc a bit more verbose. People in workshops could not find this method which points to poor documentation

lrg code works if there are lrg xrefs
there are lrg xrefs when the regular expression to fetch the data from hgnc is correct

Added meta insert as otherwise any schema generated from this file would break when being patched. Also changed the ordering of the fields in protein_feature to avoid poor patch performance

Test schema now matches live. Any future patching should be done using the ensembl-test/scripts/patch_test_databases.pl script.

use Test::More rather than old Test library. Avoids breaking tests when we change the numbers of tests run

New patch which brings back the data_file's missing auto_increment declaration from patched databases. This does affect new databases created from the table.sql file.

[ENSCORESW-302]. TranslationAdaptor did not deal with multispecies databases properly when querying for IDs.

Added missing parameter to allow secondary database password. Otherwise it defaults to none and fails.

[ENSCORESW-301]. Adding INSERT IGNORE to a lot of statements as EFO can repeat terms and subsets from other ontologies.