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

when projecting a symbol onto a gene, use the same symbol for all attached transcripts, with version number in format -201
for all species now, not just pig

Uniprot_genename has been added to RFAM and miRBase as a trusted source for gene name assignement

used in OfficialNaming mapper for merged species
Uniprot_genename is now a valid source for gene display assignment, along with RFAM and miRBase

Names can exceed 255 characters. Switched to TEXT which gives us 64K strings and added a 50 char prefix index to the table

Added GOA webservice call, timeout response, and subsequent usage of the blacklist to the projections.

updated priority for ZFIN_ID data: priority for directly mapped ZFIN_ID over those imported from Vega

Adding column edits for columns which have now diverged in their definitions. Also making sure data_file's collate is set correctly

release version updated to 70
table mapping_set updated to include build information about external and internal databases

when the script is run, adds new entries for each seq_region id which has changed between current and previous release
but also updated existing entries so that all rows internal_seq_region_id in seq_region_mapping correspond to a seq_region_id which is in the current database

patch a is the release patch
patch b updates the mapping_set table to fit the new storing format
now, stores both release versions of seq_region id change to link back to the initial id

count_by_Slice renamed to count_by_Slice_constraint to be more in keeping with existing naming patterns.

code_action() was prematurely switching mode on /sub/ but substr also matched. Added following character pattern to allow sub{, sub , but not substr.

Removed reference to $SERVERROOT because it's just confusing and makes things harder. Just have your Perl5Lib properly set.

has a relationship with seq_region table, not contig table

Added support for multi-line inheritence where commas are used to separate things. Chiefly for Matthieu's use base () in Compara code.

[ENSCORESW-284]. Fixing registry lookups for compara gene trees. Also refactored it slightly; we will rip this out soon as we need a clearer separation.

this is provided by the xref_config.ini file