removing ensembl-core versions

removing ensembl-core copy

retiring ensembl-core version

removed species-specific configuration file which do not have anything different from the main mapper

Uniprot_genename replaced with Uniprot_gn
_transcript_name suffix replaced with _trans_name suffix

_transcript_name suffix replaced with _trans_name suffix
Uniprot_genename source replaced with Uniprot_gn

gene names can be duplicated, so use of a insert ignore when adding the corresponding transcript name

do not attempt to ref object as it could be its id

for each object, methods are explicitly defined

[ENSCORESW-499]. schemaPatches.t checks that the table.sql patch set matches what is in the patched database

there should not be any, and we end up adding data which is not an ontology

miscellaneous section removed
removed hard coded html tags for schema file, this is now at the top of the file
merged two description tags for interpro table, was only using the second one

[ENSCORESW-494]. IN statement is now generically handled rather than repeating the same logic over and over again

[ENSCORESW-493]. Fixing a number of naming issues in ontology schema. Also had to introduce a patch for is_obsolete

Renamed 'old' reference to the coord_system variable. coord_system had been renamed to central_coord_system.

[ENSCORESW-490]. Point raised by Dan. Default GFF3 for source is . not ensembl. Using . and supporting basic features

[ENSCORESW-490]. Fixing the GFF serializer which would add an additional ; at times and now supports a custom source field. Gene and transcript now both emit this