Remove deprecated GOTermAdaptor and SOTermAdaptor modules

Deprecated since 2011, non-functional since March 2018. See ENSCORESW-2871.

Note that there is still a reference to GOTermAdaptor in the xref parser
GOSlimParser. However, the parser in question seems to be no longer used
and in any case has not been updated, other than changing the copyright
notices, for years.

modules/Bio/EnsEMBL/DBSQL/GOTermAdaptor.pm

-=head1 LICENSE
-
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2019] EMBL-European Bioinformatics Institute
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-     http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-
-=cut
-
-
-=head1 CONTACT
-
-  Please email comments or questions to the public Ensembl
-  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
-
-  Questions may also be sent to the Ensembl help desk at
-  <http://www.ensembl.org/Help/Contact>.
-
-=cut
-
-=head1 NAME
-
-Bio::EnsEMBL::DBSQL::GOTermAdaptor
-
-=head1 DESCRIPTION
-
-A specialization of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor,
-specifically for Gene Ontology (GO) terms.  See the documentation of
-Bio::EnsEMBL::DBSQL::OntologyTermAdaptor for further information.
-
-=head1 METHODS
-
-=cut
-
-package Bio::EnsEMBL::DBSQL::GOTermAdaptor;
-
-use strict;
-use warnings;
-
-use base qw( Bio::EnsEMBL::DBSQL::OntologyTermAdaptor );
-
-=head2 new
-
-  Arg [1]       : Bio::EnsEMBL::DBSQL::DBAdaptor
-                  Argument required for parent class
-                  Bio::EnsEMBL::DBSQL::BaseAdaptor.
-
-  Description   : Creates an ontology term adaptor for GO terms.
-
-  Example       :
-
-    my $go_adaptor = Bio::EnsEMBL::DBSQL::GOTermAdaptor->new( $dba );
-
-  Return type   : Bio::EnsEMBL::DBSQL::GOTermAdaptor
-
-=cut
-
-sub new {
-  my ( $proto, $dba ) = @_;
-
-  my $this = $proto->SUPER::new( $dba, 'GO' );
-
-  return $this;
-}
-
-1;

modules/Bio/EnsEMBL/DBSQL/SOTermAdaptor.pm

-=head1 LICENSE
-
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2019] EMBL-European Bioinformatics Institute
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-     http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-
-=cut
-
-
-=head1 CONTACT
-
-  Please email comments or questions to the public Ensembl
-  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
-
-  Questions may also be sent to the Ensembl help desk at
-  <http://www.ensembl.org/Help/Contact>.
-
-=cut
-
-=head1 NAME
-
-Bio::EnsEMBL::DBSQL::SOTermAdaptor
-
-=head1 DESCRIPTION
-
-A specialization of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor,
-specifically for Sequence ontology (SO) terms.  See the
-documentation of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor for
-further information.
-
-=head1 METHODS
-
-=cut
-
-package Bio::EnsEMBL::DBSQL::SOTermAdaptor;
-
-use strict;
-use warnings;
-
-use base qw( Bio::EnsEMBL::DBSQL::OntologyTermAdaptor );
-
-=head2 new
-
-  Arg [1]       : Bio::EnsEMBL::DBSQL::DBAdaptor
-                  Argument required for parent class
-                  Bio::EnsEMBL::DBSQL::BaseAdaptor.
-
-  Description   : Creates an ontology term adaptor for SO terms.
-
-  Example       :
-
-    my $go_adaptor = Bio::EnsEMBL::DBSQL::SOTermAdaptor->new( $dba );
-
-  Return type   : Bio::EnsEMBL::DBSQL::SOTermAdaptor
-
-=cut
-
-sub new {
-  my ( $proto, $dba ) = @_;
-
-  my $this = $proto->SUPER::new( $dba, 'SO' );
-
-  return $this;
-}
-
-1;

modules/Bio/EnsEMBL/OntologyTerm.pm

@@ -34,10 +34,8 @@ Bio::EnsEMBL::OntologyTerm
 
 =head1 DESCRIPTION
 
-An ontology term object, (most often) created by
-Bio::EnsEMBL::DBSQL::GOTermAdaptor and used in querying for
-transcripts, genes, and translations using the relevant adaptors and
-methods.
+An ontology term object, used in querying for transcripts, genes,
+and translations using the relevant adaptors and methods.
 
 =head1 METHODS