Merge pull request #391 from Ensembl/ENSCORESW-2871

Remove deprecated GOTermAdaptor and SOTermAdaptor modules

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