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API Support for Regulatory Features

As of release 49 of Ensembl, support for regulatory features has been migrated from the core databases into the functional genomics databases.

This change should be transparent for those of you who access this data via the website, but for those of you who use the API or MySQL database access will need to note the following changes:

API

The following objects and adaptors have been removed from the core API:

  • RegulatoryFactor.pm
  • RegulatoryFeature.pm
  • RegulatorySearchRegion.pm
  • RegulatoryFactorAdaptor.pm
  • RegulatorySearchRegionAdaptor.pm
  • RegulatoryFeatureAdaptor.pm

Additionally, all regulatory feature-related calls have been removed from BaseAdaptor.pm and its subclasses.

The data can be extracted via the functional genomics API, as follows:

# Grab the eFG DB
my $efg_db = Bio::EnsEMBL::Registry->get_DBAdaptor->('Human','funcgen');

# Get the FeatureSetAdaptor
my $fset_adaptor = $efg_db->get_FeatureSetAdaptor();

#External FeatureSet names are:
# miRanda miRNA         
# cisRED search regions  
# VISTA enhancer set     
# cisRED motifs   

# Get the FeatureSet
my $fset = $fset_adaptor->fetch_by_name('cisRED motifs');

my @cisred_features = @{$fset->get_Features_by_Slice($slice)};

# You can retrieve features from more than one set at a time by using
# the ExternalFeatureAdaptor directly e.g.

my $ext_feature_Adaptor = $efg_db->get_ExternalFeatureAdaptor;
my @mixed_features =
@{$ext_feature_adaptor->fetch_all_by_Slice_FeatureSets($slice,
@feature_sets)};

Schema

The following tables have been removed from the core database schema:

  • regulatory_feature
  • regulatory_factor
  • regulatory_factor_coding
  • regulatory_feature_object

The data is now stored in the functional genomics database, as follows.

external_feature
contains the individual feature information e.g. display label, locus, feature_type etc...
feature_set
contains summary information about a given set of features e.g. name, feature_type. The feature sets of the old core regulatory features are named as follows:
  • miRanda miRNA
  • cisRED group motifs
  • cisRED search regions
  • VISTA enhancer set
feature_type
contains detailed information about a given feature_type efg xref schema (xref, object_xref, identity_xref,
go_xref, external_db, external_synonym)
Similar to the core xref schema, references to entities external to the eFG DB are stored here. e.g. Target genes for miRNAs, coding