LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] 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

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CONTACT

  Please email comments or questions to the public Ensembl
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NAME

Bio::EnsEMBL::OntologyXref

DESCRIPTION

This class extends the DBEntry in order to associate Evidence Tags to the relationship between EnsEMBL objects and ontology accessions (primarily GO accessions).

The relationship to GO that is stored in the database is actually derived through the relationship of EnsEMBL peptides to SwissProt peptides, i.e. the relationship is derived like this:

  ENSP -> SWISSPROT -> GO

And the evidence tag describes the relationship between the SwissProt Peptide and the GO entry.

In reality, however, we store this in the database like this:

  ENSP -> SWISSPROT
  ENSP -> GO

and the evidence tag hangs off of the relationship between the ENSP and the GO identifier. Some ENSPs are associated with multiple closely related Swissprot entries which may both be associated with the same GO identifier but with different evidence tags. For this reason a single 'OntologyXref' can have multiple evidence tags.

SYNOPSIS

  my $ontology_xref = Bio::EnsEMBL::OntologyXref->new();
  $ontology_xref->add_linkage_type('IEA');

  foreach my $evtag ( @{ $ontology_xref->get_all_linkage_types() } ) {
    print "$evtag\n";
  }

METHODS

get_OntologyTerm

  Example    : $ontology_xref->get_OntologyTerm();
  Description: Queries the OntologyTermAdaptor for a term which is the same 
               as the primary id of this object. This method requires a
               OntologyDBAdaptor to be available in the Bio::EnsEMBL::Registry. 
               If you have loaded data from an Ensembl release using
               Bio::EnsEMBL::Registry->load_registry_from_db() then this should
               work.
  Returntype : Bio::EnsEMBL::OntologyTerm
  Exceptions : None
  Caller     : general
  Status     : Experimantal

add_linkage_type

  Arg [1]    : string $value
               allowed values:
               'IC', 'IDA', 'IEA', 'IEP', 'IGI', 'IMP', 'IPI',
               'ISS', NAS', 'ND', 'TAS', 'NR', 'RCA'
  Arg [2]    : (optional) Bio::EnsEMBL::DBEntry $source
  Example    : $ontology_xref->add_linkage_type('IGI');
  Description: Associates a linkage type and source DBEntry with
               this ontology_xref
  Returntype : integer; number of linkages
  Exceptions : thrown if $linkage_type argument not supplied or
               the optional DBEntry is not a DBEntry object.
  Caller     : DBEntryAdaptor
  Status     : Experimantal

get_all_linkage_info

  Arg [1]    : none
  Example    :

    foreach ( @{ $ontology_xref->get_all_linkage_info() } ) {
      print "evidence: $_->[0] via $_->[1]->display_id";
    }

  Description: Retrieves a list of evidence-tag/source-DBEntry pairs
               associated with this ontology_xref
  Returntype : listref of listrefs
  Exceptions : none
  Caller     : geneview? general.
  Status     : Experimental

get_all_linkage_types

  Arg [1]    : none
  Example    :

    print( join( ' ', @{ $ontology_xref->get_all_linkage_types() } ),
           "\n" );

  Description: Retrieves a unique list of evidence tags associated with
               this ontology_xref
  Returntype : none
  Exceptions : none
  Caller     : geneview? general
  Status     : Stable

flush_linkage_types

  Arg [1]    : none
  Example    : $ontology_xref->flush_linkage_types();
  Description: Removes any associated evidence tags
  Returntype : none
  Exceptions : none
  Caller     : general 
  Status     : Stable

add_associated_xref

  Arg [1]    : Bio::EnsEMBL::DBEntry $associated_xref
               or an Array of Bio::EnsEMBL::DBEntry for compound annotations
  Arg [2]    : Bio::EnsEMBL::DBEntry $source_dbentry
  Arg [3]    : string $condition_type or an Array of string $condition_types
               matching the order of Arg[1] for compound queries.
  Arg [4]    : (optional) Integer $group id for compound annotations.
  Arg [5]    : (optional) Integer $rank order for a term within a compound annotation.
  Example    : $ontology_xref->add_associated_xref(
                                  $associated_xref,
                                  $source_dbentry,
                                  'with',
                                  42,
                                  5);
  Description: Associates a linkage type and source DBEntry with
               this ontology_xref
  Returntype : none
  Exceptions : thrown if $linkage_type argument not supplied or
               the optional DBEntry is not a DBEntry object.
  Caller     : DBEntryAdaptor
  Status     : Experimantal

add_linked_associated_xref

  Arg [1]    : Bio::EnsEMBL::DBEntry $associated_xref
               or an Array of Bio::EnsEMBL::DBEntry for compound annotations
  Arg [2]    : Bio::EnsEMBL::DBEntry $source_dbentry
  Arg [3]    : string $condition_type or an Array of string $condition_types
               matching the order of Arg[1] for compound queries.
  Arg [4]    : Integer $group id.
  Arg [5]    : Integer $rank id.
  Example    : $ontology_xref->add_associated_xref(
                                  $associated_xref,
                                  $source_dbentry,
                                  'with',
                                  42,
                                  5);
  Description: Associates a linkage type and source DBEntry with this
               ontology_xref that have come from the same annotation source
  Returntype : none
  Exceptions : thrown if $linkage_type argument not supplied or
               the optional DBEntry is not a DBEntry object.
  Caller     : DBEntryAdaptor
  Status     : Experimantal

get_all_associated_xrefs

  Arg [1]    : none
  Example    :

    foreach ( @{ $ontology_xref->get_all_associated_xref() } ) {
      print "evidence: $_->[0] via $_->[1]->display_id";
    }

  Description: Retrieves a list of associated-DBEntry/source-DBEntry/condition
               sets associated with this ontology_xref
  Returntype : listref of listrefs
  Exceptions : none
  Caller     : geneview? general.
  Status     : Experimental

get_extensions Arg [1] : none Example :

    use Data::Dumper;
    print Dumper @{ $ontology_xref->get_extensions_for_web() }
    
  Returns    :
    $VAR1 = {
              'source' => '<a href="<Link to CiteXplore>">11937031</a>',
              'evidence' => 'IDA',
              'description' => '<strong>has_direct_input</strong> 
                   <a href="http://www.pombase.org/gene/SPBC32F12.09">
                     SPBC32F12.09
                   </a>'
            };

  Description: Retrieves a list of associated-DBEntry/source-DBEntry/condition
               sets associated with this ontology_xref and formats them ready
               for web display in a group per row fashion.
               The accessions for ontologies are linkable. Extra links need to
               be added for each distinct database that is reference. 
  Returntype : listref of hashrefs
  Exceptions : none
  Caller     : 
  Status     : Experimental

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL