Inheritance diagram for Bio::EnsEMBL::OntologyXref:

Public Member Functions
public Bio::EnsEMBL::OntologyTerm	get_OntologyTerm ()

public Int	add_linkage_type ()

public Listref	get_all_linkage_info ()

public void	get_all_linkage_types ()

public void	flush_linkage_types ()

public void	add_associated_xref ()

public void	add_linked_associated_xref ()

public Listref	get_all_associated_xrefs ()

public	get_extensions ()

Public Member Functions inherited from Bio::EnsEMBL::DBEntry
public Bio::EnsEMBL::DBEntry	new ()

public String	primary_id ()

public String	display_id ()

public String	optional_id ()

public String	dbname ()

public String	database ()

public String	release ()

public String	version ()

public String	db_version ()

public String	description ()

public Bio::EnsEMBL::Analysis	analysis ()

public String	comment ()

public String	priority ()

public String	db_display_name ()

public String	info_type ()

public String	info_text ()

public String	linkage_annotation ()

public String	type ()

public String	secondary_db_name ()

public String	secondary_db_table ()

public void	add_synonym ()

public Listref	get_all_synonyms ()

public Listref	get_all_dependents ()

public Listref	get_all_masters ()

public void	flush_synonyms ()

public String	status ()

Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()

public Instance	new_fast ()

public Int	dbID ()

public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()

public Boolean	is_stored ()

public	get_all_DAS_Features ()

Detailed Description

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";
}

Definition at line 41 of file OntologyXref.pm.

Member Function Documentation

◆ add_associated_xref()

public void Bio::EnsEMBL::OntologyXref::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

Code:

click to view

◆ add_linkage_type()

public Int Bio::EnsEMBL::OntologyXref::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

Code:

click to view

◆ add_linked_associated_xref()

public void Bio::EnsEMBL::OntologyXref::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

Code:

click to view

sub add_linked_associated_xref {
  my ( $self, $associated_xref, $source_dbentry, $condition_type, $associate_group_id, $associate_group_rank ) = @_;
  
  if ( !defined($associated_xref) )
  {
    $self->throw("associated_xref must be a Bio::EnsEMBL::DBEntry or an Array
                  of Bio::EnsEMBL::DBEntry objects.");
  }
  
  if ( defined($associated_xref)
       && !$associated_xref->isa('Bio::EnsEMBL::DBEntry') )
  {
    $self->throw("associated_xref must be a Bio::EnsEMBL::DBEntry or an Array
                  of Bio::EnsEMBL::DBEntry objects.");
  }
  
  if ( defined($source_dbentry)
       && !$source_dbentry->isa('Bio::EnsEMBL::DBEntry') )
  {
    $self->throw("source_dbentry must be a Bio::EnsEMBL::DBEntry");
  }
  
  if ( !defined $condition_type ) {
      $self->throw("condition must be a string");
  }
  
  if ( !defined $associate_group_id )
  {
    $self->throw("$associate_group_id must be an integer");
  }
  
  if ( !defined $associate_group_rank )
  {
    $self->throw("$associate_group_rank must be an integer");
  }
  
#  print "\t" . $associate_group_id;
#  print "\t" . $associate_group_rank;
#  print "\t|" . defined($associated_xref) . '|';
#  #print "\t" . defined($associated_xref->primary_id);
#  print "\t" . $associated_xref->primary_id;# . ' (' . $associated_xref->display_id . ')';
#  print "\t" . $source_dbentry->primary_id;
#  print "\t" . $condition_type . "\n"; 
  
  my $associated_xref_array = {};
  my $matching_link = 0;
  
  my $load_postion = 0;
  if ( !defined $self->{'associated_xref'} ) {
    $associated_xref_array->{$associate_group_id}->{$associate_group_rank} = [
      $associated_xref,
      $source_dbentry,
      $condition_type
    ];
    $load_postion = 1;
  } else {
    $associated_xref_array = $self->{'associated_xref'};
    
    if (!defined $associated_xref_array->{$associate_group_id} ) {
      $associated_xref_array->{$associate_group_id}->{$associate_group_rank} = [
        $associated_xref,
        $source_dbentry,
        $condition_type
      ];
      $load_postion = 2;
    } else {
      my $already_loaded = 0;
      foreach my $rank ( keys %{$associated_xref_array->{$associate_group_id}} ) {
        my @ax_gr_set = @{ $associated_xref_array->{$associate_group_id}->{$rank} };
        if (
          $ax_gr_set[0]->primary_id eq $associated_xref->primary_id && 
          $ax_gr_set[1]->primary_id eq $source_dbentry->primary_id &&
          $ax_gr_set[2] eq $condition_type
        ) {
          $already_loaded = 1;
          $load_postion = 4;
          #last;
        }
      }
      if ( !$already_loaded ) {
        if (!defined $associated_xref_array->{$associate_group_id}->{$associate_group_rank} ) {
          $associated_xref_array->{$associate_group_id}->{$associate_group_rank} = [
            $associated_xref,
            $source_dbentry,
            $condition_type
          ];
          $load_postion = 5;
        } else {
          $associated_xref_array->{$associate_group_id}->{scalar keys %{ $associated_xref_array->{$associate_group_id} }} = [
            $associated_xref,
            $source_dbentry,
            $condition_type
          ];
          $load_postion = 3;
        }
      }
    }
  }
  $self->{'associated_xref'} = $associated_xref_array;
#  print "\t\tLoaded at " . $load_postion . "\n";
#  if ($associate_group_id == 28792 || $associate_group_id == 28793) {
#    print Data::Dumper->Dumper([$self->{'associated_xref'}]);
#  }
}

◆ flush_linkage_types()

public void Bio::EnsEMBL::OntologyXref::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

Code:

click to view

◆ get_all_associated_xrefs()

public Listref Bio::EnsEMBL::OntologyXref::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

Code:

click to view

◆ get_all_linkage_info()

public Listref Bio::EnsEMBL::OntologyXref::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

Code:

click to view

◆ get_all_linkage_types()

public void Bio::EnsEMBL::OntologyXref::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

Code:

click to view

◆ get_extensions()

public Bio::EnsEMBL::OntologyXref::get_extensions ( )

  Arg [1]    : none
  Example    :

use Data::Dumper;

print Dumper @{ $ontology_xref->get_extensions_for_web() }

  Returns    :
    $VAR1 = {
              'source' => '11937031',
              'evidence' => 'IDA',
              'description' => 'has_direct_input 
                   
                     SPBC32F12.09
                   '
            };

  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

Code:

click to view

sub get_extensions {
  my ($self) = @_;
  
  if ( !defined $self->{'associated_xref'} ) {
    return [];
  }
  
  my @annotExtRows = ();
  
  my %external_urls = (
    'GO'     => 'http://www.ebi.ac.uk/ego/GTerm?id=',
    'GO_REF' => 'http://www.geneontology.org/cgi-bin/references.cgi#',
    'SO'     => 'http://www.sequenceontology.org/miso/current_cvs/term/',
    #'MOD'    => 'href=mod',
    'PomBase' => 'http://www.pombase.org/gene/',
    'PomBase_Systematic_ID' => 'http://www.pombase.org/gene/',
    'PUBMED' => 'http://europepmc.org/abstract/MED/'
  );
  
  foreach my $groupId (keys %{ $self->{'associated_xref'} } ) {
    my $description = '';
    my $evidence    = '';
    my $source      = '';
    
    foreach my $rank ( keys %{ $self->{'associated_xref'}->{$groupId} } ) {
      if ( $self->{'associated_xref'}->{$groupId}->{$rank}->[2]
           eq 'evidence' ) {
        if ( exists $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname} ) {
          $evidence = '<a href="' . $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname}
                    . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->primary_id . '">'
                    . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id
                    . '</a>';
        } else {
          $evidence = $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id;
        }
      } else {
        if (length $description > 0) {
          $description .= ', ';
        }
        $description .= '<strong>' . $self->{'associated_xref'}->{$groupId}->{$rank}->[2] . '</strong> ';
        
        if (exists $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname} ) {
          $description .= '<a href="' . $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[0]->dbname}
                        . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->primary_id . '">'
                        . $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id
                        . '</a>';
        } else {
          $description .= $self->{'associated_xref'}->{$groupId}->{$rank}->[0]->display_id;
        }
        
        
      }
      
      if ( !undef $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[1]} ) {
        if ( exists $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[1]->dbname} ) {
          $source = '<a href="' . $external_urls{$self->{'associated_xref'}->{$groupId}->{$rank}->[1]->dbname}
                  . $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->primary_id . '">';
          if ( $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->dbname ne 'GO_REF' ) {
            $source .= 'PMC:';
          }
          $source .= $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->display_id . '</a>';
        } elsif ($self->{'associated_xref'}->{$groupId}->{$rank}->[1]->display_id eq 'PMPB:0') {
          $source = '';
        } else {
          $source = $self->{'associated_xref'}->{$groupId}->{$rank}->[1]->display_id;
        }
      }
    }
    
    if ($evidence ne '' and $description ne '') {
      my %row =  ('description' => $description,
                  'evidence'    => $evidence,
                  'source'      => $source);
      push @annotExtRows, (\%row);
    }
  }
  
  return \@annotExtRows;
}

◆ get_OntologyTerm()

public Bio::EnsEMBL::OntologyTerm Bio::EnsEMBL::OntologyXref::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

Code:

click to view

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/OntologyXref.pm

Public Member Functions

Detailed Description

Description

Synopsis

Member Function Documentation

◆ add_associated_xref()

◆ add_linkage_type()

◆ add_linked_associated_xref()

◆ flush_linkage_types()

◆ get_all_associated_xrefs()

◆ get_all_linkage_info()

◆ get_all_linkage_types()

◆ get_extensions()

◆ get_OntologyTerm()