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

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NAME

Bio::EnsEMBL::DBSQL::DBEntryAdaptor - MySQL Database queries to load and store external object references.

SYNOPSIS

$db_entry_adaptor =
  $registry->get_adaptor( 'Human', 'Core', 'DBEntry' );

$db_entry = $db_entry_adaptor->fetch_by_dbID($id);

my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );

my $gene = $gene_adaptor->fetch_by_stable_id('ENSG00000101367');

@db_entries = @{ $db_entry_adaptor->fetch_all_by_Gene($gene) };
@gene_ids   = $db_entry_adaptor->list_gene_ids_by_extids('BAB15482');

METHODS

fetch_by_dbID

Arg [1]    : int $dbID
             the unique database identifier for the DBEntry to retrieve
Example    : my $db_entry = $db_entry_adaptor->fetch_by_dbID($dbID);
Description: Retrieves a dbEntry from the database via its unique
             identifier.
Returntype : Bio::EnsEMBL::DBEntry
Exceptions : none
Caller     : general
Status     : Stable

get_all_dependents

Args[1]    : dbID of the DBentry to get the dependents of.
Args[2]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
Example    : my @dependents = @{ $dbe_adaptor->get_all_dependents(1234) };
Description: Get a list of DBEntrys that are depenednet on the DBEntry.
             if an ensembl gene transcript or translation is given then only
             the ones on that object will be given
Returntype : listref of DBEntrys. May be empty.
Exceptions : none
Caller     : DBEntry->get_all_dependnets
Status     : UnStable

get_all_masters

Args[1]    : dbID of the DBentry to get the masters of.
Args[2]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
Example    : my @masters = @{ $dbe_adaptor->get_all_masters(1234) };
Description: Get a list of DBEntrys that are the masters of the DBEntry.
             if an ensembl gene transcript or translation is given then only
             the ones on that object will be given.
Returntype : listref of DBEntrys. May be empty.
Exceptions : none
Caller     : DBEntry->get_all_masters
Status     : UnStable

Arg [1]    : string $name - The name of the external reference.
             found in accession, display_label or synonym
Arg [2]    : (optional) string $dbname  - The name of the database which 
             the provided name is for.

Example    : my $xref = @{$dbea->fetch_all_by_name('BRAC2','HGNC')}[0];
             print $xref->description(), "\n" if($xref);
Description: Retrieves list of DBEntrys (xrefs) via a name.
             The accesion is looked for first then the synonym and finally
             the display_label.
             NOTE $dbname this is optional but adding this speeds the
             process up if you know what you are looking for.

             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
Returntype : Bio::EnsEMBL::DBSQL::DBEntry
Exceptions : thrown if arguments are incorrect
Caller     : general, domainview
Status     : Stable

fetch_by_db_accession

Arg [1]    : string $dbname - The name of the database which the provided
             accession is for.
Arg [2]    : string $accession - The accesion of the external reference to
             retrieve.
Example    : my $xref = $dbea->fetch_by_db_accession('Interpro','IPR003439');
             print $xref->description(), "\n" if($xref);
Description: Retrieves a DBEntry (xref) via the name of the database
             it is from and its primary accession in that database.
             Undef is returned if the xref cannot be found in the
             database.
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
Returntype : Bio::EnsEMBL::DBSQL::DBEntry
Exceptions : thrown if arguments are incorrect
Caller     : general, domainview
Status     : Stable

store

Arg [1]    : Bio::EnsEMBL::DBEntry $dbEntry
             The DBEntry (xref) to be stored
Arg [2]    : Int $ensID
             The dbID of an EnsEMBL object to associate with this external
             database entry
Arg [3]    : string $ensType ('Transcript', 'Translation', 'Gene')
             The type of EnsEMBL object that this external database entry is
             being associated with.
Arg [4]    : boolean $ignore_release
             If unset or zero, will require that the release string
             of the DBEntry object is identical to the release of the
             external database.  If set and non-zero, will ignore the
             release information.
Example    : $dbea->store($db_entry, $transcript_id, 'Transcript');
Description: Stores a reference to an external database (if it is not stored
             already) and associates an EnsEMBL object of a specified type
             with the external identifier.
Returntype : int - the dbID of the newly created external refernce
Exceptions : thrown when invalid dbID is passed to this method
Caller     : scripts which load Xrefs and ObjectXrefs, etc. into Ensembl
Status     : Stable

update

Arg [1]    : Bio::EnsEMBL::DBEntry $dbentry
             The dbentry to update
Example    : $dbentry_adaptor->update($dbentry);
Description: Updates the dbprimary_acc, display_label, version, description, info_type
             and info_text of a dbentry in the database.
Returntype : None
Exceptions : thrown if the $dbentry is not a Bio::EnsEMBL::DBEntry
Caller     : general
Status     : Stable

get_external_db_id

Arg [1]    : String
             The external DB name to query by. Supports LIKE statements
Arg [2]    : String (optional) 
             External DB release to use. If not specified then we 
             will search for NULL db_release entries
Arg [3]    : Boolean (optional)
             If true we will never look at the db_release value 
             when querying for an external db id
Description: Looks for the internal identifier of an external DB. You can
             search using direct equality or using like statements specify. We
             only return one value from this method.

             If you want more than one entry use get_external_db_ids().
Exceptions : None
Returntype : Int

get_external_db_ids

Arg [1]    : String
             The external DB name to query by. Supports LIKE statements
Arg [2]    : String (optional) 
             External DB release to use. If not specified then we 
             will search for NULL db_release entries
Arg [3]    : Boolean (optional)
             If true we will never look at the db_release value 
             when querying for an external db id
Description: Looks for the internal identifier of an external DB. You can
             search using direct equality or using like statements specify. We
             only return one value from this method. Returns more than one value
Exceptions : None
Returntype : ArrayRef of Int

get_distinct_external_dbs

Description: Queries the external_db table for all unique 
             DB names
Exceptions : None
Returntype : ArrayRef of String

_check_external_db

Arg [1]    : DBEntry object
Arg [2]    : Ignore version flag
Description: Looks for a record of the given external database
Exceptions : Throws on missing external database entry
Returntype : Int

_store_or_fetch_xref

Arg [1]    : DBEntry object
Arg [2]    : Database accession for external database
Description: Thread-safe method for adding xrefs, or otherwise returning
             an xref ID for the inserted or retrieved xref. Also inserts
             synonyms for that xref when entire new 
Returns    : Int - the DB ID of the xref after insertion

exists

Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
Example    : if($dbID = $db_entry_adaptor->exists($dbe)) { do stuff; }
Description: Returns the db id of this DBEntry if it exists in this database
             otherwise returns undef.  Exists is defined as an entry with
             the same external_db and display_id
Returntype : int
Exceptions : thrown on incorrect args
Caller     : GeneAdaptor::store, TranscriptAdaptor::store
Status     : Stable

fetch_all_by_Gene

Arg [1]    : Bio::EnsEMBL::Gene $gene
             (The gene to retrieve DBEntries for)
Arg [2]    : optional external database name. SQL wildcards are accepted
Arg [3]    : optional external_db type. SQL wildcards are accepted
Example    : @db_entries = @{$db_entry_adaptor->fetch_all_by_Gene($gene)};
Description: This returns a list of DBEntries associated with this gene.
             Note that this method was changed in release 15.  Previously
             it set the DBLinks attribute of the gene passed in to contain
             all of the gene, transcript, and translation xrefs associated
             with this gene.
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
             there is mapping data, or OntologyXref if there is linkage data.
Exceptions : thows if gene object not passed
Caller     : Bio::EnsEMBL::Gene
Status     : Stable

fetch_all_by_Operon

Arg [1]    : Bio::EnsEMBL::Operon $operon
             (The operon to retrieve DBEntries for)
Arg [2]    : optional external database name. SQL wildcards are accepted
Arg [3]    : optional external_db type. SQL wildcards are accepted
Example    : @db_entries = @{$db_entry_adaptor->fetch_all_by_Operon($operon)};
Description: This returns a list of DBEntries associated with this operon.
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
             there is mapping data, or OntologyXref if there is linkage data.
Exceptions : thows if operon object not passed
Caller     : general

fetch_all_by_Transcript

Arg [1]    : Bio::EnsEMBL::Transcript
Arg [2]    : optional external database name. SQL wildcards are accepted
Arg [3]    : optional external_db type. SQL wildcards are accepted
Example    : @db_entries = @{$db_entry_adaptor->fetch_all_by_Transcript($trans)};
Description: This returns a list of DBEntries associated with this
             transcript. Note that this method was changed in release 15.
             Previously it set the DBLinks attribute of the gene passed in
             to contain all of the gene, transcript, and translation xrefs
             associated with this gene.
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
             there is mapping data, or OntologyXref if there is linkage data.
Exceptions : throes if transcript argument not passed
Caller     : Bio::EnsEMBL::Transcript
Status     : Stable

fetch_all_by_Translation

Arg [1]    : Bio::EnsEMBL::Translation $trans
             (The translation to fetch database entries for)
Arg [2]    : optional external database name. SQL wildcards are accepted
Arg [3]    : optional externaldb type. SQL wildcards are accepted
Example    : @db_entries = @{$db_entry_adptr->fetch_all_by_Translation($trans)};
Description: Retrieves external database entries for an EnsEMBL translation
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
             there is mapping data, or OntologyXref if there is linkage data.
Exceptions : throws if translation object not passed
Caller     : general
Status     : Stable

fetch_all_by_RNAProduct

Arg [1]    : Bio::EnsEMBL::RNAProduct $rp
             (The rnaproduct to fetch database entries for)
Arg [2]    : optional external database name. SQL wildcards are accepted
Arg [3]    : optional externaldb type. SQL wildcards are accepted
Example    : @db_entries = @{$db_entry_adptr->fetch_all_by_RNAProduct($rp)};
Description: Retrieves external database entries for an EnsEMBL rnaproduct
Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
             there is mapping data, or OntologyXref if there is linkage data.
Exceptions : throws if rnaproduct object not passed
Caller     : general
Status     : Stable

remove_from_object

Arg [1]    : Bio::EnsEMBL::DBEntry $dbe - The external reference which
             is to be disassociated from an ensembl object.
Arg [2]    : Bio::EnsEMBL::Storable $object - The ensembl object the
             external reference is to be disassociated from
Arg [3]    : string $object_type - The type of the ensembl object.
             E.g. 'Gene', 'Transcript', 'Translation'
Example    :
             # remove all dbentries from this translation
             foreach my $dbe (@{$translation->get_all_DBEntries()}) {
               $dbe_adaptor->remove($dbe, $translation, 'Translation');
             }
Description: Removes an association between an ensembl object and a
             DBEntry (xref).  This does not remove the actual xref from
             the database, only its linkage to the ensembl object.
Returntype : none
Exceptions : Throw on incorrect arguments.
             Warning if object or dbentry is not stored in this database.
Caller     : TranscriptAdaptor::remove, GeneAdaptor::remove,
             TranslationAdaptor::remove
Status     : Stable

_fetch_by_object_type

Arg [1]    : string $ensID
Arg [2]    : string $ensType (object type to be returned)
Arg [3]    : optional $exdbname (external database name)
             (may be an SQL pattern containing '%' which matches any
             number of characters)
Arg [4]    : optional $exdb_type (external database type)
             (may be an SQL pattern containing '%' which matches any
             number of characters)
Example    : $self->_fetch_by_object_type( $translation_id, 'Translation' )
Description: Fetches DBEntry by Object type
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.


Returntype : arrayref of DBEntry objects; may be of type IdentityXref if
             there is mapping data, or OntologyXref if there is linkage data.
Exceptions : none
Caller     : fetch_all_by_Gene
             fetch_all_by_Translation
             fetch_all_by_Transcript
Status     : Stable

list_gene_ids_by_external_db_id

Arg [1]    : string $external_id
Example    : @gene_ids = $dbea->list_gene_ids_by_external_db_id(1020);
Description: Retrieve a list of geneid by an external identifier that
             is linked to any of the genes transcripts, translations
             or the gene itself.
             NOTE:  If more than one external identifier has the
             same primary accession then genes for each of these is
             returned.
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
Returntype : list of ints
Exceptions : none
Caller     : unknown
Status     : Stable

list_gene_ids_by_extids

Arg [1]    : string $external_name
Arg [2]    : (optional) string $external_db_name
Arg [3]    : Boolean override, see _type_by_external_id
Example    : @gene_ids = $dbea->list_gene_ids_by_extids('CDPX');
Description: Retrieve a list of geneid by an external identifier that is
             linked to  any of the genes transcripts, translations or the
             gene itself
Returntype : list of ints
Exceptions : none
Caller     : unknown
Status     : Stable

list_transcript_ids_by_extids

Arg [1]    : string $external_name
Arg [2]    : (optional) string $external_db_name
Arg [3]    : Boolean override, see _type_by_external_id
Example    : @tr_ids = $dbea->list_transcript_ids_by_extids('BCRA2');
Description: Retrieve a list transcript ids by an external identifier that
             is linked to any of the genes transcripts, translations or the
             gene itself
Returntype : list of ints
Exceptions : none
Caller     : unknown
Status     : Stable

list_translation_ids_by_extids

Arg [1]    : string $external_name
Arg [2]    : (optional) string $external_db_name
Arg [3]    : Boolean override, see _type_by_external_id
Example    : @tr_ids = $dbea->list_translation_ids_by_extids('GO:0004835');
Description: Gets a list of translation IDs by external display IDs
Returntype : list of Ints
Exceptions : none
Caller     : unknown
Status     : Stable

list_rnaproduct_ids_by_extids

Arg [1]    : string $external_name
Arg [2]    : (optional) string $external_db_name
Arg [3]    : Boolean override, see _type_by_external_id
Example    : @rp_ids = $dbea->list_rnaproduct_ids_by_extids('GO:0004835');
Description: Gets a list of rnaproduct IDs by external display IDs
Returntype : list of Ints
Exceptions : none
Caller     : unknown
Status     : Stable

_type_by_external_id

Arg [1]    : string $name - dbprimary_acc
Arg [2]    : string $ensType - ensembl_object_type
Arg [3]    : (optional) string $extraType
Arg [4]    : (optional) string $external_db_name
	           other object type to be returned
Arg [5]    : Boolean override to force _ to be treated as an SQL 'any'
             This is usually optimised out for query speed due to 
             large numbers of names like NM_00...
Example    : $self->_type_by_external_id($name, 'Translation');
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
             SQL wildcards can be used in the external id, 
             but overly generic queries (two characters) will be prevented.
Description: Gets
Returntype : list of dbIDs (gene_id, transcript_id, etc.)
Exceptions : none
Caller     : list_translation_ids_by_extids
             translationids_by_extids
	           geneids_by_extids
Status     : Stable

_type_by_external_db_id

Arg [1]    : integer $type - external_db_id
Arg [2]    : string $ensType - ensembl_object_type
Arg [3]    : (optional) string $extraType
	       other object type to be returned. This references the _id fields of
	       the transcript table, and if left unset defaults to the translation_id
	       from the translation table.
Arg [4]    : (optional) string $linkage_type
             provides a link to ontology_xref and limits by an ontology linkage type
Example    : $self->_type_by_external_db_id(1030, 'Translation');
Description: Gets.
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
Returntype : list of dbIDs (gene_id, transcript_id, etc.)
Exceptions : none
Caller     : list_translation_ids_by_extids
             translationids_by_extids
	           geneids_by_extids
Status     : Stable

fetch_all_by_description

Arg [1]    : string description to search for. Include % etc in this string
Arg [2]    : <optional> string $dbname. Name of the database to search

Example    : @canc_refs = @{$db_entry_adaptor->fetch_all_by_description("%cancer%")};
             @db_entries = @{$db_entry_adaptor->fetch_all_by_description("%cancer%","MIM_MORBID")};
Description: Retrieves DBEntries that match the description.
             Optionally you can search on external databases type.
             NOTE:  In a multi-species database, this method will
             return all the entries matching the search criteria, not
             just the ones associated with the current species.
Returntype : ref to array of Bio::EnsEMBL::DBSQL::DBEntry
Exceptions : None.
Caller     : General
Status     : At Risk

fetch_all_by_source

Arg [1]    : string source to search for. Include % etc in this string
             if you want to use SQL patterns

Example    : @unigene_refs = @{$db_entry_adaptor->fetch_all_by_source("%unigene%")};
Description: Retrieves DBEntrys that match the source name.
Returntype : ref to array of Bio::EnsEMBL::DBSQL::DBEntry
Exceptions : None.
Caller     : General
Status     : At Risk

fetch_all_synonyms

Arg [1]    : dbID of DBEntry to fetch synonyms for. Used in lazy loading of synonyms.

Example    : @canc_refs = @{$db_entry_adaptor->fetch_all_synonyms(1234)};
Description: Fetches the synonyms for a particular DBEntry.
Returntype : listref of synonyms. List referred to may be empty if there are no synonyms.
Exceptions : None.
Caller     : General
Status     : At Risk

get_db_name_from_external_db_id

Arg [1]    : external_dbid of database to get the database_name
Example    : my $db_name = $db_entry_adaptor->get_db_name_from_external_db_id(1100);
Description: Gets the database name for a certain external_db_id
Returntype : scalar
Exceptions : None.
Caller     : General
Status     : At Risk

1 POD Error

The following errors were encountered while parsing the POD:

Around line 385:: Unknown directive: =head

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