Bio::Chado::Schema::Cv::Cvterm

RELATIONS

acquisitionprops
acquisition_relationships
analysisfeatureprops
analysisprops
arraydesign_platformtypes
arraydesign_substratetypes
arraydesignprops
assayprops
biomaterialprops
biomaterial_relationships
biomaterial_treatments
cell_line_cvterms
cell_line_cvtermprops
cell_lineprops
cell_line_relationships
contacts
contact_relationships
controls
cv
dbxref
cvterm_dbxrefs
cvtermpath_types
cvtermpath_objects
cvtermpath_subjects
cvtermprop_types
cvtermprop_cvterms
cvterm_relationship_types
cvterm_relationship_objects
cvterm_relationship_subjects
cvtermsynonym_types
cvtermsynonym_cvterms
dbxrefprops
elements
element_relationships
elementresult_relationships
environment_cvterms
expression_cvterm_cvterms
expression_cvterm_cvterm_types
expression_cvtermprops
expressionprops
features
feature_cvterms
feature_cvtermprops
feature_expressionprops
feature_genotypes
featuremaps
featureprops
feature_pubprops
feature_relationships
feature_relationshipprops
libraries
library_cvterms
libraryprops
nd_experiments
nd_experimentprops
nd_experiment_stocks
nd_experiment_stockprops
nd_geolocationprops
nd_protocolprops
nd_protocol_reagents
nd_reagents
nd_reagentprops
nd_reagent_relationships
organismprops
phendescs
phenotype_assays
phenotype_attrs
phenotype_observables
phenotype_cvalues
phenotype_comparison_cvterms
phenotype_cvterms
phenstatements
phylonodes
phylonodeprops
phylonode_relationships
phylotrees
projectprops
project_relationships
protocols
protocolparam_unittypes
protocolparam_datatypes
pubs
pubprops
pub_relationships
quantificationprops
quantification_relationships
stocks
stockcollections
stockcollectionprops
stock_cvterms
stockprops
stock_relationships
stock_relationship_cvterms
studydesignprops
studyfactors
studyprops
studyprop_features
synonyms
treatments

ADDITIONAL RELATIONS

cvtermprops
cvtermsynonyms

ADDITIONAL METHODS

add_synonym
delete_synonym
get_secondary_dbxrefs
add_secondary_dbxref
delete_secondary_dbxref
create_cvtermprops
create_with

AUTHOR
COPYRIGHT AND LICENSE

NAME

Bio::Chado::Schema::Cv::Cvterm

DESCRIPTION

A term, class, universal or type within an ontology or controlled vocabulary. This table is also used for relations and properties. cvterms constitute nodes in the graph defined by the collection of cvterms and cvterm_relationships.

NAME

Bio::Chado::Schema::Cv::Cvterm

ACCESSORS

cvterm_id

  data_type: 'integer'
  is_auto_increment: 1
  is_nullable: 0
  sequence: 'cvterm_cvterm_id_seq'

cv_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 0

The cv or ontology or namespace to which this cvterm belongs.

name

  data_type: 'varchar'
  is_nullable: 0
  size: 1024

A concise human-readable name or label for the cvterm. Uniquely identifies a cvterm within a cv.

definition

  data_type: 'text'
  is_nullable: 1

A human-readable text definition.

dbxref_id

  data_type: 'integer'
  is_foreign_key: 1
  is_nullable: 0

Primary identifier dbxref - The unique global OBO identifier for this cvterm. Note that a cvterm may have multiple secondary dbxrefs - see also table: cvterm_dbxref.

is_obsolete

  data_type: 'integer'
  default_value: 0
  is_nullable: 0

Boolean 0=false,1=true; see GO documentation for details of obsoletion. Note that two terms with different primary dbxrefs may exist if one is obsolete.

is_relationshiptype

  data_type: 'integer'
  default_value: 0
  is_nullable: 0

Boolean 0=false,1=true relations or relationship types (also known as Typedefs in OBO format, or as properties or slots) form a cv/ontology in themselves. We use this flag to indicate whether this cvterm is an actual term/class/universal or a relation. Relations may be drawn from the OBO Relations ontology, but are not exclusively drawn from there.

RELATIONS

ADDITIONAL RELATIONS

cvtermprops

Type: has_many

cvtermsynonyms

Type: has_many

ADDITIONAL METHODS

add_synonym

 Usage:        $self->add_synonym($synonym , { type => 'exact' , autocreate => 1} );
 Desc:         adds the synonym $new_synonym to this cvterm
               If the synonym $new_synonym already exists,
               nothing is added.
 Args:         a synonym name  and
    options hashref as:
          {
            synonym_type => [e.g. exact, narrow, broad, related],
            autocreate => 0,
               (optional) boolean, if passed, automatically create cv,
               cvterm, and dbxref rows if one cannot be found for the
               given synonym name.  Default false.

            cv_name => cv.name to use for the given synonym type.
                       Defaults to 'synonym_type',

            db_name => db.name to use for autocreated dbxrefs,
                       default 'null',

            definitions => optional hashref of:
                { cvterm_name => definition,
                }
             to load into the cvterm table when autocreating cvterms
                      }
             Ret:          a Cvtermsynonym object
             Example:

delete_synonym

 Usage: $self->delete_synonym($synonym)
 Desc:  delete synonym $synonym from cvterm object
  Ret:  nothing
 Args: $synonym
 Side Effects: Will delete all cvtermsynonyms with synonym=$synonym. Case insensitive
 Example:

get_secondary_dbxrefs

 Usage: $self->get_secondary_dbxrefs()
 Desc:  find all secondary accessions associated with the cvterm
         These are stored in cvterm_dbxref table as dbxref_ids
 Ret:    a list of accessions (e.g. GO:0000123)
 Args:   none
 Side Effects: none
 Example:

add_secondary_dbxref

 Usage: $self->add_secondary_dbxref(accession, 1)
 Desc:  add an alternative id to cvterm. Stores in cvterm_dbxref
 Ret:   a CvtermDbxref object
 Args:  an alternative id (i.e. "GO:0001234"). A second arg will store a is_for_definition=1 (default = 0)
 Side Effects: stores a new dbxref if accession is not found in dbxref table
 Example:

delete_secondary_dbxref

 Usage: $self->delete_secondary_dbxref($accession)
 Desc:  delete a cvterm_dbxref from the database
 Ret:   nothing
 Args:  full accession (db_name:dbxref_accession e.g. PO:0001234)
 Side Effects:
 Example:

create_cvtermprops

  Usage: $set->create_cvtermprops({ baz => 2, foo => 'bar' });
  Desc : convenience method to create cvterm properties using cvterms
          from the ontology with the given name
  Args : hashref of { propname => value, ...},
         options hashref as:
          {
            autocreate => 0,
               (optional) boolean, if passed, automatically create cv,
               cvterm, and dbxref rows if one cannot be found for the
               given cvtermprop name.  Default false.

            cv_name => cv.name to use for the given cvtermprops.
                       Defaults to 'cvterm_property',

            db_name => db.name to use for autocreated dbxrefs,
                       default 'null',

            dbxref_accession_prefix => optional, default
                                       'autocreated:',
            definitions => optional hashref of:
                { cvterm_name => definition,
                }
             to load into the cvterm table when autocreating cvterms

             rank => force numeric rank. Be careful not to pass ranks that already exist
                     for the property type. The function will die in such case.

             allow_duplicate_values => default false.
                If true, allow duplicate instances of the same cvterm
                and value in the properties of the cvterm.  Duplicate
                values will have different ranks.
                       }
               Ret  : hashref of { propname => new cvtermprop object }

create_with

 Usage: $schema->resultset('Cv::Cvterm')->create_with(
                  { name   => 'cvterm name',
                    cv     => $cv  || 'cv name',
                    db     => $db  || 'db name',
                    dbxref => $dbx || 'accession',
                  });

 Desc: convenience method to create a cvterm, linking it to the CV and
       DB that you name or provide.  For any cv, db, or dbxref that
       you call only by name, does a find_or_create() using that name.
 Ret : a new Cvterm row
 Args: hashref of:
         { name   => 'cvterm name',
           cv     => 'cv name' or L<Bio::Chado::Schema::Cv::Cvterm> row,
           db     => 'db name' or L<Bio::Chado::Schema::General::Db> row,
           dbxref => 'accession' or L<Bio::Chado::Schema::General::Dbxref> row,
         }

AUTHOR

Robert Buels <rbuels@cpan.org>

COPYRIGHT AND LICENSE

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.

Bio::Chado::Schema::Cv::Cvterm