NAME

Bio::Chado::Schema::Cv::Cvterm - 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.

ACCESSORS

cvterm_id

  data_type: integer
  default_value: nextval('cvterm_cvterm_id_seq'::regclass)
  is_auto_increment: 1
  is_nullable: 0
  size: 4

cv_id

  data_type: integer
  default_value: undef
  is_foreign_key: 1
  is_nullable: 0
  size: 4

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

name

  data_type: character varying
  default_value: undef
  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
  default_value: undef
  is_nullable: 1
  size: undef

A human-readable text definition.

dbxref_id

  data_type: integer
  default_value: undef
  is_foreign_key: 1
  is_nullable: 0
  size: 4

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
  size: 4

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 Note that two terms with different primary dbxrefs may exist if one is obsolete.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
  size: 4

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

acquisitionprops

Type: has_many

acquisition_relationships

Type: has_many

analysisfeatureprops

Type: has_many

analysisprops

Type: has_many

arraydesign_platformtype_ids

Type: has_many

Related object: Bio::Chado::Schema::Mage::Arraydesign

arraydesign_substratetype_ids

Type: has_many

Related object: Bio::Chado::Schema::Mage::Arraydesign

arraydesignprops

Type: has_many

assayprops

Type: has_many

Related object: Bio::Chado::Schema::Mage::Assayprop

biomaterialprops

Type: has_many

biomaterial_relationships

Type: has_many

biomaterial_treatments

Type: has_many

cell_line_cvterms

Type: has_many

cell_line_cvtermprops

Type: has_many

cell_lineprops

Type: has_many

cell_line_relationships

Type: has_many

contacts

Type: has_many

Related object: Bio::Chado::Schema::Contact::Contact

contact_relationships

Type: has_many

controls

Type: has_many

Related object: Bio::Chado::Schema::Mage::Control

cv

Type: belongs_to

Related object: Bio::Chado::Schema::Cv::Cv

dbxref

Type: belongs_to

Related object: Bio::Chado::Schema::General::Dbxref

cvterm_dbxrefs

Type: has_many

Related object: Bio::Chado::Schema::Cv::CvtermDbxref

cvtermpath_type_ids

Type: has_many

Related object: Bio::Chado::Schema::Cv::Cvtermpath

cvtermpath_object_ids

Type: has_many

Related object: Bio::Chado::Schema::Cv::Cvtermpath

cvtermpath_subject_ids

Type: has_many

Related object: Bio::Chado::Schema::Cv::Cvtermpath

cvtermprop_type_ids

Type: has_many

Related object: Bio::Chado::Schema::Cv::Cvtermprop

cvtermprop_cvterm_ids

Type: has_many

Related object: Bio::Chado::Schema::Cv::Cvtermprop

cvterm_relationship_type_ids

Type: has_many

cvterm_relationship_object_ids

Type: has_many

cvterm_relationship_subject_ids

Type: has_many

cvtermsynonym_type_ids

Type: has_many

Related object: Bio::Chado::Schema::Cv::Cvtermsynonym

cvtermsynonym_cvterm_ids

Type: has_many

Related object: Bio::Chado::Schema::Cv::Cvtermsynonym

dbxrefprops

Type: has_many

Related object: Bio::Chado::Schema::Cv::Dbxrefprop

elements

Type: has_many

Related object: Bio::Chado::Schema::Mage::Element

element_relationships

Type: has_many

elementresult_relationships

Type: has_many

environment_cvterms

Type: has_many

expression_cvterm_cvterm_ids

Type: has_many

expression_cvterm_cvterm_type_ids

Type: has_many

expression_cvtermprops

Type: has_many

expressionprops

Type: has_many

features

Type: has_many

Related object: Bio::Chado::Schema::Sequence::Feature

feature_cvterms

Type: has_many

feature_cvtermprops

Type: has_many

feature_expressionprops

Type: has_many

feature_genotypes

Type: has_many

featuremaps

Type: has_many

Related object: Bio::Chado::Schema::Map::Featuremap

featureprops

Type: has_many

feature_pubprops

Type: has_many

feature_relationships

Type: has_many

feature_relationshipprops

Type: has_many

libraries

Type: has_many

Related object: Bio::Chado::Schema::Library::Library

library_cvterms

Type: has_many

libraryprops

Type: has_many

organismprops

Type: has_many

phendescs

Type: has_many

Related object: Bio::Chado::Schema::Genetic::Phendesc

phenotype_assay_ids

Type: has_many

phenotype_attr_ids

Type: has_many

phenotype_observable_ids

Type: has_many

phenotype_cvalue_ids

Type: has_many

phenotype_comparison_cvterms

Type: has_many

phenotype_cvterms

Type: has_many

phenstatements

Type: has_many

phylonodes

Type: has_many

phylonodeprops

Type: has_many

phylonode_relationships

Type: has_many

phylotrees

Type: has_many

protocols

Type: has_many

Related object: Bio::Chado::Schema::Mage::Protocol

protocolparam_unittype_ids

Type: has_many

protocolparam_datatype_ids

Type: has_many

pubs

Type: has_many

Related object: Bio::Chado::Schema::Pub::Pub

pubprops

Type: has_many

Related object: Bio::Chado::Schema::Pub::Pubprop

pub_relationships

Type: has_many

quantificationprops

Type: has_many

quantification_relationships

Type: has_many

stocks

Type: has_many

Related object: Bio::Chado::Schema::Stock::Stock

stockcollections

Type: has_many

stockcollectionprops

Type: has_many

stock_cvterms

Type: has_many

stockprops

Type: has_many

Related object: Bio::Chado::Schema::Stock::Stockprop

stock_relationships

Type: has_many

studydesignprops

Type: has_many

studyfactors

Type: has_many

Related object: Bio::Chado::Schema::Mage::Studyfactor

studyprops

Type: has_many

Related object: Bio::Chado::Schema::Mage::Studyprop

studyprop_features

Type: has_many

synonyms

Type: has_many

Related object: Bio::Chado::Schema::Sequence::Synonym

treatments

Type: has_many

Related object: Bio::Chado::Schema::Mage::Treatment

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 featureprop 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:

To install Bio::Chado::Schema, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Chado::Schema

CPAN shell

perl -MCPAN -e shell
install Bio::Chado::Schema

For more information on module installation, please visit the detailed CPAN module installation guide.

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