NAME
Bio::Chado::Schema::Pub::Pub
DESCRIPTION
A documented provenance artefact - publications, documents, personal communication.
ACCESSORS
pub_id
data_type: 'integer'
is_auto_increment: 1
is_nullable: 0
sequence: 'pub_pub_id_seq'title
data_type: 'text'
is_nullable: 1Descriptive general heading.
volumetitle
data_type: 'text'
is_nullable: 1Title of part if one of a series.
volume
data_type: 'varchar'
is_nullable: 1
size: 255series_name
data_type: 'varchar'
is_nullable: 1
size: 255Full name of (journal) series.
issue
data_type: 'varchar'
is_nullable: 1
size: 255pyear
data_type: 'varchar'
is_nullable: 1
size: 255pages
data_type: 'varchar'
is_nullable: 1
size: 255Page number range[s], e.g. 457--459, viii + 664pp, lv--lvii.
miniref
data_type: 'varchar'
is_nullable: 1
size: 255uniquename
data_type: 'text'
is_nullable: 0type_id
data_type: 'integer'
is_foreign_key: 1
is_nullable: 0The type of the publication (book, journal, poem, graffiti, etc). Uses pub cv.
is_obsolete
data_type: 'boolean'
default_value: false
is_nullable: 1publisher
data_type: 'varchar'
is_nullable: 1
size: 255pubplace
data_type: 'varchar'
is_nullable: 1
size: 255RELATIONS
cell_line_cvterms
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineCvterm
cell_line_features
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineFeature
cell_line_libraries
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineLibrary
cell_lineprop_pubs
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLinepropPub
cell_line_pubs
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLinePub
cell_line_synonyms
Type: has_many
Related object: Bio::Chado::Schema::CellLine::CellLineSynonym
expression_pubs
Type: has_many
Related object: Bio::Chado::Schema::Expression::ExpressionPub
feature_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureCvterm
feature_cvterm_pubs
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureCvtermPub
feature_expressions
Type: has_many
Related object: Bio::Chado::Schema::Expression::FeatureExpression
featureloc_pubs
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeaturelocPub
featuremap_pubs
Type: has_many
Related object: Bio::Chado::Schema::Map::FeaturemapPub
featureprop_pubs
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeaturepropPub
feature_pubs
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeaturePub
feature_relationshipprop_pubs
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureRelationshippropPub
feature_relationship_pubs
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureRelationshipPub
feature_synonyms
Type: has_many
Related object: Bio::Chado::Schema::Sequence::FeatureSynonym
library_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Library::LibraryCvterm
libraryprop_pubs
Type: has_many
Related object: Bio::Chado::Schema::Library::LibrarypropPub
library_pubs
Type: has_many
Related object: Bio::Chado::Schema::Library::LibraryPub
library_synonyms
Type: has_many
Related object: Bio::Chado::Schema::Library::LibrarySynonym
nd_experiment_pubs
Type: has_many
Related object: Bio::Chado::Schema::NaturalDiversity::NdExperimentPub
phendescs
Type: has_many
Related object: Bio::Chado::Schema::Genetic::Phendesc
phenotype_comparisons
Type: has_many
Related object: Bio::Chado::Schema::Genetic::PhenotypeComparison
phenotype_comparison_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Genetic::PhenotypeComparisonCvterm
phenstatements
Type: has_many
Related object: Bio::Chado::Schema::Genetic::Phenstatement
phylonode_pubs
Type: has_many
Related object: Bio::Chado::Schema::Phylogeny::PhylonodePub
phylotree_pubs
Type: has_many
Related object: Bio::Chado::Schema::Phylogeny::PhylotreePub
project_pubs
Type: has_many
Related object: Bio::Chado::Schema::Project::ProjectPub
protocols
Type: has_many
Related object: Bio::Chado::Schema::Mage::Protocol
type
Type: belongs_to
Related object: Bio::Chado::Schema::Cv::Cvterm
pubauthors
Type: has_many
Related object: Bio::Chado::Schema::Pub::Pubauthor
pub_dbxrefs
Type: has_many
Related object: Bio::Chado::Schema::Pub::PubDbxref
pubprops
Type: has_many
Related object: Bio::Chado::Schema::Pub::Pubprop
pub_relationship_objects
Type: has_many
Related object: Bio::Chado::Schema::Pub::PubRelationship
pub_relationship_subjects
Type: has_many
Related object: Bio::Chado::Schema::Pub::PubRelationship
stock_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Stock::StockCvterm
stockprop_pubs
Type: has_many
Related object: Bio::Chado::Schema::Stock::StockpropPub
stock_pubs
Type: has_many
Related object: Bio::Chado::Schema::Stock::StockPub
stock_relationship_cvterms
Type: has_many
Related object: Bio::Chado::Schema::Stock::StockRelationshipCvterm
stock_relationship_pubs
Type: has_many
Related object: Bio::Chado::Schema::Stock::StockRelationshipPub
studies
Type: has_many
Related object: Bio::Chado::Schema::Mage::Study
create_pubprops
Usage: $set->create_pubprops({ baz => 2, foo => 'bar' });
Desc : convenience method to create pubprop 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 pubprop name. Default false.
cv_name => cv.name to use for the given pubprops.
Defaults to 'pub_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 pubprop. Duplicate
values will have different ranks.
}
Ret : hashref of { propname => new pubprop object }