Provided by: libgo-perl_0.15-9_all 
NAME
GO::Model::Term - a term or concept in an ontology
SYNOPSIS
# From a file
use GO::Parser;
my $parser = new GO::Parser({handler=>'obj'}); # create parser object
$parser->parse("gene_ontology.obo"); # parse file -> objects
my $graph = $parser->handler->graph; # get L<GO::Model::Graph> object
my $term = $graph->get_term("GO:0001303"); # fetch a term by ID
printf "Term %s %s\n", $term->name, $term->acc;
# From a GO Database (requires go-db-perl)
my apph = GO::AppHandle->connect(-dbname=>$dbname);
my $term = $apph->get_term({acc=>00003677});
printf "Term:%s (%s)\nDefinition:%s\nSynonyms:%s\n",
$term->name,
$term->public_acc,
$term->definition,
join(", ", @{$term->synonym_list});
DESCRIPTION
Represents an Ontology term; the same class is used for process, compartment and function
currently, a Term is not aware of its Relationships; to find out how a term is related to
other terms, use the a GO::Model::Graph object, which will give you the
GO::Model::Relationship objects; for example
$rels = $graph->get_parent_relationships($term->acc);
SEE ALSO
GO::Model::Relationship GO::Model::Graph GO::Model::Xref GO::Model::Association
NOTES
Like all the GO::Model::* classes, this uses accessor methods to get or set the
attributes. by using the accessor method without any arguments gets the value of the
attribute. if you pass in an argument, then the attribuet will be set according to that
argument.
for single-valued attributes
# this sets the value of the attribute
$my_object->attribute_name("my value");
# this gets the value of the attribute
$my_value = $my_object->attribute_name();
for lists:
# this sets the values of the attribute
$my_object->attribute_name(\@my_values);
# this gets the values of the attribute
$my_values = $my_object->attribute_name();
acc
Usage - print $term->acc()
Alias - public_acc
Returns -
Args -
accessor: gets/sets GO ID/accession [as an integer]
throws: exception if you try to pass in a non-integer
if you want to use IDs in the format GO:0000nnn, then use the method public_acc()
name
Usage - print $term->name;
Returns -
Args -
accessor: gets/sets "name" attribute
subset_list
Usage - foreach (@{$term->subset_list || []}) { printf " $_\n" }
Returns - list of strings
Args - list of strings [optional]
List of subset Accs for a term
Subsets are also known as GO Slims
in_subset
Usage - if ($term->in_subset('goslim_prok');
Returns - bool
Args - subset-name str
Tests if the term belongs to a subset
definition
Usage - print $term->definition;
Returns -
Args -
accessor: gets/sets "definition" attribute
primary_xref
Title : primary_xref
Usage :
Function:
Example :
Returns : GO::Model::Xref
Args :
The same as acc(), except the ID is returned as a GO::Model::Xref rather than a string
comment
Title : comment
Usage : $obj->comment($newval)
Function:
Example :
Returns : value of comment (a scalar)
Args : on set, new value (a scalar or undef, optional)
definition_dbxref_list
Title : definition_dbxref_list
Usage : $obj->definition_dbxref(\@xrefs)
Function:
Example :
Returns : definition_dbxref_list hashlist (of GO::Model::Xref)
Args : on set, new values (GO::Model::Xref hashlist)
GO::Model::Xref
add_definition_dbxref
- Usage : $term->add_definition_dbxref($xref);
- Args : GO::Term::Xref
GO::Model::Xref
has_synonym
Usage - if ($term->has_synonym("autotrophy") {...}
Returns - bool
Args - string
add_synonym
Usage - $term->add_synonym("calcineurin");
Usage - $term->add_synonym(@synonym_strings);
Returns -
Args -
Adds a synonym; loses type information (the synonym type in blank)
synonym_list
Usage - my $syn_l = $term->synonym_list;
Usage - $term->synonym_list([$syn1, $syn2]);
Returns - arrayref
Args - arrayref [optional]
accessor: gets/set list of synonyms [array reference]
each synonym is represented as a string - this method loses synonym typing information. If
used as a setter, will set the type for each synonym to null
add_synonym_by_type
Usage - $term->add_synonym_by_type('exact', $syn);
Returns -
Args -
synonyms_by_type
Usage - $synstrs = $term->synonyms_by_type('exact');
Usage - $term->synonyms_by_type('exact', \@exact_syns);
Returns - arrayref of strings
Args - type string, arrayref of strings [optional]
in getter mode, gets a list of synonyms of a particular type
in setter mode, sets a list of synonyms for a particular type
alt_id_list
Usage - my $syn_l = $term->alt_id_list;
Usage - $term->alt_id_list([$syn1, $syn2]);
Returns - arrayref
Args - arrayref [optional]
accessor: gets/set list of synonyms [array reference]
add_alt_id
Usage - $term->add_alt_id('GO:0000001');
Returns -
Args - id string, or list of id strings
namespace (INHERITED)
Usage - print $term->namespace(); # getting the type
Usage - $term->namespace("molecular_function"); # setting the type
Alias - type
Alias - term_type
Alias - category
Alias - ontology
Returns - string representing type
Args - string represnting type [optional]
The OBO namespace for the GO::Model::Term or GO::Model::Relationship
This method is inherited from the superclass
set_namespace_by_code
Usage - $term->set_namespace_by_code("P");
Returns -
Args - String: M, P or C
Currently the mapping is hardcoded
('F'=>'molecular_function',
'P'=>'biological_process',
'C'=>'cellular_component');
get_code_from_namespace
Usage - $code = $term->get_code_from_namespace;
Returns - String: M, P or F
Args - String (if omitted will use current namespace)
Returns the code for the current namespace (or any given namespace if supplied)
add_dbxref
- Usage : $term->add_dbxref($xref);
- Args : GO::Term::Xref
GO::Model::Xref
dbxref_list
- Usage : $term->dbxref_list($xref);
- Args : optional listref of GO::Term::Xref
- Returns : listref of GO::Term::Xref
accessor: gets/sets list of dbxref [array reference]
is_obsolete
accessor: gets/set obsolete flag [boolean
is_root
accessor: gets/set is_root flag [boolean]
TERM ASSOCIATION METHODS
association_list
Usage - $assoc_l = $term->association_list
Returns - arrayref of GO::Model::Association
Args - arrayref of GO::Model::Association [optional]
accessor: gets/set list of associations [array reference]
if this is undefined, the datasource will be queried for the associations
selected_association_list
Usage - $assoc_l = $term->selected_association_list
Returns - arrayref of GO::Model::Association
Args - arrayref of GO::Model::Association [optional]
accessor: gets list of SELECTED associations [array reference]
[this method is only of use if you are using it in conjunction with GO::AppHandle in the
go-db-perl distro]
this in not the total list of all associations associated with a term; if the term was
created via a query on products, this will include those associations
GO::Model::Association
add_association
Usage - $term->add_association($assoc);
Returns -
Args - GO::Model::Association
GO::Model::Association
add_selected_association
Usage -
Returns -
Args -
GO::Model::Association
association_hash
returns associations as listref of unique GeneProduct objects
GO::Model::Association
get_all_associations
Usage - my $al = $term->get_all_associations
Returns - GO::Model::Association list
Args -
returns all associations for the term and the terms beneath it in the GO DAG
same as $apph->get_all_associations($term)
GO::Model::Association
n_associations
Usage - my $n = $term->n_associations
Returns -
Args -
product_list
Usage - $prods = $term->product_list
Returns - L<GO::Model::GeneProduct> listref
Args -
Returns a reference to an array of gene products that are attached directly to this term.
(if the products have not been fetched, this method will call $term->association_list,
cache the results, and use the associations to build the product list. succeeding calls of
product_list to this term will hence be faster)
See GO::Model::GeneProduct
deep_product_list
Usage -
Returns - GO::Model::GeneProduct listref
Args -
finds all products attached to this term and all terms below in the graph
GO::Model::GeneProduct
n_deep_products
Usage - my $count = $term->n_deep_products;
Returns - int
Args - filter (hashref) - or string "recount"
gets the count for the *dsitinct* number of GO::Model::GeneProduct entries annotated at OR
BELOW this level. if you have set the filters in GO::AppHandle then these filters will be
used in determining the count.
Remember, if you did not explicitly set the filters, then the default filter will be used,
which is [!IEA] (i.e. curated associations only, see www.geneontology.org for a discussion
of evidence codes).
Note: currently only the speciesdb filter is respected. It turns out to be very expensive
to do the set arithmetic for distinct recursive gene counts with different evidence
combinations. Because each product belongs to one speciesdb only, the speciesdb counts are
mutually exclusive, which makes this easier.
# get the number of gene products that have been annotated
# as transcription factors in worm and fly discounting
# uncurated automatic annotations
$apph->filters({evcodes=>["!IEA"], speciesdbs=>["SGD", "FB"]});
$term = $apph->get_term({name=>"transcription factor"});
print $term->n_deep_products;
The count will be cached, so if you alter the filter parameters be sure to get a recount
like this:
my $count = $term->n_deep_products("recount");
TODO: make the recount automatic if the filter is changed
PERFORMANCE NOTE 1: When you ask the AppHandle to give you a list of GO::Model::Term
objects, it may decide to populate this attribute when building the terms in a fast and
efficient way. Therefore you should avoid setting the filters *after* you have created the
objects otherwise it will have to refetch all these values slowing things down.
PERFORMANCE NOTE 2: If you are using the SQL GO::AppHandle implementation, then this call
will probably involve a query to the *gene_produc_count* table. If you populated the
database you are using yourself, make sure this table is filled otherwise this will be an
expensive query.
GO::Model::GeneProduct
n_products
Usage - as n_deep_products
Returns -
Args -
see docs for n_deep_products
gets a count of products AT THIS LEVEL ONLY
GO::Model::GeneProduct
loadtime
Title : loadtime
Usage :
Function:
Example :
Returns : time term was loaded into datasource
Args : none