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 either the GO::AppHandle object or a GO::Model::Graph object, which will give you the GO::Model::Relationship objects
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 instance
# 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();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
type
Alias - term_type
Alias - category
Alias - ontology
Usage - print $term->type(); # getting the type
Usage - $term->type("function"); # setting the type
Returns - string representing type
Args - string represnting type [optional]in_subset
Usage - if ($term->in_subset('goslim_prok');
Returns - bool
Args - subset-name strdefinition
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)add_definition_dbxref
- Usage : $term->add_definition_dbxref($xref);
- Args : GO::Term::Xref
has_synonym
Usage - if ($term->has_synonym("autotrophy") {...}
Returns - bool
Args - stringadd_synonym
Usage - $term->add_synonym("calcineurin");
Returns -
Args -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]
add_synonym_by_type
Usage - $term->add_synonym_by_type('exact', $syn);
Returns -
Args -synonyms_by_type
Usage - $synstrs = $term->synonyms_by_type('exact');
Returns -
Args -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_dbxref
- Usage : $term->add_dbxref($xref);
- Args : GO::Term::Xrefdbxref_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]
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
add_association
Usage - $term->add_association($assoc);
Returns -
Args - GO::Model::Associationadd_selected_association
Usage -
Returns -
Args -association_hash
returns associations as listref of unique GeneProduct objects
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)
n_associations
Usage - my $n = $term->n_associations
Returns -
Args -product_list
Usage -
Returns - 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)
deep_product_list
Usage -
Returns - GO::Model::GeneProduct listref
Args -finds all products attached to this term and all terms below in the graph
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.
n_products
Usage - as n_deep_products
Returns -
Args -see docs for n_deep_products
gets a count of products AT THIS LEVEL ONLY
loadtime
Title : loadtime
Usage :
Function:
Example :
Returns : time term was loaded into datasource
Args : none