man GO::Model::Term (3): 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);

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

SYNOPSIS

DESCRIPTION

NOTES

acc

name

subset_list

in_subset

definition

primary_xref

comment

definition_dbxref_list

add_definition_dbxref

has_synonym

add_synonym

synonym_list

add_synonym_by_type

synonyms_by_type

alt_id_list

add_alt_id

namespace (INHERITED)

set_namespace_by_code

get_code_from_namespace

add_dbxref

dbxref_list

is_obsolete

is_root

TERM ASSOCIATION METHODS

association_list

selected_association_list

add_association

add_selected_association

association_hash

get_all_associations

n_associations

product_list

deep_product_list

n_deep_products

n_products

loadtime

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