GO::AppHandle GO::AppHandle is a Gene Ontology Data API handler.
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GO::AppHandle Tags

Perl module api ontology gene Gene Ontology API handler

GO::AppHandle Description

GO::AppHandle is a Gene Ontology Data API handler. GO::AppHandle is a Gene Ontology Data API handler.SYNOPSIS use GO::AppHandle; my $dbname = "go"; # connect to a database on a specific host $apph = GO::AppHandle->connect(-dbname=>$dbname, -dbhost=>$mysqlhost); # EXAMPLE 1 # fetching a GO term from the datasource $term = $apph->get_term({acc=>"GO:0003677"}); printf "GO term; name=%s GO ID=%sn", $term->name(), $term->public_acc(); # EXAMPLE 2 # fetching a list of associations to the ER # (and all the GO terms that are subtypes of the ER, or # located within the ER) # for which there is reasonably good evidence # (traceable author / direct assay) $assocs = $apph->get_associations({name=>"endoplasmic reticulum"}, {evcodes=>}); foreach my $assoc (@$assocs) { printf "Gene: %s evidence for association: %s %s", $assoc->gene_product->symbol, $assoc->evidence->code(), $assoc->evidence->xref->xref_key(); } # EXAMPLE 3 # fetching a subgraph of GO $graph = $apph->get_graph(-acc=>3677, -depth=>3); foreach my $term (@ {$graph->get_all_nodes}) { printf "GO term; name=%s GO ID=%sn", $term->name(), $term->public_acc(); } # EXAMPLE 4 # fetching a subgraph of GO, # and using a graph iterator to # display the graph $graph = $apph->get_graph_by_search("DNA helicase*"); $it = $graph->create_iterator; while (my $ni = $it->next_node_instance) { $depth = $ni->depth; $term = $ni->term; printf "%s Term = %s (%s) // n_assocs=%s // depth=%dn", "----" x $depth, $term->name, $term->public_acc, $term->n_associations || 0, $depth; } # EXAMPLE 5 # fetching a subgraph of GO, # constraining by gene products # get all terms that were used to annotate these two SGD genes $terms = $apph->get_terms({products=>}); # build a graph all the way to the leaf nodes # from the above terms $graph = $apph->get_graph_by_terms($terms, -1); # create an iterator on the graph $it = $graph->create_iterator; # iterate through every node in graph while (my $ni = $it->next_node_instance) { $depth = $ni->depth; $term = $ni->term; printf "%s Term = %s (%s) // ASSOCS=%sn", "----" x $depth, $term->name, $term->public_acc, join("; ", map {$_->gene_product->acc} @{$term->association_list}); } Requirements: · Perl

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