<commit_before>package Bio::KBase::OntologyService::OntologyServiceImpl;
use strict;
use Bio::KBase::Exceptions;
# Use Semantic Versioning (2.0.0-rc.1)
# http://semver.org 
our $VERSION = "0.1.0";

=head1 NAME

Ontology

=head1 DESCRIPTION

This module provides public interface/APIs for KBase plant ontology services. It encapsulates the basic functionality of extracting domain ontologies (e.g. biological process, molecular function, cellular process) from ontology types (such as GO, PO, TO, EO etc) of interest for a given set of species specific genes. Additionally, it also allows ontology enrichment analysis to be performed on a set of genes that may be, say for example, over-expressed in drought stress in plant roots. To support these key features, currently this modules provides five API-functions that are backed by custom defined data structures. Majority of these API-functions accept a list of input items (majority of them being text strings) such as list of gene-ids, list of go-ids, list of ontology-domains, and list of ontology-types and return the requested results as tabular dataset.

=cut

#BEGIN_HEADER
use DBI;
use POSIX;
use OntologySupport;
use Text::NSP::Measures::2D::Fisher::twotailed;
#use IDServerAPIClient;
#END_HEADER

sub new
{
    my($class, @args) = @_;
    my $self = {
    };
    bless $self, $class;
    #BEGIN_CONSTRUCTOR
    #END_CONSTRUCTOR

    if ($self->can('_init_instance'))
    {
	$self->_init_instance();
    }
    return $self;
}

=head1 METHODS



=head2 getGOIDList

  $results = $obj->getGOIDList($sname, $geneIDList, $domainList, $ecList)<commit_msg>service folder name to be consistent<commit_after>package Bio::KBase::OntologyService::OntologyServiceImpl;
use strict;
use Bio::KBase::Exceptions;
# Use Semantic Versioning (2.0.0-rc.1)
# http://semver.org 
our $VERSION = "0.1.0";

=head1 NAME

Ontology

=head1 DESCRIPTION

This module provides public interface/APIs for KBase plant ontology services. It encapsulates the basic functionality of extracting domain ontologies (e.g. biological process, molecular function, cellular process) from ontology types (such as GO, PO, TO, EO etc) of interest for a given set of species specific genes. Additionally, it also allows ontology enrichment analysis to be performed on a set of genes that may be, say for example, over-expressed in drought stress in plant roots. To support these key features, currently this modules provides five API-functions that are backed by custom defined data structures. Majority of these API-functions accept a list of input items (majority of them being text strings) such as list of gene-ids, list of go-ids, list of ontology-domains, and list of ontology-types and return the requested results as tabular dataset.

=cut

#BEGIN_HEADER
use DBI;
use POSIX;
use Bio::KBase::OntologyService::OntologySupport;
use Text::NSP::Measures::2D::Fisher::twotailed;
#use IDServerAPIClient;
#END_HEADER

sub new
{
    my($class, @args) = @_;
    my $self = {
    };
    bless $self, $class;
    #BEGIN_CONSTRUCTOR
    #END_CONSTRUCTOR

    if ($self->can('_init_instance'))
    {
	$self->_init_instance();
    }
    return $self;
}

=head1 METHODS



=head2 getGOIDList

  $results = $obj->getGOIDList($sname, $geneIDList, $domainList, $ecList)
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{'dir': 'git-commits-cleaned', 'id': '5895503', 'n_tokens_mistral': 1015, 'n_tokens_neox': 961, 'n_words': 382}