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sdk_ontology.spec
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sdk_ontology.spec
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/*
A KBase module: sdk_ontology
This module convert given KBase annotations of a genome to GO terms.
*/
module sdk_ontology {
/*
workspace - the name of the workspace for input/output
ontology_dictionary - reference to ontology dictionary
*/
typedef structure {
string ontology_dictionary_ref;
} ListOntologyTermsParams;
typedef structure {
string ontology;
string namespace;
list <string> term_id;
}OntlogyTermsOut;
funcdef list_ontology_terms (ListOntologyTermsParams params) returns (OntlogyTermsOut output) authentication required;
/*
Ontology overview
*/
typedef structure {
list <string> ontology_dictionary_ref;
} OntologyOverviewParams;
typedef structure {
string ontology;
string namespace;
string data_version;
string format_version;
int number_of_terms;
string dictionary_ref;
}overViewInfo;
typedef structure{
list <overViewInfo> dictionaries_meta;
}OntlogyOverviewOut;
funcdef ontology_overview (OntologyOverviewParams params) returns (OntlogyOverviewOut output) authentication required;
/*
List public ontologies
*/
typedef list <string> public_ontologies;
funcdef lsit_public_ontologies () returns (public_ontologies) authentication required;
/*
List public translations
*/
typedef list <string> public_translations;
funcdef list_public_translations () returns (public_translations) authentication required;
/*
get ontology terms
*/
typedef structure{
string ontology_dictionary_ref;
list <string> term_ids;
}GetOntologyTermsParams;
typedef structure{
string name;
string id;
}term_info;
typedef structure {
mapping <string, list<string>> term_info;
}GetOntologyTermsOut;
funcdef get_ontology_terms (GetOntologyTermsParams params) returns (GetOntologyTermsOut output) authentication required;
/*
get equivalent terms
*/
typedef structure{
string ontology_trans_ref;
list <string> term_ids;
}GetEqTermsParams;
typedef structure{
string name;
list <string> terms;
}term_info_list;
typedef structure {
mapping <string, list<string>> term_info_list;
}GetEqTermsOut;
funcdef get_equivalent_terms (GetEqTermsParams params) returns (GetEqTermsOut output) authentication required;
/*
workspace - the name of the workspace for input/output
input_genome - reference to the input genome object
ontology_translation - optional reference to user specified ontology translation map
output_genome - the name of the mapped genome annotation object
@optional ontology_translation
*/
typedef structure {
string workspace;
string input_genome;
string ontology_translation;
string translation_behavior;
string custom_translation;
string clear_existing;
string output_genome;
} ElectronicAnnotationParams;
typedef structure {
string report_name;
string report_ref;
string output_genome_ref;
int n_total_features;
int n_features_mapped;
} ElectronicAnnotationResults;
funcdef annotationtogo(ElectronicAnnotationParams params) returns (ElectronicAnnotationResults output)
authentication required;
};