Package index • ontoProc2

All functions

PREDICATES: Standard predicate CURIEs used in OBO ontologies
SemsqlConn(): SemsqlConn: S7 connection wrapper for SemanticSQL databases
count_by_prefix(): Count labeled terms grouped by CURIE prefix
count_descendants(): Count the number of descendants of a term
describe_table(): Describe the columns of a table in a SemsqlConn database
disconnect(): Disconnect a SemsqlConn from its database
find_by_restriction(): Find terms that have a given OWL someValuesFrom restriction
find_intersection(): Find terms that are descendants of a superclass and have a given restriction
get_ancestors(): Get all ancestors of a term via entailed edges
get_ancestors_partonomy(): Get ancestors traversing both is-a and part-of relationships
get_definition(): Get the text definition for a term
get_descendants(): Get all descendants of a term via entailed edges
get_descendants_partonomy(): Get descendants traversing both is-a and has-part relationships
get_direct_edges(): Get direct edges in the ontology graph for a term
get_direct_subclasses(): Get direct subclasses of a term
get_direct_superclasses(): Get direct superclasses of a term
get_label(): Get the rdfs:label for a term
get_prefix(): Retrieve the ontology prefix from a SemsqlConn
get_restrictions(): Get OWL someValuesFrom restrictions for a term
get_synonyms(): Get synonyms for a term
get_term_info(): Retrieve a summary of information about a term
improveNodes(): inject linefeeds for node names for graph, with textual annotation from ontology
is_connected(): Test whether a SemsqlConn has a valid open connection
list_tables(): List tables in a SemsqlConn database
make_graphNEL_from_ontology_plot(): obtain graphNEL from ontology_plot instance of ontologyPlot
ncit_map: a named vector with values rdfs labels in NCI thesaurus, and names the corresponding formal ontology tags
onto_plot2(): high-level use of graph/Rgraphviz for rendering ontology relations
print: setup print
reconnect(): Reconnect a SemsqlConn to its database
report(): Display a detailed report of a SemsqlConn object
retrieve_semsql_conn(): return a SQLite connection (read only) to an INCAtools Semantic SQL ontology
run_query(): Run an arbitrary SQL query against a SemsqlConn database
search_labels(): Search term labels in a SemsqlConn database
semsql_connect(): Create a SemsqlConn connection
semsql_to_oi(): produce an ontology_index instance from semantic sql sqlite connection
semsql_url(): produce INCAtools distribution URL
with_connection(): Execute code with an automatically managed SemsqlConn