Package index • ontoProc2

All functions
`PREDICATES`	Standard predicate CURIEs used in OBO ontologies
`SemsqlConn()`	SemsqlConn: S7 connection wrapper for SemanticSQL databases
`bbop_sqlite_db_gz()`	retrieve and cache all filenames of Semantic SQL ontologies available, checking for updated content relative to cache via ETag
`cells_with_pmp()`	produce a table with cells exhibiting given proteins on plasma membrane according to CL
`cn2tag`	a named vector with mapping from cell type phrase to CURIE for CL.owl of 2025-12-17
`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_present_pmp()`	produce a table with list of proteins from protein ontology identified as present on cell membranes for input cell type CURIEs
`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
`improve_nodes()`	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()`	Show method for SemsqlConn. Concise one-line summary displayed when a `SemsqlConn` object is auto-printed at the R prompt.
`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
`tag2cn`	a named vector with mapping from CURIE to cell type phrase for CL.owl of 2025-12-17
`with_connection()`	Execute code with an automatically managed SemsqlConn

Reference

All functions