Ontology Facilities Based on INCAtools Semantic SQL

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Documentation for package ‘ontoProc2’ version 0.99.28

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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
PREDICATES	Standard predicate CURIEs used in OBO ontologies
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
report-method	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
SemsqlConn	SemsqlConn: S7 connection wrapper for SemanticSQL databases
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