# Ontology Facilities Based on INCAtools Semantic SQL

## Documentation for package ‘ontoProc2’ version 0.99.30

- 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
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
with_connection | Execute code with an automatically managed SemsqlConn