Retrieves an ontology database with relations in the desired data
structure. The database is automatically loaded and the requested data
structure is constructed if necessary. The databases stay loaded up to a
certain time period (see the option omnipathr.db_lifetime). Hence
the first one of repeated calls to this function might take long and the
subsequent ones should be really quick.
Arguments
- key
Character: key of the ontology database. For the available keys see
omnipath_show_db.- rel_fmt
Character: the data structure of the ontology relations. Posible values are 1) "tbl" a data frame, 2) "lst" a list or 3) "gra" a graph.
- child_parents
Logical: whether the ontology relations should point from child to parents (
TRUE) or from parent to children (FALSE).
Value
A list with the following elements: 1) "names" a table with term IDs and names; 2) "namespaces" a table to connect term IDs and namespaces they belong to; 3) "relations" a table with relations between terms and their parent terms; 4) "subsets" a table with terms and the subsets they are part of; 5) "obsolete" character vector with all the terms labeled as obsolete.