NEWS.md
In ontologyIndex: Reading Ontologies into R

ontologyIndex 2.9

Attempting to create ontologies containing cycles now fails with an error message and get_ontology now has option merge_equivalent_terms (TRUE by default) so that terms that are marked equivalent_to other terms are merged and properties aggregated (thanks to feedback from Vincent Carey).
get_ancestors now returns an empty character vector rather than NULL when terms argument is empty.

The *_branches functions have all been renamed to *_descendants and their branch_roots argument to roots.
The get_descendants function has had two arguments renamed: ancestor is now roots and can accept a vector of root terms, returning the set of all terms which descend from them; remove_ancestor is now exclude_roots, determining whether or not to exclude the given roots terms from the result.
A check function which checks whether an ontology is valid has been added.
XML encoded 'OWL' files can now be read in as ontology_indexes.

get_ontology now only requires a file argument.
ontology_index objects now contain an obsolete slot - a logical vector.
prune_branches, exclude_branches and intersection_with_branches now use the same signature and are renamed to reflect the possibilit of passing multiple branch roots.
get_term_property, get_term_parents, get_term_ancestors and get_term_children functions with as_names argument to get descriptive names added for convenience.
swap_out_alt_ids replaced with force_compatibility which optionally throws an error if non-matchable term IDs are passed.
GO now included: data(go) now loads an ontology_index of the Gene Ontology (2015-11-27).