As I was investigating the data formats in swo_data.owl I noticed that there were two classes that overlapped: SBML and SBML file.
Both of these classes were present as children of data format specification. Perhaps the original intention of SBML file was to represent an actual file (rather than the format), but in any case they are sibling classes now. All axioms from SBML file were moved to SBML , and SBML file was placed in the obsolete hierarchy.
This resulting in the obsoleting of http://www.ebi.ac.uk/efo/swo/SWO_0000379.