Semsimian should be aware of obsolete terms and ignore either by default or when specified.
An example from the Monarch API:
http://api-dev.monarchinitiative.org/v3/api/semsim/search/HP%3A0002104%2CHP%3A0012378%2CHP%3A0012378%2CHP%3A0012378/Human%20Diseases?limit=10
The top hit here is an obsolete.