Deprecated classes: to include or not to include?

[matentzn]

There is a big questionmark around deprecated classes. We can either include or ignore them. Right now, the mondo.sssom.tsv still contains them (see for example this PR).

@kevinschaper what is your sense?

1. Case 1: Mondo class is deprecated, external (eg OMIM) class is not
2. Case 2: Mondo and external class is deprecated
3. Case 3: Mondo is not deprecated, but external one is

For our use cases, I think its obvious that 3 will be included.

1. Is tougher. I personally think this helps with transparency.
2. No idea. What if a datasource uses an OMIM class that is deprecated without replacement, Mondo also decided to deprecate it?