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monarch-initiative / monarch-mapping-commons

Building a fully exectuable workflow for boomer
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Deprecated classes: to include or not to include? #45

Open matentzn opened 11 months ago

matentzn commented 11 months ago

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?