Reapply previous pull requests and commits that were undone by PR #143

[alexskr]

Merge of PR #143 undid a number of pull requests and commits:

• PR Feature: enhance zipped submissions support #144
• PR Fix: Enhance zipped submissions support - follow up  #174
• 629aa39

Done:

• 29e3028
• b208745 for PR Notifications sends separate emails for archived status with vague content #190
• a3f6cf0 for PR Feature: extract ontology URI automatically in submissions process #153
• da1642e for PR use max_depth calculated by owlapi_wrapper for UMLS ontologies #182

[alexskr]

enhanced zip submissions support is re-implemented with a4bfc7f and 6dc0ab9