WebPhenote must archive assertions

[cmungall]

At a meeting with @DoctorBud @drseb @kltm

We want to be able to delete assertions, but we never want to lose them. They should be obsoleted/deprecated, using the same annotation properties we use for classes, etc

This will probably be implemented entirely in minerva, cc @hdietze

[hdietze]

Summarizing a discussion with @kltm and @cmungall about implementation options:

• Use the OWL built-in deprecated annotation approach
  • Pro: out-of-the box support, no/minimal changes required in minerva
  • Con: reasoners usually ignore the deprecation annotations and will use 'deleted' axioms, pre-processing of the ontology is possible, but not transparent for downstream users/consumers
• Remove the axioms and store a shortform/alternate representation somewhere
  • Pro: No special handling for the reasoner
  • Con: How do we store the deleted axioms? (We want to avoid introducing an obsolete-relation counter-part for each existing one)
  • At least the ID and type of each individual and the relations (or the object property assertion) are required, preferably also the evidence is preserved.
  • A simple list/text field is not sufficient, as we probably need a machine readable format (to create redirects, obsolete pages, prevent duplicate annotation or at least warn users about it)
  • Where do we persist that information? In the model or as separate file?
• Use a full log of edits, persist this change history The most extreme would be to track all edits, WebProtege for example uses a binary-owl representation to append each axiom change.
  • Question: How do you quickly find all the relevant (deleted individuals and types) for validation or rendering (e.g. AmiGO) purposes in the log.
  • Pro: Persistent Undo-Redo over a server restart for free
  • Con: Relevant information about a model is split over multiple (at least two) files. Could this work with a triple store or other non-file persistence solutions