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New command: ROBOT migrate

Open matentzn opened this issue 4 years ago • 3 comments

I am developing a new command for a few use cases that allows migrating terms easily from one IDSPACE to another, preserving provenance and the likes. Use cases include:

  1. IAO wants to cede 20 terms to ENVO. ROBOT migrate will select those terms, migrate them include the axiomatisation, and (configurable) mint new ids.
  2. Two overlapping ontologies want to sync up (ECTO and NCIT, NCIT and DO)

I am using ROBOT for this as it gives me most of the functionality I need - I don't want to discuss the design etc yet in too much detail, but I need an issue where I can collect some thoughts while I am doing the initial design.

matentzn avatar Jul 17 '21 13:07 matentzn

  • [ ] Ensure no accidental proxy merges
  • [ ] Ensure full provenance on all imported axioms, including term level

matentzn avatar Jul 17 '21 13:07 matentzn

This would be v useful for COB https://github.com/OBOFoundry/COB/issues/147

cmungall avatar Jul 29 '21 21:07 cmungall

@matentzn - did you make a start? for cob I am tempted to just do it using sed/perl replacements

not sure if it helps, but the analogous owltools command could help with requirements:

$ owltools --merge-equivalence-sets -h
--merge-equivalence-sets [-s PREFIX SCORE]* [-l PREFIX SCORE]* [-c PREFIX SCORE]* [-d PREFIX SCORE]* [-P PREFIX] [-x]      merges sets of equivalent classes. Prefix-based priorities used to determine representative member

cmungall avatar Aug 26 '21 21:08 cmungall