Automate mapping of deprecated terms in use

[dosumis]

This is, IMO, a major missing component of the ODK

• MVP - generate a report of mappings for obsoleted terms every time imports are updated. We already have suitable SPARQL for finding mappings src/sparql/obsoletes.sparql.

  • This should be extended to:
    • Report label and comments on obsoleted term if present
    • Report label of mapped term
    • Report if ID of obsolete term is the value of an OboInOWL#alt_id axiom (this indicates obsoletion was due to OBO merge.
  • Potential problems:
    • lack of range restrictions or checks on the value of replaced_by & consider axioms could cause problems for mapping to term referred to. We need to support the following possibilities:
      • OBO curie - type string
      • IRI (typed)
      • short_form ID (?)
    • Too complex to support all of above in SPARQL?

• Complete functionality

  • ODK option to auto-update editors file & template tsvs for every obsolete term for which there is a single replacement mapped via 'replaced_by'. Automated update should be accompanied by a report of all mappings.

[dosumis]

@matentzn - can this be added to board for Monday tech calls?

[matentzn]

Ok, but lower priority, @shawntanzk

[shawntanzk]

covered by: https://github.com/INCATools/ubergraph/issues/77