Grouping: omimFormerly, omimIncluded, & includedEntryInOMIM

[joeflack4]

Overview

Sub-tasks

• "Included" Decide if we want just want 1 property or 2
  • Update 12/16: Nico thinks 2.
• Decide implementation of omimFormerly and omimIncluded
  • a. Joe and Nico think best as synonym types. Edit: So far this is what Joe has done in create candidate mappings for ORDO based on OMIM equiv xrefs #167
  • b. We're currently (tentatively?) using them as annotation properties.
• Decide camelCase vs snake_case
  • Edit: Joe took liberty of of changing to UPPER_SNAKE_CASE per that comment, in create candidate mappings for ORDO based on OMIM equiv xrefs #167
• Remove redundant rdf:comments?
  • rdfs:comment "This term has one or more labels that end with ', INCLUDED'."
  • Edit: Joe took the liberty of removing in included / formerly refactor omim#167 due to us already having omimIncluded and omimFormerly

Sub-issues

• MONDO:omim_formerly mondo#8235
• "Alternative symbol" synonyms & "Formerly" - props rename omim#168
• included / formerly refactor omim#167
• Rename OMIM axiom annotation properties #698

[matentzn]

Just to reiterate:

[Term]
id: NI:CO
synonym: "Big G" EXACT ["MONDO:IncludedEntryInOMIM"]

Is something very different from

[Term]
id: NI:CO
synonym: "Big G" OMIM_INCLUDED EXACT []

Do not mix these two things up! The first case is source evidence. The second case is a synonym type property!

[joeflack4]

Nico says this usage is bad, e.g.:

• TERM MONDO:omimIncluded true
• TERM MONDO:includedEntryInOMIM true

Do this:

• synonym: "Big G" EXACT ["MONDO:IncludedEntryInOMIM"]
  • Should be an oboInOwl:source property

Want to do this way (using omim repo's new functional code):

            add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, title,
                [(oboInOwl.source, Literal('MONDO:includedEntryInOMIM')])

            add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, title,
                [(oboInOwl.hasSynonymType, URIRef(MONDONS['omimIncluded'])])

Edit 2025/01/03: I think actually it is:

            add_triple_and_optional_annotations(graph, omim_uri, oboInOwl.hasExactSynonym, title [
                 (oboInOwl.hasSynonymType, URIRef(MONDONS['omimIncluded'])),
                 (oboInOwl.source, Literal('MONDO:includedEntryInOMIM'))
            ])