Harmonize CHMO with OBI

[NRayya]

This issue summerizes the discussion and decisions made on the OBI Development Call on 09.02.2026. Please assign me.

CHMO was designed as an extension of OBI. Over the time, terms have been minted in CHMO that are also in scope of OBI. This caused the following issues:

1. Circular import in CHMO resulting from OBI importing from CHMO.
2. CHMO and OBI have equivalent classes

We propose the following solutions to be applied in OBI:

• Mint new term in OBI as a replacement to the same ones in CHMO. Here is the list of terms to be replaced:

  • light microscopy assay
  • fluorescence microscopy assay
  • fluorescence laser scanning microscopy
  • confocal fluorescence microscopy assay

• For all minted terms:

  • Reuse current CHMO hierarchy if more specific than in OBI (e.g., with CHMO:confocal laser scanning microscopy vs OBI:confocal fluorescence microscopy assay) as we agreed in the call that a full harmonization of such braches will be deferred to a later stage
  • Use CHMO definitions. Make sure to use Aristotelean structure in term definiton
  • Add an editor note explaining the the CHMO history
  • Add a term tracker item linking to this issue.

• Update the annotations (e.g. definition, synonyms, ..) of the following terms if CHMO equivalents provide better annotations:

  • OBI:microscopy assay to CHMO:microscopy
  • OBI:electron microscopy imaging assay to CHMO:electron microscopy
  • OBI:microscope to CHMO:microscope
  • OBI:electron microscope to CHMO:electron microscope
  • OBI:optical microscope to CHMO:optical microscope

• Update CHMO import module to exclude the matching terms from task 1

• Announce this upcoming change on OBO discuss mailing list

• Document this in the release notes of the resulting new OBI version

Here are all the issues that can be closed by closing this one:

• Harmonize CHMO:microscopy and OBI:microscopy assay #29
• harmonize CHMO_0000953 (microscope) with OBI_0400169 (microscope) branch #14