dr. M.S. (Matthijs) BerendsandClaude Opus 5.5 d683b9e7c6 (v3.0.1.9096) MO code registry: codes never change meaning, are never guessed, and are validated ...

- data-raw/microorganisms_files/: registry of all MO codes of every release since v2.0.0
  (78,992 codes, built from the git tags), approved renames, and README with the rules;
  decision by Matthijs S. Berends: MO codes from before v2.0.0 are not supported
- as.mo(): codes of earlier releases are translated deterministically via the internal
  MO_RETIRED_CODES (generated from the registry); unknown codes are no longer guessed
  (previously F_TRCHP, Trichophyton in v3.0.1, became Talaromyces chlamydosporus)
- synonym_mo_to_accepted_mo(): a missing target of one source no longer overwrites a valid
  target of another source (e.g. Chaetomium abuense), and no 'renamed to itself'
- taxonomy build: codes are reused and reserved from the registry instead of the development
  data (fixes 40 codes reused in the 2026 development data), also for phylum to family;
  synonym cycles are broken; dangling 'renamed to' identifiers are removed; the build stops
  on any broken integrity rule before saving
- run_microorganisms_build.R: runs the build in chunks at its checkpoints in one R process,
  with progress logging and resuming from any checkpoint; prompt updated accordingly
- tests: shared integrity rules (helper-microorganisms.R) used by build and testthat, registry
  tests over all codes, sentinel organisms, regression tests; current defects of the data on
  main are listed in microorganisms_known_defects.csv until the next rebuild

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

2026-10-03 11:45:25 +02:00

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