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AMR/data-raw/microorganisms_files/README.md
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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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MO code registry

MO codes (such as B_ESCHR_COLI) are stored by users in their own data, sometimes for years. A code must therefore always mean the same taxon, in every future version of the AMR package. This folder contains the registry that guarantees this.

Files

File Contents
mo_code_registry.csv Every MO code that was ever part of a released version of the AMR package since v2.0.0, with the taxon it denotes (name, rank, domain, genus, species, subspecies), the first and last release it was in, and older names of the same code (e.g. a corrected spelling).
build_mo_code_registry.R Recreates mo_code_registry.csv from the git tags of all releases. Run it after every new release.
mo_code_renames.csv The only allowed exceptions: registered codes that get another name, because it is the same taxon (e.g. a corrected spelling or a renamed species group). Every row needs approved_by and approved_date.

Rules

  1. Only releases count. Development versions (the main branch) are never part of the registry. Codes that only existed in a development version carry no weight and may be reassigned.
  2. Codes from before v2.0.0 are not supported. Decision by Matthijs S. Berends, 3 October 2026: MO codes from releases before v2.0.0 (12 March 2023) are not supported. Every code in all releases since v2.0.0 has always meant the same taxon (checked on 3 October 2026), so the registry starts without conflicts.
  3. A registered code is never given to another taxon. The taxonomy build (data-raw/_reproduction_scripts/reproduction_of_microorganisms.R) reuses the code of every taxon in the registry (most recent release first), never gives a registered code to a new taxon, and stops if a registered code would get another name than in the registry, unless that is listed and approved in mo_code_renames.csv.
  4. A registered code that is no longer in the data still works. as.mo() translates it to the current code of the same taxon (by its name, so also if the taxon moved to another domain), using an internal lookup table (MO_RETIRED_CODES) that is created from the registry in data-raw/_pre_commit_checks.R. If the taxon is no longer in the data at all, the result is NA with a warning. The package never guesses.
  5. Tests enforce all of this. tests/testthat/test-data-microorganisms.R checks the current data against the registry and the renames, and checks that every registered code resolves to its own taxon.

After a release

  1. Make sure the git tag of the release exists (e.g. v3.1.0).
  2. Run source("data-raw/microorganisms_files/build_mo_code_registry.R") from the root of the repository.
  3. Review the changes to mo_code_registry.csv (git diff): only new codes may be added, and existing codes may only get a later last_release. Commit the result.
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