ARBA00027430 alcohol metabolic process (GO:0006066)

id: ARBA00027430
description: >-
  ARBA rule assigning GO:0006066 alcohol metabolic process through 83 alternative condition sets built
  from InterPro, CATH FunFam, PANTHER and taxon conditions.
status: IN_PROGRESS
rule_type: ARBA
rule:
  rule_id: ARBA00027430
  condition_sets:
  - number: 2
    conditions:
    - condition_type: INTERPRO
      value: IPR005522
      curie: InterPro:IPR005522
      label: Inositol polyphosphate kinase
      negated: false
    - condition_type: INTERPRO
      value: IPR038286
      curie: InterPro:IPR038286
      label: Inositol polyphosphate kinase superfamily
      negated: false
    - condition_type: TAXON
      value: Haplorrhini
      label: Haplorrhini
      negated: false
    notes: Inositol polyphosphate kinase family, Haplorrhini.
  - number: 4
    conditions:
    - condition_type: INTERPRO
      value: IPR004294
      curie: InterPro:IPR004294
      label: Carotenoid oxygenase
      negated: false
    - condition_type: PANTHER
      value: PTHR10543:SF57
      curie: PANTHER:PTHR10543:SF57
      label: RETINOID ISOMEROHYDROLASE
      negated: false
    - condition_type: TAXON
      value: Eukaryota
      label: Eukaryota
      negated: false
    notes: Carotenoid oxygenase family with a PANTHER subfamily, Eukaryota.
  - number: 5
    conditions:
    - condition_type: INTERPRO
      value: IPR008901
      curie: InterPro:IPR008901
      label: Alkaline ceramidase
      negated: false
    - condition_type: TAXON
      value: Chordata
      label: Chordata
      negated: false
    notes: Alkaline ceramidase family, Chordata.
  go_annotations:
  - go_id: GO:0006066
    go_label: alcohol metabolic process
    aspect: BP
  entries: []
  reviewed_protein_count: 0
  unreviewed_protein_count: 0
  created_date: '2021-10-20'
  modified_date: '2026-07-18'
  retrieved_date: '2026-11-09'
  source_condition_set_count: 83
review_summary: >-
  The live rule has 83 condition sets. Three (sets 2, 4 and 5) were read for the identity of their
  InterPro families; none was checked against annotated proteins. In GO, ethanol metabolic process
  (GO:0006067), thiamine metabolic process (GO:0006772), thiamine biosynthetic process (GO:0009228)
  and cholesterol metabolic process (GO:0008203) are is_a descendants of GO:0006066, so enzymes of
  those pathways are correctly described by the term. No false positive has been identified. No verdict
  is given.
action: UNDECIDED
action_rationale: >-
  The rule was not examined set by set. The term is general, but a general true term is not a wrong
  one, and no wrongly annotated protein is known.
suggested_modifications:
- Examine the condition sets against curated annotations of their Swiss-Prot members.
- >-
  Where a condition set selects one pathway, a more specific descendant of GO:0006066 (for example
  GO:0006067 or GO:0009228) could replace the general term for that set.
annotation_assessments:
- annotation_kind: GO_TERM
  value: GO:0006066
  label: alcohol metabolic process
  assessment: UNDECIDED
  notes: >-
    QuickGO is_a ancestors (2026-11-09): GO:0006067 ethanol metabolic process, GO:0006772 thiamine
    metabolic process, GO:0009228 thiamine biosynthetic process and GO:0008203 cholesterol metabolic
    process all have GO:0006066 as an ancestor. GO:0016126 sterol biosynthetic process and GO:0016125
    sterol metabolic process do not. No matched protein was checked.
corrections:
- date: '2026-11-10'
  withdrawn_claim: >-
    Enzymes of thiamine metabolism and ethanol metabolism are only tangentially related to alcohol
    metabolism and would be false positives.
  correction: >-
    These processes are is_a descendants of GO:0006066 in GO, so the annotation is true for them.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - >-
    QuickGO: GO:0006772 thiamine metabolic process is_a GO:0034308 primary alcohol metabolic process
    is_a GO:0006066
  - 'QuickGO: GO:0006067 ethanol metabolic process has ancestor GO:0006066'
  - 'QuickGO: GO:0008203 cholesterol metabolic process has ancestor GO:0006066'
- date: '2026-11-10'
  withdrawn_claim: Sterol biosynthesis sets should use GO:0016126 as a more specific term.
  correction: >-
    GO:0016126 sterol biosynthetic process is not a descendant of GO:0006066, so it is not a refinement
    of the rule's term.
  error_type: ONTOLOGY_MISREAD
  evidence:
  - QuickGO is_a ancestors of GO:0016126 do not include GO:0006066
- date: '2026-11-10'
  withdrawn_claim: The term is too broad, so the rule should be deprecated.
  correction: >-
    The previous text itself proposed descendant terms, which concedes the annotation is true; that
    supports refinement, not deprecation.
  error_type: GENERAL_IS_NOT_WRONG
  evidence:
  - GO:0006067 and GO:0009228 are descendants of GO:0006066
- date: '2026-11-10'
  withdrawn_claim: Literature contradicts the rule.
  correction: >-
    The cited source was a note that no literature search had been run; the assessment is removed.
  error_type: UNSUPPORTED_SOURCE
  evidence:
  - 'Previous supported_by reference_id: ANALYSIS_LIMITATION'
- date: '2026-11-10'
  withdrawn_claim: >-
    89 condition sets and inconsistent taxon restrictions show the rule is flawed (confidence 0.1).
  correction: >-
    No condition set had been recorded and no protein checked; size and taxon variety are not evidence.
  error_type: SIZE_AS_EVIDENCE
  evidence:
  - 'Previous file recorded condition_sets: []'
  - 'rest.uniprot.org/arba/ARBA00027430, 2026-11-09: 83 sets'