---
pathways:
  - id: urea_cycle
    module: urea_cycle
    reactome_root: R-HSA-70635
    organism: Homo sapiens
    scope: whole_subtree
    description: >-
      Import the full current Reactome urea-cycle subtree and compare it to the
      local urea_cycle module.

  - id: purine_nucleotide_interconversion
    module: purine_nucleotide_interconversion
    reactome_root: R-HSA-73817
    organism: Homo sapiens
    scope: curated_slice
    include_events:
      - R-HSA-111524
      - R-HSA-73794
      - R-HSA-73792
      - R-HSA-76590
    description: >-
      Keep the import focused on the four IMP-branch interconversion reactions
      that the local module cites under its executable reaction nodes.

  - id: bile_acid_synthesis_ring_modification
    module: bile_acid_synthesis_ring_modification
    reactome_root: R-HSA-192105
    organism: Homo sapiens
    scope: curated_slice
    include_events:
      - R-HSA-192051
      - R-HSA-192065
      - R-HSA-192097
      - R-HSA-192033
    description: >-
      Import the ring-modification slice of the larger Reactome bile-acid
      synthesis pathway so side-chain and conjugation reactions remain out of
      scope.
    manual_verdicts:
      - reactome_event: R-HSA-192033
        module_node: akr1d1_step
        module_annoton: akr1d1_activity
        verdict: wrong_go_branch
        reason: >-
          Reactome's own event evidence supports AKR1D1 delta4-3-oxosteroid
          5beta-reductase chemistry; the event is mapped to the
          alcohol-dehydrogenase NADP+ branch rather than the CH-CH donor branch.

  - id: gpi_anchor_core_glycan_assembly
    module: gpi_anchor_core_glycan_assembly
    reactome_root: R-HSA-162710
    organism: Homo sapiens
    scope: curated_slice
    include_events:
      - R-HSA-162857
      - R-HSA-162683
      - R-HSA-162830
      - R-HSA-162873
      - R-HSA-162821
    description: >-
      Import the GlcNAc-PI de-N-acetylation, inositol acylation, and first
      three mannosyltransferase reactions that form the local core-glycan
      assembly slice of the larger Reactome GPI-anchor biosynthesis pathway.

  - id: glycosphingolipid_lysosomal_degradation
    module: glycosphingolipid_lysosomal_degradation
    reactome_root: R-HSA-1660661
    organism: Homo sapiens
    scope: curated_slice
    include_events:
      - R-HSA-1606807
      - R-HSA-1606564
      - R-HSA-1605591
      - R-HSA-9769742
      - R-HSA-1606602
    description: >-
      Import the ARSA, GALC, GBA, SMPD1, and ASAH1 lysosomal reactions cited by
      the local degradation module; PSAP deliberately reuses the ARSA sulfatide
      reaction as lipid-presentation evidence.