# Per-organism flags for failing pathway terms.
# O = suspect over-annotation (organism appears to lack the ligand or receptor the term names).
# G = misapplied or generic term (another lineage's term, a regulation-type subterm, or a generic parent).
# Manual judgement (Claude Code, Oct 2026); the O calls rest on background knowledge, not checked data.
organism_flags:
  human:
  - term: GO:0008063
    name: Toll signaling pathway
    category: G
    note: Drosophila Toll pathway term applied to human IRAK/MYD88; TLR terms are the human equivalents.
  - term: GO:0033626
    name: positive regulation of integrin activation by cell surface receptor linked signal transduction
    category: G
    note: A regulation term that sits under the pathway branch; only CDH17 and P2RY12 annotated.
  - term: GO:1990117
    name: B cell receptor apoptotic signaling pathway
    category: G
    note: Annotated genes (BAX, NFKBIZ) are downstream apoptosis machinery.
  - term: GO:0038097
    name: positive regulation of mast cell activation by Fc-epsilon receptor signaling pathway
    category: G
    note: Single NR4A3 annotation to a regulation-flavoured subterm.
  fly:
  - term: GO:0031663
    name: lipopolysaccharide-mediated signaling pathway
    category: O
    note: Flies do not sense LPS through a TLR4-like route.
  - term: GO:0034142
    name: toll-like receptor 4 signaling pathway
    category: O
    note: No TLR4 orthology in flies.
  - term: GO:0048011
    name: neurotrophin TRK receptor signaling pathway
    category: O
    note: Flies have no Trk receptors.
  - term: GO:0033211
    name: adiponectin-activated signaling pathway
    category: O
    note: Flies have AdipoR but no adiponectin.
  - term: GO:0038158
    name: granulocyte colony-stimulating factor signaling pathway
    category: O
    note: Flies have no G-CSF.
  - term: GO:0038180
    name: nerve growth factor signaling pathway
    category: O
    note: Flies have no NGF.
  pombe:
  - term: GO:0007166
    name: cell surface receptor signaling pathway
    category: G
    note: Only pathway term used in pombe (on wsc1). The pheromone pathway has no pathway term at all;
      see the pombe section.