Found reviewing the fix commit on PR #345 — it says the previous fix was cosmetic, and it is right.
1. #348's fix bought no auditable honesty. auditor.py does connected_taxa.update(taxonomy_by_term) for any COMMUNITY_LEVEL interaction. Interaction 3 is still COMMUNITY_LEVEL, so it credits all four taxa regardless of what interaction 1 does. The auditor reports 0 issues on the record both before and after the change. Removing that one scope: line from interaction 3 immediately yields DISCONNECTED: Archaea.
Archaea is named as source or target of exactly zero interactions. The change moved one blanket to a pairwise and left the blanket that was actually doing the hiding.
The real fix is interaction 4 (PREDATION, source_taxon: Viruses, no target_taxon): the record states hosts are bacterial/archaeal, so supplying the target connects Archaea for a stated reason rather than by blanket.
2. Interaction 1 as PAIRWISE MUTUALISM over-claims relative to its evidence. Its sole snippet is "Warming promoted saprophytic fungi and chemoorganoheterotrophic bacteria in root-associated environments" — co-occurrence under a treatment, not a directed relation. The description says bacteria "synergize with fungal decomposition by metabolizing low-molecular-weight organic compounds released during fungal litter breakdown": a one-directional benefit, so COMMENSALISM (+/0) or CROSS_FEEDING, not MUTUALISM (+/+). No fungal benefit from bacteria is stated anywhere in the record.
The interaction's own name, "Warming-Enhanced Saprophytic Decomposition", describes an abiotic-driver phenomenon — which is what COMMUNITY_LEVEL exists for. The fix made the record more specific without making it better supported.
Found reviewing the fix commit on PR #345 — it says the previous fix was cosmetic, and it is right.
1. #348's fix bought no auditable honesty.
auditor.pydoesconnected_taxa.update(taxonomy_by_term)for anyCOMMUNITY_LEVELinteraction. Interaction 3 is still COMMUNITY_LEVEL, so it credits all four taxa regardless of what interaction 1 does. The auditor reports 0 issues on the record both before and after the change. Removing that onescope:line from interaction 3 immediately yieldsDISCONNECTED: Archaea.Archaea is named as source or target of exactly zero interactions. The change moved one blanket to a pairwise and left the blanket that was actually doing the hiding.
The real fix is interaction 4 (
PREDATION,source_taxon: Viruses, notarget_taxon): the record states hosts are bacterial/archaeal, so supplying the target connects Archaea for a stated reason rather than by blanket.2. Interaction 1 as PAIRWISE MUTUALISM over-claims relative to its evidence. Its sole snippet is "Warming promoted saprophytic fungi and chemoorganoheterotrophic bacteria in root-associated environments" — co-occurrence under a treatment, not a directed relation. The description says bacteria "synergize with fungal decomposition by metabolizing low-molecular-weight organic compounds released during fungal litter breakdown": a one-directional benefit, so
COMMENSALISM(+/0) orCROSS_FEEDING, notMUTUALISM(+/+). No fungal benefit from bacteria is stated anywhere in the record.The interaction's own name, "Warming-Enhanced Saprophytic Decomposition", describes an abiotic-driver phenomenon — which is what COMMUNITY_LEVEL exists for. The fix made the record more specific without making it better supported.