Model ROS detoxification as the process it was already described as (#297) - #495
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…297) #296 rehomed an orphaned note onto a `metabolites` entry reading "Reactive oxygen species detoxification is an inferred interaction process" - a note that says *process* while sitting on a compound. #297 recorded that as a modelling question rather than a defect, and left the choice open: compound, process, or both. Both, because the record already asserted both in prose. CHEBI:26523 is the species; GO:0098869 `cellular oxidant detoxification` is what is done to it. Grounding the process adds no new claim - it makes the claim the note already made machine-readable. GO:0098869 chosen over two nearer-looking terms: * GO:0141082 "symbiont-mediated detoxification of host-generated reactive oxygen species" would assert a host-symbiont relation this consortium does not have - Trichodesmium and Alteromonas are a consortium, and the ROS is photosynthetic rather than host-generated. * GO:0061692 is hydrogen peroxide only, where the record says ROS generally. GO:0098869's definition - "reduces or removes the toxicity of superoxide radicals or hydrogen peroxide" - is the general oxidant case and matches. Verified non-obsolete, canonical label; the id-label gate goes 6094 -> 6095 OK_CANONICAL with no exceptions added. #297 also asks whether the other two "inferred interaction axis" metabolites - phosphate and iron(2+) - want the same treatment. Checked, and the answer is no, for a reason worth recording: clean GO terms exist (GO:0006826 iron ion transport, GO:0006817 phosphate ion transport) but both are *cellular transport* processes, while the record's notes describe ecological *acquisition axes*. Grounding them would introduce a claim the record does not make - the same over-claiming that rules out GO:0141082 above. The ROS case is different precisely because its note already named the process. The new entry inherits the interaction's COMPUTATIONAL evidence; this is the inferred axis the source names, not a measured one. docs/ regenerated - the #477 gate caught the stale page, which is what it is for. 2364 passed, validate-strict 0 errors.
Network integrity findingsWarnings only — a member with no interaction yet, or a participant matched by ontology id rather than by name, or one on a community-level interaction that resolves to no member. Reported, but does not fail the build. The full report is attached to the workflow run as an artifact. |
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Closes #297, taking the "both" option.
The choice
#296 rehomed an orphaned note onto a
metabolitesentry reading "Reactive oxygen species detoxification is an inferred interaction process" — a note that says process while sitting on a compound. #297 recorded that as a modelling question and left it open: compound, process, or both.Both, because the record already asserted both in prose.
CHEBI:26523is the species;GO:0098869cellular oxidant detoxification is what is done to it. Grounding the process adds no new claim — it makes the claim the note already made machine-readable, which is the objection #297 raised against introducing a GO term on a record whose sourcing is inferential.Why GO:0098869 and not the nearer-looking terms
GO:0141082symbiont-mediated detoxification of host-generated ROSGO:0061692cellular detoxification of hydrogen peroxideGO:0098869's definition — "reduces or removes the toxicity of superoxide radicals or hydrogen peroxide" — is the general oxidant case and matches the note exactly. Verified non-obsolete with canonical label; the id↔label gate goes 6094 → 6095 OK_CANONICAL with no exception added.The follow-up question #297 asks
Checked — and the answer is no, for a reason worth recording. Clean terms exist (
GO:0006826iron ion transport,GO:0006817phosphate ion transport), but both are cellular transport processes while the record's notes describe ecological acquisition axes. Grounding them would introduce a claim the record does not make — the same over-claiming that rules outGO:0141082above.The ROS case is different precisely because its note already named the process. That distinction is the whole basis for treating one differently from the other two, so it is in the record's notes rather than only here.
Verification
linkml-validate: no issuesvalidate-strict: 0 ERROR rows✅ All id↔label pairs correspond2364 passed, 16 skippeddocs/regenerated — the Stop publishing a plant's taxon id for a bacterium, and gate docs/ (#442) #477 gate caught the stale page and refused until it was committed, which is exactly what it exists for.The new entry inherits the interaction's
COMPUTATIONALevidence; this is the inferred axis the source names, not a measured one.🤖 Generated with Claude Code