Both arms of the biofilm consortium, not an average of them (#183) - #536
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Both arms of the biofilm consortium, not an average of them (#183)#536realmarcin wants to merge 1 commit into
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Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortium gets two cultivation_setup entries, because the paper ran two experiments on the same consortium and its result is the contrast between them. The planktonic arm: 18 x 150 mm Balch anaerobic tubes, 10 mL mGS-2, 150 rpm, 37 °C, with medium held under 5% H2 / 5% CO2 / 90% N2 in a Bactron II chamber until use. The biofilm arm: biofilms on medium plates moved to a fresh plate every two days, 37 °C, in an anoxic chamber, an oxic incubator, or both depending on the experiment — the oxygen regime is the variable, not a setting, so it is described rather than reduced to a field. Two enum approximations are labelled as such rather than left to look exact. A Balch tube is recorded as SERUM_BOTTLE, the nearest value for a butyl-stoppered anaerobic vessel, with the real vessel in instrument_detail. A surface-attached biofilm on a plate is OTHER, because FLASK or any reactor type would assert a containment this had none of. Unlike the last two records, neither arm here is a preculture — both are experiments on the consortium — so both belong. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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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What
Clostridium_Phytofermentans_Ecoli_Cellobiose_Biofilm_Consortiumgets twocultivation_setupentries, because the paper ran two experiments on the same consortium and its result is the contrast between them — temporal partitioning of anaerobic and aerobic metabolism within the biofilm.Planktonic arm: 18 × 150 mm Balch anaerobic culture tubes, 10 mL mGS-2 medium, 150 rpm, 37 °C, with medium held under 5% H₂ / 5% CO₂ / 90% N₂ in a Bactron II chamber until use.
Biofilm arm: biofilms on medium plates, transferred to a fresh plate every 2 days, 37 °C, in an anoxic chamber, an oxic incubator, or both depending on the experiment. The oxygen regime is the variable rather than a setting, so it is described rather than reduced to a field.
Two enum approximations, labelled as such
cultivation_setuphas no value for either vessel, and both notes say so rather than letting the approximation look exact:SERUM_BOTTLE— the nearest value for a butyl-stoppered anaerobic culture vessel — with the actual vessel ininstrument_detail.OTHER.FLASKor any reactor type would assert a containment this had none of.Different from the last two records
The previous two (#534, #535) both had preculture conditions sitting next to the community's in the same paper, and the work was deciding which to exclude. Here neither arm is a preculture — both are experiments on the consortium — so both belong, and the work was deciding not to collapse them into one.
Same underlying question each time: what is this number about. It just resolves the opposite way.
Checks
just validate— no issuesjust validate-references— 0 issues; all three snippets verbatimjust validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2375 passed, 16 skippedPart of #183.
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