A deliberately partial setup, labelled as one (#183) - #542
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Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeeding gets a cultivation_setup with no system_type, no working_volume and no operating_temperature. What the source does state, for "all cultivation work", is the atmosphere: a Coy Labs anaerobic chamber under 70% N2 / 25% CO2 / 5% H2, with media sparged and reduced with l-cysteine and sugar solutions equilibrated in the chamber for 48 h before use. That phrasing covers the B. breve / R. gnavus cocultures, so it is theirs. For a strict-anaerobe gut community the chamber composition is a real fact about how it was grown, not a placeholder. The paper then defers the coculture's vessel, volume and temperature to "(Methods)", which the cached text does not carry. The 37 °C with shaking that does appear belongs to a 48 h inoculum recovery step, so recording it would be #529 for the sixth time in this batch. Padding the block out would have been easy and wrong. The empty fields and the reason for each are in notes, so a later curator with the full methods knows exactly what to add rather than having to re-derive what was already checked. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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What
Bifidobacterium_Ruminococcus_Infant_HMO_CrossFeedinggets acultivation_setupwith nosystem_type, noworking_volume, and nooperating_temperature.That is the point of this one.
What the source does state
The atmosphere, for "all cultivation work": a Coy Labs anaerobic chamber under 70% N₂ / 25% CO₂ / 5% H₂, with media sparged with N₂ and reduced with l-cysteine hydrochloride, and sugar solutions equilibrated in the chamber for at least 48 h before mixing — so the carbon source itself was anoxic when it reached the culture.
That phrasing covers the B. breve / R. gnavus cocultures, so it is theirs. And for a strict-anaerobe gut community the chamber composition is a real, citable fact about how it was grown — not a placeholder for the fields that are missing.
Atmosphere is in
controls_notesrather than as a per-culture setting, because it is controlled by the chamber, not by a headspace in each vessel.What it doesn't state
The paper defers the coculture's vessel, volume and temperature to "(Methods)", which the cached text does not carry. The 37 °C with shaking that does appear belongs to a 48 h inoculum recovery step — recording it would be #529 for the sixth time in this batch.
Why record anything at all
Padding the block out would have been easy and wrong. Leaving the record untouched would have thrown away a fact that is unambiguous and useful.
So the empty fields and the reason for each are written into
notes. A later curator with the full methods knows exactly what to add, and does not have to re-derive which numbers in that paper were already checked and rejected.Checks
just validate— no issuesjust validate-references— 0 issues; both 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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