Cheese rind: the in vitro arm only, and OMM12 refused (#183, #543) - #545
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Cheese rind: the in vitro arm only, and OMM12 refused (#183, #543)#545realmarcin wants to merge 1 commit into
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Cheese_Rind_InSitu_InVitro_Model_Community: communities reconstructed on cheese curd agar from roughly equal inocula, followed over time by pulling agar plugs from 96-well plates and counting CFUs, plates at room temperature. Only the in vitro arm is recorded. The record also covers an in situ survey, and sampled cheese rind is not a cultivation — the same distinction that made Avena_Rhizosphere unenrichable, except that here one paper supplies both and only one belongs in this slot. system_type is OTHER: an agar-plug community in a 96-well plate has no enum value, and FLASK or a reactor type would assert a liquid culture this is not. No operating_temperature either — the source says "room temperature", and turning that into 20 or 25 °C would invent precision the paper declined to give. OMM12_Gnotobiotic_Mouse_Gut_Community was checked and refused. Its in vitro step is per-strain revival from glycerol cryostocks into 100 ml serum bottles before the mixture is inoculated into germ-free mice; the community itself lives in the animal. Recording those bottles would be the preculture error, and a gnotobiotic mouse is not a CultivationSetup. Two of the thirteen full-text candidates in #543 are now known to be host-associated or environmental rather than cultured. The remaining plant SynComs and the second gut community likely need the same check before anyone treats that list as a work queue. 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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The record curated
Cheese_Rind_InSitu_InVitro_Model_Community— communities reconstructed on cheese curd agar from roughly equal inocula, followed over time by pulling agar plugs from 96-well plates and counting CFUs, plates at room temperature.Only the in vitro arm. The record also covers an in situ survey, and sampled cheese rind is not a cultivation — the same distinction that made
Avena_Rhizosphereunenrichable, except that here one paper supplies both and only one belongs in this slot.The medium is treated as the point rather than a detail: cheese curd agar is what makes the in vitro system recapitulate in situ succession, which is the paper's central claim.
Two fields left empty with reasons:
system_typeisOTHERbecause an agar-plug community in a 96-well plate has no enum value, andFLASKor a reactor type would assert a liquid culture this is not. Nooperating_temperature, because the source says "room temperature" and turning that into 20 or 25 °C would invent precision the paper declined to give.OMM12 checked and refused
OMM12_Gnotobiotic_Mouse_Gut_Communityhas a "Bacterial Cultivation" section with everything you could want: anaerobic chamber at 3% H₂/rest N₂, 100 mL Wheaton glass serum bottles with butyl rubber stoppers, 10 mL of Anaerobic Akkermansia Medium.All of it is per-strain revival from glycerol cryostocks, before the mixture is inoculated into germ-free mice. The community lives in the animal. Those bottles are precultures, and a gnotobiotic mouse is not a
CultivationSetup.The list in #543 is not a work queue
Two of thirteen candidates now refused, one partially curatable. I've added a predicted classification of the remaining ten to #543 — five likely refusals (plant SynComs and a second gut community, all with OMM12's shape), three likely curatable, one possibly in silico. If that holds, the tractable remainder is three or four records, not thirteen.
The pattern underneath is worth stating: in every refusal, the paper does contain real cultivation numbers — for the strains individually. That is exactly why these records rank highly on any automated filter, and why the refusal always takes reading. A SynCom paper almost always describes growing its members; describing growing the community is a different sentence, and sometimes it does not exist.
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. Advances #543.
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