My #543 prediction was wrong, and that is the useful part (#183, #543) - #549
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realmarcin wants to merge 2 commits into
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My #543 prediction was wrong, and that is the useful part (#183, #543)#549realmarcin wants to merge 2 commits into
realmarcin wants to merge 2 commits into
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Cyprus_Copper_Sulphide_Bioleaching_Consortium: sampled from packed bioleaching column SC3 at the Skouriotissa Mine, then maintained at 28 °C without agitation and sub-cultured ten times at 5% inoculum every two months in MAM with 0.25 g of unsterilised chalcopyrite, before being split onto chalcocite as well. The mineral is in the setup rather than only among environmental factors because it is the growth substrate and the experimental variable at once — the study is about how mineral type drives composition. It is also deliberately unsterilised, which is a choice about what the community is allowed to encounter. Static, recorded for the same reason as the thermophilic cellulose and TCE records: a mineral-attached acidophile consortium grows on a settled solid surface, so "without agitation" is a design decision, not an omission. No system_type or working_volume — the source names neither for the sub-cultures. The packed column is the field source, not the laboratory setup; recording it would describe where the community was found rather than how it was grown. This completes the three "likely curatable" predictions in #543, and it is the closest call of them. The community originates in a column at a mine, which is the shape that made Avena_Rhizosphere unenrichable. What separates them is that this one was carried into the laboratory and propagated for ten passages. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
ORNL_PMI_Populus_PD10_SynCom: the ten-member community was assembled and passaged in liquid medium — each strain grown alone for 48 h, normalised to the lowest OD600, equal volumes mixed, then triplicate cultures incubated 48 h at 30 °C with shaking at 200 rpm and passaged every 48 h at 1:10. I predicted this one a likely refusal in #543, reasoning that a plant-associated SynCom lives on the plant. It does not, in this study: it never touches a Populus root here. The prediction was a guess dressed as a classification, and it took one grep to falsify. That matters more than the record. #543 lists five "likely refuse" candidates on the same reasoning, and one of the five has now failed. The remaining four need reading rather than inheriting the guess, which is exactly the point that issue was filed to make about automated ranking. Both media are named rather than one: the study asks whether the same ten strains form different stable communities in R2A and in MOPS, so recording one would misrepresent the design. No system_type or working_volume. The 10 mL test tubes in the source are the individual seed cultures; the paper does not say what the community passages ran in, and carrying the seed vessel across would be the preculture error again. 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
ORNL_PMI_Populus_PD10_SynCom— the ten-member community was assembled and passaged in liquid medium: each strain grown alone for 48 h, normalised to the lowest OD₆₀₀ in that medium, equal volumes mixed so all ten started at roughly equal concentration, then triplicate cultures incubated 48 h at 30 °C with shaking at 200 rpm and passaged every 48 h at 1:10.The prediction it falsifies
I classified this one "likely refuse" in #543, reasoning that a plant-associated SynCom lives on the plant. It does not, in this study — it never touches a Populus root here.
That was a guess dressed as a classification, and it took one grep to falsify.
This matters more than the record. #543 lists five "likely refuse" candidates resting on that same single inference — plant-associated ⇒ grown on a plant — and one of the five has now failed. The remaining four need reading rather than inheriting the guess, which is precisely the point that issue was filed to make about automated ranking. The correction is the same lesson applied to my own shortcut: a plausible rule over record names is still a rule over record names.
Running tally after six of thirteen read: 2 refused, 1 partial, 4 curated — and the only wrong call was the one made without reading.
Two curation notes
Both media are named, not one. The study asks whether the same ten strains form different stable communities in R2A versus MOPS, so recording a single medium would misrepresent the design.
No
system_typeorworking_volume. The 10 mL test tubes in the source are the individual seed cultures; the paper does not say what the community passages ran in. Carrying the seed vessel across would be the preculture error (#529) — the same one avoided in six other records this batch.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. Corrects #543.
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