Two records I curated from abstracts were wrong, not just thin (#183) - #577
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Acting on the lesson from the dental-biofilm record: I had been treating "abstract-only cache" as a property of the source rather than of the cache. Re-ran cache_fulltext.py over the seven records I had judged thin. Two fetched (+59 KB and +60 KB), four are genuinely not OA in Europe PMC, and one already had 95 KB cached that I had failed to search properly. Both fetched records turned out to contain errors, not just gaps. PET_Artificial_FourSpecies_Degradation_Consortium: cultivation_mode was BATCH. The methods show 10 mL of fresh Wn medium supplemented on days 2, 3 and 4 of a 7-day degradation. That is FED_BATCH. Also gained the UV-irradiated film, the wash-and-dilute-to-OD600=2 assembly, and triplicate runs. Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture: system_type was FLASK, inferred from the abstract's "50 mL shake cultures". The full text shows a sealed 100 mL serum bottle with the oxygen line entering through the seal. The seal is the point — a flask cannot hold a controlled oxygen transfer rate, and that rate is the entire mechanism of this mutualism. Corrected to SERUM_BOTTLE with the 50 mL recorded as working volume in a 100 mL vessel. Both errors were plausible readings of an abstract, and both would have stood indefinitely: linkml-validate accepts either value and the snippets validated throughout. The only thing that surfaced them was fetching text I had assumed did not exist. 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. |
This was referenced Aug 13, 2026
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The sweep
Acting on the lesson from #576: I had been treating "abstract-only cache" as a property of the source rather than of the cache. Re-ran
cache_fulltext.pyover the seven records I had judged thin on that basis.Both fetched records turned out to contain errors, not just gaps.
PET_Artificial_FourSpecies_Degradation_Consortium:BATCH→FED_BATCHThe methods show 10 mL of fresh Wn medium supplemented on days 2, 3 and 4 of a 7-day degradation. That is feeding, not a single charge.
Also gained: the PET film is UV-irradiated for 24 h before use, members are washed into Wn and diluted to OD₆₀₀ = 2 before combining, and each experiment is triplicate.
Clostridium_Saccharomyces_Cellulose_Ethanol_Coculture:FLASK→SERUM_BOTTLEI had inferred
FLASKfrom the abstract's "50 mL shake cultures". The full text shows a sealed 100 mL serum bottle with the oxygen line entering through the seal.The seal is the point. A flask cannot hold a controlled oxygen transfer rate — and that rate is the entire mechanism of this mutualism, since the yeast protects the anaerobe from oxygen in exchange for sugars. The 50 mL is the working volume in a 100 mL vessel.
Why this matters beyond two records
Both errors were plausible readings of an abstract, and both would have stood indefinitely:
linkml-validateacceptsBATCHandFED_BATCHequally, andFLASKandSERUM_BOTTLEequallyThe only thing that surfaced them was fetching text I had assumed did not exist. That is now a step in the workflow rather than an afterthought, and the four confirmed-not-OA records are recorded as such so the check is not repeated pointlessly.
Checks
just validateon both records — no issuesjust validate-referenceson both — 0 issuesjust validate-strict,just lint,just check-docs-current— exit 0uv run pytest tests/— 2422 passed, 16 skippedPart of #183.
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