Resolve canonical examples for the 30 resolvable remaining traits (corpus 312/312 microbial+cited)#138
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Deep-research pass over the traits that still lacked canonical examples. Of the 173 CLASS traits without examples, ~143 genuinely cannot take a single-organism example (numerical bins like ph_optimum_mid1 / temperature_range_*, gc_* and genome-size value bins, the 20 observation/ measurement classes, quantitative_property/, abstract parents such as pigmentation / gram_stain / cell_shape / metabolism / *_preference / habitat_association, and biosafety_level_4/5) and are intentionally left empty; the 94 OBJECT_PROPERTY and 7 DATATYPE_PROPERTY relational predicates likewise have no organism exemplar. The ~30 genuinely-resolvable phenotype classes get 1-2 representative microbes each (225 traits / 312 entries total now): - fine-grained trophic types (chemo/litho/photo-litho/photo-organo/phototrophic, chemoheterotrophic, organotrophic, copiotrophic, ...) - distinctive shapes/pigments (curved, spindle, black-pigmented, green-pigmented) - electron_transfer, lignin_degradation, substrate_level_phosphorylation - categorical tolerances (alkaphilic, obligately_acidophilic, facultatively_alkaphilic, piezotolerant, non_halophilic, euryhaline) - genomics features (genomic_island, prophage, transposable_element, mobile_genetic_element, plasmid_carriage, rrna_operon_copy_number) - Microbe gate: every taxon_id verified under Bacteria/Archaea via ncbitaxon.db entailed-edge closure. Full corpus now 312 entries, 312 microbial, 312 cited. - Citations from a deep-research confirmation workflow (each agent verified the organism fits the trait and the identifier resolves). 2 uncited entries (Clostridium botulinum for spindle_shaped, Enterococcus faecium for mobile_genetic_element) were dropped in favour of their cited co-representatives. - just validate-strict: 0 errors. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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What
A deep-research pass over the traits that still lacked canonical examples, answering "what about the remaining traits?"
Triage of the 173 CLASS traits without examples
~143 genuinely cannot take a single-organism example and are intentionally left empty:
ph_optimum_mid1,temperature_range_*,*_delta_*,gc_*,genome_size, all*_phenotype_with_numerical_limitsobservation/measurement classes +quantitative_property/pigmentation,gram_stain,cell_shape,metabolism,*_preference,habitat_associationbiosafety_level_4/5(no standard bacterial exemplar)(The 94
OBJECT_PROPERTY+ 7DATATYPE_PROPERTYrelational predicates —uses_as_carbon_source,has_observation,does_not_*— likewise have no organism exemplar.)The ~30 resolvable phenotype classes → 1–2 representative microbes each
fine-grained trophic types (chemo/litho/photo-litho/photo-organo/phototrophic, chemoheterotrophic, organotrophic, copiotrophic); distinctive shapes/pigments (curved, spindle, black-/green-pigmented);
electron_transfer,lignin_degradation,substrate_level_phosphorylation; categorical tolerances (alkaphilic, obligately-acidophilic, facultatively-alkaphilic, piezotolerant, non-halophilic, euryhaline); genomics features (genomic island, prophage, transposable element, mobile genetic element, plasmid carriage, rRNA-operon copy number).Method & integrity
ncbitaxon.dbentailed-edge closure.falconwas also run as a cross-check (it produces causal-graph research reports rather than example organisms).Final corpus
just validate-strict: 0 errors.🤖 Generated with Claude Code