Thiele-Palsson score mapping + verified ECO ids - #80
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Add thiele_palsson_score(reaction): the Thiele & Palsson reconstruction confidence score (0-4) derived from the gene_association facet's basis (gpr+literature -> 3, gpr -> 2, no-gpr -> 1), the facet that captures reaction-inclusion evidence. Grounded in the correspondences already asserted in score_gene_association_confidence. Respects the study doc's two cautions: the map runs forward only (basis -> score), so the ambiguous Thiele-Palsson 2 is never reverse-mapped to an evidence class, and curated is left unmapped (a curator's assertion does not name its evidence class). The ECO evidence-class ids in §9 were each verified against EBI's ECO (OLS) - ECO:0000044 sequence similarity, ECO:0000015 mutant phenotype, ECO:0000002 direct assay - and the assertion-method term ECO:0000305 is explicitly excluded as it is not an evidence class. Docs: §9 gains the concrete basis -> score -> ECO table; §10.3 marked mapping-shipped. Tests for the mapping and the end-to-end basis path.
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Maps the confidence facets onto the field's standard vocabulary — the Thiele & Palsson reconstruction score and ECO evidence terms — so the confidence record is interoperable rather than bespoke.
Changes
thiele_palsson_score(reaction) -> int | None— the Thiele & Palsson reconstruction confidence score (0–4), derived from thegene_associationfacet'sbasis:gpr+literature→ 3,gpr→ 2,no-gpr→ 1. It maps from the evidencebasis, not from a support-strengthlevel. The map runs forward only, so the ambiguous Thiele-Palsson 2 is never reverse-mapped to an evidence class, and acuratedcall (which names no evidence class) maps toNone.ECO:0000044(sequence similarity),ECO:0000015(mutant phenotype),ECO:0000002(direct assay).ECO:0000305("curator inference used in manual assertion") is flagged as an assertion method, not an evidence class.