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…ddressed); review committed Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…or addressed) Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…covery pass (B1): 27 Onygenales, 7 Aspergillaceae, 612 background Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
… (16 files); background is 619 genera, all pass Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
… adapter writes raw tables from them Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
… adapter writes raw tables from them Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…am join (B3), with tests Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…ts per pool and target (B4); gains and losses on the rooted tree still to wire in Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…asidiomycota; target and elsewhere counted apart Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
… (B5); tables; hand-off Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…gillus supplement (40 species, 8 clades); 52 new proteomes, 6 jobs Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…host-interaction tier Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…with UniLectin3D fungal table Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
… outputs Apply the 11 required changes of review 1: FleA role dispute, paracoccin (no lectin Pfam hit; GH18 only), one M1/M2 rule (host evidence and ubiquity), M1 coverage (16/43 sequences, 7/25 clusters), smoke caveat, N1 and six-proteome scan, Emp46/47 paper, wording fixes, D5 precedent, report text. Commit recount script, sequences, clusters and scan files. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Whole-proteome scan of the 653 discovery proteomes: PF07938 hits 392 genera (60%), not 28 (4%, pool S). The ungated call and the ubiquity rule do not match, so the stated rule gives an empty M1. Paracoccin identity and GH18 overlap, D7 label conflict, missed papers (Coltri 2006, Avr4, four Aspergillus papers). Review scripts and hits in analysis/lectin_class_spec/review2/. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
…akes extra model sets Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
… CBM_14 and Chitin_bind_1 whole-proteome scan, Avr4 and PF07938 truth scores Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…, options a/b/c, paracoccin, family label, Avr4 check, new papers) Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…eeds revision 4) Re-ran whole-proteome counts, a 25-proteome PF07938 rescan, SignalP 6, MMseqs2 clustering and a Pfam seed leakage check. Findings: option (c) has no build path in the current Pfam module code; CBM_14 meets the spec's own M1 rule; the pool S PF07938 set is 6 full-length Onygenales proteins plus 26 weak hits; Sakai 2019 measured knockout adhesion. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Option (c) rewritten against the code (c-i, c-ii), H1b rule made explicit with CBM_14 option, option (a2) and the pool S PF07938 population added, Sakai 2019 adhesion test, seed leakage, Candida_ALS_N, Slp1 and CBM18 papers, owner question 3 split. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…wo text fixes before owner) Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Pool S wording for the PF07938 Onygenales set, CBM_14 and Chitin_bind_1 in M2, Sakai 2019 detail in F14, F27 lengths and Pfam 38.2 count, (a2) floor note, small text fixes. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…revision 5 edits) Thirteen owner-approved edits: F14, F17, F20, F27, D7, D9, L3b row, sections 1 and 10, 6.2 item 6, and a change table. No decision is changed. Kerr 2016 dermatophyte genus names are marked not independently verified. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
This was referenced Oct 11, 2026
…dd owner questions 10 to 15 Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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Spec for a lectin class of cellsurface_sorting_hat (task 09). Spec only: no code, no change to categories.yaml, family_table.tsv, status files or adhesins.tsv.
Weakest points: the ranking of options is reasoning only (no performance data); the Sakai 2019 adhesion direction is not read in the full PDF; the 6 Onygenales PF07938 proteins come from the discovery pass and have no function paper or truth; most papers were read at abstract level only (spec section 10).
Do not merge: needs owner review.
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