Review · Biological notes · Original-reading scope · Evidence inventory · Context archive
The review contains 71 original contexts: 25 ACCEPT, 20 KEEP_AS_NON_CORE, 12 MODIFY, 7 REMOVE, 4 UNDECIDED and 3 MARK_AS_OVER_ANNOTATED. There is one catalytic core, four natural products, 53 reference assessments and no NEW annotation. The raw NOT lipopolysaccharide context is retained with an explicit endpoint-specific consistency exception; the source comparison is documented in the original-reading page. Seven literal location/cell-type atoms are restored without inventing a natural-product assignment.
The current parser produces 70 keys because two positive AHSA1 interaction records differ only in original ID, date and assigning database. Both remain existing annotations. The archive keeps every raw field, null, ordering and extension expression, the raw-to-planned permutation, exact product sequences, and historical Git locators. It also retains all 63 historical quotation associations with their verification outcomes; three nonmatching old strings are preserved as historical locators, not endorsed as current quotations. Eight source-retired old contexts remain accessible in the immutable old review. Retirement alone is not a biological refutation.
The three IBA assertions were checked against the actual PANTHER tree, alignment, target sequence and ancestral placements. Source URLs and hashes in the evidence inventory identify the original tree/MIA/MSA/attribute files; the PAINT TSV alone is not evidence for all those claims. Human self-donor entries are legitimate experimental grounding. Typed refinements distinguish is_a from part_of.
Five short current excerpts are centralized in the core and reference findings. Their exact source bytes, offsets and aggregate word counts are recorded in the evidence inventory. Annotation-level reference-only links point to the same assessed sources without repeating quotations. Reference availability flags describe reviewer access to original text; normal-cache coverage and the exact inspected sections are documented separately. A full-text cache flag does not mean every figure, supplement or experiment was inspected.
The published fad08 predecessor's genuine refresh and native seeding reproduced all 71 original contexts and 70 parser keys. Both distinct AHSA1 originals are retained in the 71-row review, with seven exact atoms and the NOT qualifier. All 65 source records are present: 36 reused unchanged and 29 acquired only because they were missing. All selected titles and five excerpts match the native caches. Reviewer availability remains distinct from cache extraction scope. Default validation, strict matching of all 71 original GOA contexts, computed-status audit, history validation, scoped whitespace and private rendering passed. That predecessor's computed status was DRAFT, with four annotation advisories: positive/NOT LPS contexts, differing source-specific LPS actions, missing structured IBA metadata and the unused inherited Falcon report. All 65 source bytes and the ontology cache remain unchanged after acquisition. No provider report was generated during this review; the inherited falcon report and its historical role remain preserved.
The follow-up specifies GO:0034615 for the catalytic assembly and core complex membership. The current 71 machine contexts, five exact excerpts, four products and complete archive are unchanged. Default validation and strict matching of all 71 original GOA contexts passed. Computed status remains DRAFT with three annotation advisories: differing source-specific LPS actions, missing structured IBA refinement metadata and the unused inherited Falcon report. The positive/NOT LPS pair is informational under its explicit consistency exception. History, status audit, private rendering and scoped whitespace passed; all 65 source records remain unchanged. The only generated cache addition is GO:0034615 GCH1 complex.