jaccard-signature-similarity: tier the Materials conditions and settle the taxonomy-coverage tension

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This issue revises ADR 0017 as part of #54; begin by reading that ADR, especially Materials and Steps 1, 2, and 4 at the cited lines. Align the requirement tiers and definitions across those sections, including taxonomy coverage and study identity. Done means the specified conditions agree and the distinction between input conditions and later steps remains clear.

Written by the indexing model from the issue text.

Description

protocol-revision

Part of #54. Validates today; this is the ADR 0017 revision.

Materials uses must three times (L56, L66, L71). The gaps:

Untiered in Materials

  • L53 "one unique identifier per signature." must; Step 1 L81 requires it.
  • L55 "Study identifiers, experiment identifiers, and direction labels for every signature." must when same_study_pairs or direction_pairing is non-default, otherwise should; the protocol does not say which.
  • L58 "a pinned taxonomy mapping capable of converting every input taxon to the selected rank." Materials implies full coverage; Step 2 L99-101 tolerates unmapped taxa by exclusion and recording. One of them should give. As written in Step 2 this is a should: warn, exclude, record.
  • L61 "taxonomic_rank: exactly one rank." must.
  • L63 "Select another rank before harmonization when scientifically justified." Prespecification; must.
  • L67 "direction_pairing: ... select only same-direction or only opposite-direction pairs before calculating the matrix." must.

Only in Steps, missing from Materials

  • L77 (Step 1): "Specify the source data version, the taxonomy version and mapping ... before inspecting similarity results." The versions are not in Materials.
  • L131 (Step 4): direction labels that match neither selected class must be defined and their handling recorded. Materials L56 covers only increased and decreased.
  • L133 (Step 4): "compare study identifiers after resolving them to the pinned study identity; do not infer study identity from a display label." A condition on what a study identifier is.

Not conditions on inputs

  • L86 "Do not select, remove, or pair signatures based on their eventual similarity values" and L162 (an output condition) stay where they are.

🤖 Drafted with Claude Code

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