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feat: minted keys, VRF seeds, RFC 9162 proofs, history roots, tag URIs and a transparency log

Keys (spec/02 §2.4), the rule paperstack settled on:
- A work key is a Scholar-style citation key, a hyphen and the first four
  Crockford base32 characters of SHA-256("scienting-key/1:" + identity),
  where the identity is the first of doi, arxiv, isbn, pmid, pmcid and
  openalex in same_as, else the folded title, year and family name. A
  collision lengthens the later key by two characters; a key is minted
  once and never recomputed. A document key adds .si, .v<seq> or .<type>
  for versions other than the version of record.
- Every fixture key is now minted (hale2026harmonic-damb,
  okafor2025solvent-acth, writer2027fixed-ynr7.v3, tiny2026tiny-j4qm), so
  every node and record ID was re-minted and the docs rewritten to match.
  The validator checks the document key against the work key and version
  (doc.key.work) and the hash part against the identifier (doc.key.suffix).
  vectors/keys.jsonl pins the cases paperstack's tests pin.

Review:
- Spot-check seeds are ECVRF-EDWARDS25519-SHA512-TAI proofs (RFC 9381),
  implemented in tools/oracle/vrf.py in plain Python and reproduced
  against the RFC's Example 16; the sample ranks by the VRF output. The
  earlier Ed25519 seed could be ground by a dishonest checker.
- RFC 9162 inclusion and consistency proofs (crypto.inclusion_path,
  verify_inclusion, consistency_proof, verify_consistency) with
  scienting-proof/1, vectors/proofs.jsonl and two fixture records.
- document.json carries `history`, the root over the corrections, with
  the empty-tree hash for none (spec/11 §11.5, rule doc.history).
- A provisional transparency log (spec/23): log entries, signed-note
  checkpoints with key hashes as transparency logs share them, the rule
  that a logged revocation beats a self-asserted time, and vectors.
- Reserved signature schemes cose and ml-dsa-65 (spec/08 §8.4).

Identifiers and text:
- urn:scienting: becomes tag:scient.ing,2026: (RFC 4151), since the URN
  namespace was never registered.
- Unicode 16.0 is pinned for normalization and categories (spec/01 §1.4);
  the checker refuses another version.

Checking:
- check.py: keys, proofs, VRF and checkpoint vectors; the proof and
  checkpoint records; a check that every ID and hash the prose quotes
  exists in the fixtures or vectors; three more broken packages
  (history-wrong, key-suffix, key-work).
- stress.py: key, VRF, proof and checkpoint properties.
- Docs: a keys section in the concepts and FAQ, rationale entries for
  keys, VRF, proofs, tag URIs and the Unicode pin, a "Looking ahead"
  section, media-type registration and OCI distribution notes.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>

2026-10-14 23:21:57 -04:00

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18. Layers and annotations

Everything people and models add to a document is an annotation, and annotations are grouped in layers. scienting-layer/1 is the W3C Web Annotation Data Model with the anchor as a selector, so any Web Annotation tool can read it. The JSON-LD context is context/scienting-1.jsonld, published at https://paperspec.scient.ing/context/scienting-1.jsonld.

18.1 One rule decides what is a claim and what is a layer

If a statement is true independently of this paper, it belongs in a claim store as a claim, where it is checked and leveled. If it is about reading this paper, it belongs in a layer, where it is attributed and signed but not checked.

18.2 The layer

A layer is a folder with layer.json and annotations.jsonl. layer.json is an AnnotationCollection with the two contexts, format, an id of the form tag:scient.ing,2026:layer:<store>/<record id>, a label, a purpose, an audience (novice, student, expert or mixed), a visibility (private, team or public), a license (CC BY 4.0 by default when public), its creator, created, its project, the docs it annotates and its total. A reader turns layers on and off, and the audience dial picks the level of glosses.

18.3 The annotation

Each line of annotations.jsonl is a W3C Annotation:

Property	Holds
`@context`	`["http://www.w3.org/ns/anno.jsonld", "https://paperspec.scient.ing/context/scienting-1.jsonld"]`.
`id`	`tag:scient.ing,2026:annotation:<store>/<record id>` (4.6).
`type`, `layer`	`Annotation`, and the layer's ID.
`motivation`	A W3C motivation: `commenting`, `describing`, `linking`, `questioning`, `assessing`, `replying` and the others.
`creator`, `created`, `modified`	An agent `{id, type, name}`, with `type` `Person` or `Software`, and times.
`body`	One body (18.4).
`target`	A `SpecificResource` whose `source` is `tag:scient.ing,2026:doc:<store>/<key>` and whose `selector` lists an `AnchorSelector` holding a `scienting-anchor/1`, optionally followed by a W3C `TextQuoteSelector` for tools that do not know ours; or, for a reply, a `SpecificResource` whose source is another annotation.
`status`	`proposed`, `confirmed`, `rejected` or `withdrawn`. A model's annotation is `proposed` until a person confirms it.
`receipt`	For a confirmed annotation, the receipt that covers it.

The TextQuoteSelector, when present, repeats the anchor quote's exact, prefix and suffix, with an empty string for a prefix or suffix the quote lacks. It is present only when the anchor's quote is plain text; an anchor whose quote is hashed or keyed (6.3) has none, so the fallback never shows text the anchor withholds.

An annotation's content hash is SHA-256 of the canonical JSON of the annotation without status, receipt and modified. A confirmed annotation is covered by its confirmer's receipt, which lists ["annotation", <record id>, <content hash>]. Replies are annotations that target annotations, so discussions are threads anchored to sentences.

18.4 Bodies

`kind`	W3C type	Adds	Says
`gloss`	`TextualBody`	`audience`	An explanation at `novice`, `student` or `expert` level.
`claim-link`	`SpecificResource`	`source` (`lode:<tag>`), `pin`, `role`	That the span `states`, `uses` or `disputes` a claim.
`symbol`	`SpecificResource`	`source`, `pin`, `symbol`	That this occurrence of a symbol is a symbol claim.
`comment`	`TextualBody`		A remark, opinion or interpretation.
`caveat`	`TextualBody`		A warning a reader should see.
`question`	`TextualBody`	`for`	A question for a `reader`, a `group` or the `authors`.
`exercise`	`TextualBody`	`exercise`	A task with a key and a rule (19).
`citation-context`	`TextualBody`	`reference`, `verdict`, `reason`	Why a sentence cites a reference, and whether it supports it.
`prerequisite`	`SpecificResource`	`source`	What to read or know first.
`crosslink`	`SpecificResource`	`source`, `selector`	That the span corresponds to a span in another document.
`translation`	`TextualBody`	`language`	The span in another language.
`description`	`TextualBody`	`role`	A description of a figure, panel or table for readers who cannot see it: `alt`, a short text equivalent, or `long`, a full description.
`generated`	`TextualBody`	`generator`	Text a model wrote about the span; never mistaken for source.

A textual body has a value, and optionally a format (text/plain or text/markdown) and a language. Nothing a model writes is ever stored as source text. A model may propose a description, and like any annotation it stays proposed until a person confirms it; an accessible export uses confirmed descriptions only, and a figure with none has no description. Other text a model writes about a span, such as a summary, is a generated annotation, which names its generator. fixtures/records/layer/ holds a layer with one annotation of each common kind and the receipt that confirms some of them.

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