paperspec/docs/glossary.md

Glossary

A scientific paper changes after it is published: errata appear, readings get corrected, annotations pile up. paperspec is a set of file formats for scientific papers that keeps each sentence findable through those changes (repository: https://git.scient.ing/infra/paperspec). This glossary defines its terms for readers from newcomer to expert, implementers included. Each entry gives the plain meaning, then the precise one, then the chapter that defines it.

A hash is a fixed-length fingerprint of data; changing one character changes it. SHA-256 is the hash function the formats use. The specification is at version 0.1.0, and each format is candidate or provisional in registry/formats.json. Format names begin with scienting-, as in scienting-doc/1; that prefix is the formats' namespace, a separate matter from the repository's name. "Outside term" marks a standard from another project.

Address

A string that names one node, optionally pinned to its state by the first six digits of its node_hash and narrowed to a span of code points (numbered characters of text): key#id@hash6[start:end]. (6.1)

Alias

A legacy ID kept so that old references still lead to the node that now holds their text. (4.3)

Align key

A hash of a node's lossy projection, used only to propose that two readings hold the same sentence; it never certifies anything. (5.1)

Anchor

The stored form of a pinned address, with its quotation and context, so that a reference can be found again after the text changes. It resolves as current, changed below, moved, reattached or stale. (6.2, 6.5)

Asset store

Where a team keeps files by SHA-256: witnesses, images, crops and withheld text. (12.6)

Bundle

One SQLite file with every table and a full-text index, which a reader or a store queries. Format scienting-bundle/1, provisional. (13.5)

Changed below

The resolution of an anchor on a container that is unchanged in itself while something inside it changed. (6.5)

Checklist

A record of checking an export, such as accessible HTML, against a named standard, criterion by criterion; it is covered by the receipt of the person who checked. Format scienting-checklist/1, provisional. (8.11)

Checkpoint

A signed note that states a transparency log's size and root hash, which a verifier checks against the last checkpoint it saw. Independent parties, the log's witnesses, cosign it, and a project says how many must. Format scienting-checkpoint/1, provisional. (23.2)

Correction

An operation on an established document, with its evidence and author; never edited, only appended. (11)

Description

An annotation that describes a figure, panel or table for readers who cannot see it, as a short text equivalent (alt) or a full description (long); an accessible export uses confirmed descriptions only. (18.4)

DID

Outside term. A decentralized identifier (W3C). A roster key may carry its did:key, which the public key alone determines, so a signer has one name inside and outside the store. (8.7)

Document

The text established for one version of one work, from one or more witnesses, as a tree of nodes. (2.1, 3)

Document key

The work key, with a dotted suffix for any version other than the version of record: .si for Supporting Information, .v2 for a second preprint. (2.4)

Drift

The amount that has changed below a container since an anchor on it was made, counted from the corrections: the share of the container's leaves touched by later corrections. It is reported as none, low or high, with a default threshold of a quarter. (6.6)

Exercise

An annotation whose body holds a prompt, an answer key and a grading rule. The key is anchors, a verdict, a chain, a value or planted errors, by exercise kind. (19.1)

Fidelity level

How far a leaf's text was checked against its source, from F0 converted to F3 proofread. (8.1)

History root

The root of the Merkle tree over a document's corrections, kept in document.json, so a consistency proof can show that a later revision extends an earlier one. (11.5)

JATS

Outside term. Journal Article Tag Suite, ANSI/NISO Z39.96-2024, an XML format in which publishers and archives exchange journal content (the NISO page). In paperspec, jats is a witness kind: the fixture okafor2025solvent-acth was established from a JATS file and a PDF that agree. The formats ingest JATS and do not replace it. (2.3)

Keyed hash

A content value computed as an HMAC (a hash mixed with a secret key) under a team key or a key derived from page fingerprints, so a short text cannot be recovered by hashing guesses. (5.8)

Layer

A named set of annotations with one purpose, audience, visibility and license. (18.2)

Leaf

A node that holds text itself: a sentence, cell, reference, author line, keyword line, equation, equation line, code or algorithm. A leaf anchor points at one whole. (6.4)

Lossy projection

A node's text with scripts flattened, citation marks, whitespace and dashes removed, and case folded; used for proposing alignments. (5.5)

Match hash

A hash of a node's strict projection. Two readings agree only when their match hashes are equal and their complex-notation keys are equal. A complex-notation key is notation:source for a piece of math too complex for the formats to normalize, with the source's whitespace removed (5.3). (5.1, 5.3)

ML-DSA-65

Outside term. The lattice-based signature scheme of FIPS 204, believed to resist quantum computers. A receipt may be signed with it today, beside Ed25519. (8.4)

Model

The record of a machine-learning model that proposed a correction or wrote an annotation: its name, provider and version, and the hashes of its weights, instructions and parameters. (11.2)

Node

An addressable part of a document: a section, paragraph, sentence, figure, panel, caption, table, row, cell, equation, footnote, reference and the rest. Each node has a permanent ID and five content values; table columns and figure-text items have IDs and are not nodes. (3, 4.2)

Own hash

A hash of a node's own content without its children, used to judge anchors on containers that have content of their own. The node_hash is a hash of the own hash and the children's node hashes. (5.1, 5.2)

Package

A document as a folder, or a zip of one, of canonical JSON (a plain-text data format) and JSON Lines (one JSON value per line) files, with a manifest whose hash pins them all. (12)

Page fingerprint

A hash of a page's size, its text with download stamps removed, and its images, so that differently stamped downloads share their pages. (7.1)

Plain projection

A node's text as one string, on which offsets, quotations and text hashes are defined. (3.6)

Policy

A project owner's signed decision that settles rights a record leaves unknown. It never overrides a use the record sets to true or false. (14.2)

Proof

An RFC 9162 inclusion proof that one item was covered by a receipt, or a consistency proof that one history extends another, each a short list of hashes. Format scienting-proof/1. (8.5)

Project

A team's curated set of documents, with its members, layers, data, reading paths and drafts. Format scienting-project/1, provisional. (20)

Receipt

One signature over a Merkle root of what a person reviewed in a sitting. The signature sets the fidelity level of what it lists. A Merkle root is a single hash that commits to a list of items; receipts build it as RFC 6962 (an internet standards document) describes, a tree that RFC 9162 obsoletes and defines identically. (8.3, 8.5)

Revision

The index of the last correction applied to a document, or 0 when there is none; anchors and receipts record it. (11)

Revocation

A signed record that withdraws a receipt, or every receipt by one signer in a period. (8.7)

Rights record

A witness's license, the basis on which the team holds it, and the uses that basis allows. (14.1)

Roster

The list of keys that may sign, with the person who holds each, that person's role in the team, and what the key may sign. (8.7)

Selector

Outside term. In the W3C Web Annotation Data Model, the part of an annotation's target that says where in the source resource the annotation applies. The model defines TextQuoteSelector (exact text, with optional prefix and suffix) and TextPositionSelector (offsets, which the model calls very brittle), among others (the W3C model). Layers use a custom AnchorSelector, which carries an anchor, followed by a TextQuoteSelector for tools that do not know it; they use neither TextPositionSelector nor FragmentSelector. (18.3)

Spot-check

A second reviewer's check of a sample of a receipt's nodes, drawn from a seed nobody can steer: the checker's deterministic signature over the receipt's record hash. (8.8)

Stamp rule

A pattern that recognizes a publisher's download stamp in a page's text, so that fingerprints ignore it. (7.2)

Strict projection

A node's text with notation folded to one canonical form and structure kept; used for certifying agreement. (5.3)

Suspect

A doubtful reading raised for a person or a review session to answer. (5.7)

Targeted F3

Proofreading the nodes a team's claims, quotations and datasets rest on, rather than every node. The target set also includes the leaves of every anchored container, every equation and, under the project's digit rule (all, anchored-sections or none), sentences and cells with a digit in a text or math run (an inline stretch of plain text, or of TeX or Typst math, within the node; 3.5). (8.10)

Text leaf

A leaf whose text a container's projections are made of: any leaf except an equation line, or an equation inside a sentence, whose text is already part of its equation or its sentence. (3.6)

Text policy

Whether a package carries its text (full) or withholds it (checks-only). (12.5)

Tile

One file of a transparency log served statically: 256 hashes of one level of the tree, or 256 entries, so a client fetches only the subtrees it needs. (23.4)

Verdict

A judgment of whether a cited passage supports a citing sentence: supports, partly, does not, or cannot tell. (19.2)

Version

One expression of a work: a preprint, the version of record, an erratum, the Supporting Information. (2.1)

VRF

A verifiable random function (RFC 9381): a keyed function with exactly one valid proof for each key and input, so that a spot-check seed can be checked but not chosen. (8.8)

Web Annotation

Outside term. The W3C Recommendation of 23 February 2017 for annotations with a body, a target and a motivation (the W3C model). It gives sentences no permanent IDs and reports no outcomes such as current or stale; for annotation in general, it and its clients are the better choice. Layers are Web Annotations. (18)

Witness

One file of one version of a work, identified by its SHA-256. (2.1, 2.3)

Work

A piece of scholarship across all its versions. (2.1)

Work key

A work's permanent name: a Scholar-style citation key, a hyphen, and the first characters of a hash of the work's identity, such as vaswani2017attention-a241; minted once and never recomputed. (2.4)