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alexmandClaude a4eecb4d5b refactor: move the reference implementation to src/paperspec 
The oracle had two import names, `tools.oracle` for the tools and
`paperspec` for other repositories, which could load the same code twice
in one process and needed a gate keyed on the module name. It now lives
in the standard src layout under its one name.

- git mv tools/oracle -> src/paperspec; the 22 rule modules are unchanged.
- The tools import `paperspec`. `tools/__init__.py` now holds the Python
  3.14 and cryptography/jsonschema check and puts src/ first on sys.path,
  so the tools run this checkout's code with or without pixi. The
  package's own __init__ checks nothing and exposes __version__.
- pyproject.toml: version from git tags via setuptools-scm
  (guess-next-dev, node-and-timestamp, src/paperspec/_version.py,
  gitignored). The packages stay listed rather than found because
  schemas/, sql/ and vectors/ stay at the root: the spec links to them and
  the site serves the schemas at their $id URLs.
- pixi.toml: a `dev` feature and environment with setuptools,
  setuptools-scm and python-build, and `pixi run -e dev wheel`.
- check.py scans src/paperspec for rule IDs; README, CONTRIBUTING, the
  FAQ, the overview, the vectors and tools READMEs and the changelog point
  at the new path. The FAQ no longer says the oracle is not a library.

pixi.lock is not re-solved in this commit: with a dynamic version, pixi
builds the package metadata to lock, which needs the conda environment
installed. Run `pixi lock` and commit the result before pushing; the site
workflow installs with --locked.

pixi run check passes; no computed value, vector, fixture, schema or SQL
file changed.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
2026-10-15 09:00:40 -04:00

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# FAQ
This page answers questions about paperspec, a set of file formats that give every sentence and table cell of a scientific paper a permanent address.
Newcomers, implementers of a reader, writer, converter or checker, and experts who know JATS (Journal Article Tag Suite), TEI (Text Encoding Initiative) or W3C Web Annotations can all use it.
Each answer gives the plain statement first, then the precise one, then the chapter that defines it.
The repository is <https://git.scient.ing/infra/paperspec>, and the formats are at version 0.1.0.
## Can I read these files without special software?
Yes.
Every file is JSON or JSON Lines (one JSON value per line), and [spec/](../spec/README.md) specifies every format. [The examples](examples.md) read a package with a few lines of Python.
## Why not keep using PDFs and page numbers?
A page number names a region, not a statement, and it changes between a preprint and the version of record.
An address names a sentence or a cell by its ID, such as `hale2026harmonic-damb#v3063qv`.
It can add a pin (the first six hex digits of the node's hash) and character offsets, which lets a reader check the address against the exact text ([spec/06 §6.1](../spec/06-anchors.md#61-addresses)).
An ID encodes no page, position or kind.
The system mints it once from the document key, kind, text hash and occurrence, then freezes it ([spec/04 §4.2](../spec/04-identity.md#42-minting-node-ids)).
## Why does a key end in four odd characters?
`hale2026harmonic-damb` is the paper's key: the citation key a reader would use, then four characters of a hash of its DOI.
Citation keys alone collide, between a preprint and its published version or two papers by one author in one year; the hash settles that, and any tool that knows the DOI can recompute it.
A key is minted once and never recomputed, so a corrected title does not change a key someone has cited ([spec/02 §2.4](../spec/02-model.md#24-work-and-document-keys)).
## Why are numbers stored as strings?
Databases and JSON libraries rewrite numbers: `310.0` becomes `310` and `1.5260` becomes `1.526`, and the printed digits are part of what a paper says.
Canonical JSON, the byte-exact form used for hashing, writes numbers as ECMAScript writes a double, so it would erase the same difference.
A decimal that carries meaning is a string.
JSON numbers are for counts, indexes, offsets, sizes and geometry ([spec/01 §1.2](../spec/01-conventions.md#12-numbers)).
## What happens when a better converter comes along?
The system aligns the new reading with the established document, sentence by sentence.
A sentence the alignment pairs keeps its ID even where the readings disagree, which catches a lost superscript instead of accepting it.
Every disagreement, and every sentence found in only one reading, becomes a suspect, a doubtful reading raised for review.
Nothing changes until a correction passes the gate, the rules that refuse, for example, a digit change with no crop of the page image as evidence.
Converting the same input again with the same converter mints the same IDs ([spec/05 §5.6](../spec/05-hashes.md#56-alignment), [spec/11 §11.4](../spec/11-corrections.md#114-the-gate), [spec/04 §4.2](../spec/04-identity.md#42-minting-node-ids)).
## Do I need receipts, rights records and spot-checks for a personal library?
You need no receipts and no spot-checks.
A receipt is a signed record that a named person compared nodes with the page image, and a spot-check is a second reviewer's sample of that work.
One person can leave both out.
Each source file still carries a rights record, though the record can say little: the license as printed, a `basis` of `unknown`, and no uses, each of which then counts as unknown ([spec/14 §14.1](../spec/14-rights.md)).
The fields are defined so that a personal library loads into a team's store later without conversion ([spec/00 §0.4](../spec/00-introduction.md#04-status)).
## Is a model allowed to correct a document?
A model may propose corrections and answer suspects, under the same gate as a person, and its corrections record the model and the run as author.
Only a named person can sign a receipt, and a model's annotation stays `proposed` until a person confirms it ([spec/11 §11.2](../spec/11-corrections.md#112-every-correction-records), [spec/18 §18.3](../spec/18-layers.md#183-the-annotation)).
## Why are annotations W3C Web Annotations?
Tools that follow the W3C Web Annotation model can read the standard parts of these annotations.
A layer, the file that groups annotations, follows the [W3C Web Annotation Data Model](https://www.w3.org/TR/annotation-model/), a W3C Recommendation of 2017.
Each target holds an `AnchorSelector` carrying a `scienting-anchor/1` record, followed by a standard `TextQuoteSelector` for tools that do not know the anchor selector.
(The `scienting-` prefix is the formats' namespace, separate from the repository's name.)
The formats use no `TextPositionSelector` or `FragmentSelector`.
The anchor adds what the standard selectors lack: the node's ID, its hashes, and a defined outcome (`current`, `changed-below`, `moved`, `reattached` or `stale`) when the text has changed.
The Web Annotation model alone is the better-established choice where an annotation needs none of that.
Whether a generic Web Annotation client displays an `AnchorSelector` is untested.
See [the comparison](comparison.md).
## What is the difference between a claim and an annotation?
A statement true independently of the paper, such as "K_r is the bond force constant of the AMBER energy", is a claim.
A claim has to be checked against evidence, so it belongs in a store of checked claims outside these formats, which define no claim semantics.
A statement about reading the paper, such as "the authors pass quickly over the scaling here", is an annotation in a layer, attributed and unchecked ([spec/18 §18.1](../spec/18-layers.md#181-one-rule-decides-what-is-a-claim-and-what-is-a-layer)).
## Can a team share notes on a paywalled paper?
Yes, without sharing the paper.
A checks-only package withholds all text and keeps IDs, labels, pages, boxes and keyed hashes.
A public layer swaps each quotation for keyed hashes, under a key derived from the paper's page fingerprints, so a reader checks and shows it only over their own copy.
The hash must be keyed because anyone can recover a plain hash of a short text such as `310.0` by hashing guesses ([spec/12 §12.5](../spec/12-package.md#125-text-policies), [spec/05 §5.8](../spec/05-hashes.md#58-keyed-hashes), [spec/06 §6.3](../spec/06-anchors.md#63-keyed-anchors)).
Whether a team may share notes on a paper this way is a question for its own counsel; nothing here is legal advice.
## How does this differ from JATS or TEI?
They overlap in subject, not in job.
JATS, the [Journal Article Tag Suite](https://www.niso.org/publications/z3996-2024-jats) (ANSI/NISO Z39.96-2024), is an XML format for publishers and archives to exchange journal content. paperspec does not replace it.
A JATS file is one kind of witness (a source file), an input from which a document is established.
None of the 312 elements in the [JATS 1.4 Archiving tag library](https://jats.nlm.nih.gov/archiving/tag-library/1.4/) marks a sentence; its smallest text unit is the paragraph, `<p>`.
TEI, the Text Encoding Initiative, has a sentence-like [`<s>` element](https://tei-c.org/release/doc/tei-p5-doc/en/html/ref-s.html) and keeps both readings of a corrected passage with [`<corr>` and `<sic>`](https://tei-c.org/release/doc/tei-p5-doc/en/html/ref-corr.html).
The encoder assigns its `xml:id`, and the guidelines [recommend it for durability](https://tei-c.org/release/doc/tei-p5-doc/en/html/SA.html).
paperspec mints and retires IDs by rule, keeps corrections as separate records with evidence, and hashes each node.
Keep JATS for publisher and archive exchange and TEI for general scholarly text encoding.
A TEI file is a witness of kind `xml` ([spec/02 §2.3](../spec/02-model.md)).
The full comparison is [docs/comparison.md](comparison.md)
## What is its status and maturity?
Version 0.1.0 has 32 formats: 19 are `candidate` and 13 are `provisional`, as [registry/formats.json](../registry/formats.json) lists.
A `candidate` format is complete, with vectors and fixtures, and ready to implement.
A `provisional` one is complete and expected to change as implementations gain experience.
The provisional formats are dataset, digitization, view, project, bundle, snapshot, draft-ids, exercise, submission, grade, checklist, log-entry and checkpoint.
The repository holds a reference checker (`tools/check.py`), 25 vector files, five valid packages, one of them also as a zip, and 31 deliberately broken packages ([spec/00 §0.4](../spec/00-introduction.md#04-status), [spec/22](../spec/22-conformance.md)).
## What does it not do?
It is built for a team-scale corpus of hundreds of documents, not hundreds of millions of papers.
It does not replace publisher interchange formats; it reads JATS as a witness.
It does not fix what a converter reads wrongly.
It records the reading and raises disagreements as suspects, and a correction is checkable.
It is not a search engine, a citation index or a recommendation feed ([docs/overview.md](overview.md)).
## How do I add a node kind or a run kind?
A node kind is a type of document part, such as `sentence`; a run kind is a type of inline content within a sentence, such as `math`.
Propose either with the vector or fixture that shows it.
A new kind is a minor version ([spec/00 §0.3](../spec/00-introduction.md#03-format-identifiers-and-versions)).
See [CONTRIBUTING.md](../CONTRIBUTING.md).
## What are the files in `tools/` for?
`build.py` builds the fixtures and vectors. `check.py` recomputes and checks every one, and `load.py` loads packages into SQLite.
The oracle's modules in `src/paperspec/` compute every expected value, so that none is typed by hand.
The other repositories of the project install them as the Python package `paperspec`; independent implementations follow the specification ([tools/README.md](../tools/README.md)).
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