indicium-standard 2.0.0__tar.gz

indicium_standard-2.0.0/.gitignore

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+.venv/
+__pycache__/
+*.pyc
+.pytest_cache/
+site/
+dist/
+.ruff_cache/
+.wheel-env/

indicium_standard-2.0.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+---
+
+## 2.0.0 — 2026-11-01
+
+First public release. These breaking changes landed *before* any Indicium package
+release. Existing downstream records may still embed the earlier context.
+
+### Breaking
+- **The `asb:` vocabulary base moved to `https://w3id.org/asb#`.** It had two
+  earlier bases. 1.x used `https://asb.holobiomics.org/ns/asb#`, a domain that was
+  never registered, so a third party could have taken it and served arbitrary
+  definitions for this standard's term IRIs. Indicium PR #4 (2026-06-14) then moved
+  it to `https://holobiomicslab.eu/ns/asb#`, and 2.0.0 settles on the permanent
+  w3id identifier. Every `asb:` term IRI therefore changes. The 2.0.0 SHACL shapes
+  target the w3id IRIs, so they do not recognise a claim typed with either earlier
+  base: such a claim goes unchecked instead of failing.
+  Released data carries the intermediate base: the 106 `indicium/*.jsonld` files of
+  the asb-skill-collections pre-release `metabolomics-v0.1.0` (2026-06-22) bind
+  `https://holobiomicslab.eu/ns/asb#` and do not validate against the 2.0.0 shapes.
+  To migrate such data, bind the `asb:` prefix of its JSON-LD context (or rewrite
+  its IRIs) to `https://w3id.org/asb#`; the local names are unchanged. Then validate
+  it with `indicium.validate_graph`. Consumers that bind the `asb:` prefix
+  themselves, notably the shape files in `indicium-adapters-metabolomics`, must be
+  updated in lockstep.
+- **The distribution is renamed `indicium` → `indicium-standard`.** The import
+  package is unchanged: `import indicium` still works. The PyPI name `indicium` is
+  held by an unrelated, abandoned key-value-store package that also ships a
+  top-level `indicium` module; installing both into one environment clobbers the
+  import. Depend on `indicium-standard`, never on `indicium`.
+- **Two SEPIO bindings are corrected before the namespace deposit.**
+  `supports_claim` now expands to `sepio:0000427` (`is_evidence_line_for`),
+  an evidence-line-to-claim relation, instead of the oppositely directed
+  `sepio:0000007`. Skill reliance `asserts` now expands to `indicium:asserts`,
+  declared in the LinkML schema, instead of `sepio:0000130` (`authored_by`).
+  JSON keys and the local `for_claim` predicate are unchanged. Refresh embedded
+  contexts and regenerate previously expanded RDF. Supporting, disputing or
+  inconclusive direction is a separate `sepio:0000183` annotation; the
+  historical `supports_claim` key alone does not establish that direction.
+
+### Added
+- `LICENSE` (MIT). 1.x declared MIT in `pyproject.toml` but shipped no licence
+  text, so a wheel would have distributed MIT-claimed code without the required
+  notice.
+- **`indicium.ASB_BASE`, `indicium.INDICIUM_BASE`, `indicium.asb_term()`** — the
+  vocabulary bases are now part of the public API, read from the generated model's
+  prefix map so they cannot drift from the SHACL shapes. Consumers that hardcoded
+  the IRI kept validating against a dead namespace after the base moved: the shapes
+  matched nothing and every graph reported `conforms=True`. Import these instead.
+- `tests/test_namespace_base.py` — guards against reintroducing an unowned
+  namespace base, and pins the metadata lookup to the declared distribution name.
+- A reproducible JSON-LD context generated from the schema, shipped in the
+  package and copied into the documentation site. OBO prefixes expand in JSON-LD
+  1.1; property IRIs and enum meanings now agree with the SHACL shapes.
+- Local release checks and a Trusted Publishing workflow with matching tag,
+  package version and dated changelog checks before publication.
+
+### Fixed
+- **`__version__` reported the wrong version.** It queried `importlib.metadata`
+  for the distribution `indicium`, which after the rename resolves either to
+  nothing (falling back to `0.0.0+unknown`) or to the unrelated squatting PyPI
+  package, reporting *its* version as ours. It now queries `indicium-standard`.
+  The `wheel-smoke` CI job asserts the installed wheel reports the built version.
+- `docs/changelog.md` is now generated from this file (`make docs-changelog`)
+  rather than hand-maintained. It had been frozen at 1.0.0 for twelve releases,
+  and `release.yml` extracts its release notes from it.
+- Installation examples now consistently name `indicium-standard`, including
+  its optional extras. Schema generation works on Linux and macOS.
+- The generated OWL ontology uses the namespace root `https://w3id.org/indicium` as
+  its document IRI and carries the version and the licence (`pav:version`,
+  `dct:license`), which the LinkML source now declares; the model and the JSON
+  Schema carry the version too. RDF serialization is deterministic for release verification.
+- The published SHACL file, `docs/schema-assets/indicium.shapes.ttl` (a release
+  asset), now holds the supplemental shapes as well as the generated ones, so a
+  SHACL processor run on it agrees with `validate_graph`: before, it accepted a
+  claim with neither `qualifier` nor `domain_qualifier`.
+- The sdist includes only package source, schema assets and release metadata;
+  internal development plans are excluded.
+- The package metadata names its author, states the licence as the SPDX
+  expression `MIT` with `LICENSE` as its licence file (instead of the full text in
+  the License field), and lists Documentation and Issues URLs.
+- SEPIO binding regression tests use an attributed excerpt of the ontology's
+  inverse, domain and range axioms. The documentation explains the target link,
+  separate evidence direction and the local reliance predicate.
+
+### Namespace registration
+- Canonical bases remain `https://w3id.org/indicium/` and
+  `https://w3id.org/asb#`. The vocabulary deposit and redirects are prepared
+  separately; registration does not create a hosted store of claim instances.
+- Prepared term redirects send HTML clients to
+  `https://holobiomicslab.eu/indicium/reference/<Name>/` and RDF clients to the
+  vocabulary representation under `/ns/indicium/`. The reference pages must be
+  live before the w3id registration is submitted.
+- ASB validation assertions use `SEPIO_0000183` with `SEPIO_0000403`,
+  `SEPIO_0000404` or `SEPIO_0000405`, and `RO_0002558` with `ECO_0000501`.
+  These are external assertion annotations, not Indicium claim-status values.
+
+---
+
+## 1.12.0 — 2026-06-10
+- New `SourceTaskKind` enum {reproduction, analysis, component_reconstruction, extension} + optional `Claim.source_task_kind` slot (`asb:sourceTaskKind`) — a claim-level reproducibility-provenance qualifier, sibling of `Evidence.workflow_coupling` (Suter et al. 2025) at claim↔source-task granularity. Canonical replacement for ASB's out-of-schema `asbext:source_task_kind`. Added to `context.jsonld` for portability. Additive, backward-compatible; SHACL non-closed.
+
+---
+
+## 1.11.0 — 2026-06-03
+- New `SSSOMMapping` class (SSSOM term mapping) + `IndiciumDocument.sssom_mappings` collection, with a `derived_from` lineage slot (cthoyt 2026-05-29). Adds sssom/semapv/skos prefixes. Additive, backward-compatible.
+
+---
+
+## 1.10.0 — 2026-06-03
+- Evidence gains optional `workflow_coupling` (`WorkflowCoupling` enum: tight/loose/ad_hoc/unknown) — a reproducibility qualifier per Suter et al. 2025 (DOI 10.1016/j.future.2025.107974). Additive, backward-compatible; SHACL non-closed.
+
+---
+
+## [1.9.0] - 2026-05-29
+
+### Added
+
+- **`VerificationResult.char_span`** — a 5th, defaulted field
+  (`tuple[int, int] | None = None`) giving `(start, end)` offsets into the
+  matched candidate's *original* (un-normalized) text. Populated for verified
+  matches from the regex span; best-effort for repaired matches (the recovered
+  span is re-located in the original candidate, and may remain `None`). Lets
+  callers highlight or re-slice the exact source region without re-searching.
+- **`verify_quote(..., punctuation_flexible=True)`** — an opt-in pass between
+  exact containment and LCS that matches the quote's alphanumeric tokens
+  (`[A-Za-z0-9]+(?:\.[A-Za-z0-9]+)*`) in order across arbitrary non-alphanumeric
+  padding, with per-token boundary guards. A hit is `verified` with `score = 1.0`
+  and a `char_span` spanning first-token-start → last-token-end. This recognises
+  a verbatim-modulo-punctuation quote (e.g. `P=0.001` ~ `P = 0.001,`) instead of
+  degrading it to a sub-threshold LCS, mirroring ASB `claim_ledger`'s
+  token-sequence matcher.
+
+### Why
+
+Lets ASB `claim_ledger` and Perspicacité consume one shared verification kernel:
+`char_span` carries the exact source offsets downstream, and the opt-in
+punctuation-flexible pass matches numeric/statistical quotes whose punctuation
+shifts between extraction and source. **Backward-compatible and additive only**:
+both changes are defaulted off / defaulted `None`, existing thresholds and the 11
+prior kernel tests are unchanged, and there are no changes to `generated/model.py`,
+the SHACL shapes, or any enum.
+
+---
+
+## [1.8.0] - 2026-05-29
+
+### Added
+
+- **`verify_quote` kernel** (`indicium.verify`, exported from the package root)
+  — a pure-Python, dependency-light, never-raises verifier that matches an
+  LLM-extracted quote against source passage texts. Returns
+  `VerificationResult(status, matched_index, quote_exact, score)` where status
+  is `verified` (whitespace-flexible, case-sensitive containment; recovers the
+  source's verbatim span, `score = 1.0`), `repaired` (no containment, but the
+  longest common substring vs the best candidate clears `near_threshold`,
+  default 0.9), or `unverified`. Structurally guarantees
+  `unverified ⇒ matched_index is None`; degenerate input (empty/whitespace
+  quote, empty candidates, or `None`/non-str entries) degrades safely instead
+  of raising.
+- Exported `verify_quote` and `VerificationResult` from the package root.
+
+### Why
+
+Lets downstream projects (Perspicacité R3, ASB) ground claim / parameter /
+failure-mode quotes against original source text — verifying provenance and
+catching paraphrase or hallucination — without depending on rdflib or the
+generated model. **Additive only**: no changes to `generated/model.py`, the
+SHACL shapes, or any enum.
+
+---
+
+## [1.7.0] - 2026-05-29
+
+### Added
+
+- **`domain_qualifier` slot** (`slot_uri: asb:domainQualifier`) — an OPEN,
+  snake_case-patterned (`^[a-z][a-z0-9_]*$`) qualifier slot for domain-adapter
+  vocabularies (e.g. transcriptomics `aligned_with`,
+  `differentially_expressed_in`). This is the standard's side-channel for
+  domain extensions, mirroring how enrichment terms ride on
+  `asb:*_ontology_term`. The closed Bucur `SuperPatternQualifier` enum on
+  `asb:qualifier` is **unchanged** — domain terms never pollute it.
+- **`QualifierPresenceShape`** (supplemental SHACL, `sh:or`) — a Claim must
+  carry at least one of `asb:qualifier` (closed Bucur SuperPattern) or
+  `asb:domainQualifier` (open domain extension).
+
+### Changed
+
+- **`qualifier` slot is no longer `required` on its own.** A Claim previously
+  had to carry a core Bucur qualifier; it may now satisfy the "at least one
+  qualifier" rule via `domain_qualifier` instead. The closed enum and its
+  `maxCount 1` are retained; only the slot-level `minCount 1` moved to the
+  either-or `QualifierPresenceShape`.
+
+### Why
+
+Resolves **indicium#1** (reported by Dina, 2026-05-29). Domain-adapter
+qualifiers extended `asb:qualifier` directly, but that slot is a CLOSED 20-term
+LinkML enum (Bucur K-CAP 2021), so the generated `sh:in` shapes rejected every
+extended qualifier — blocking all domain adapters (metabolomics, metabokg, emi,
+transcriptomics) and the ASB benchmark. SHACL merges additively
+(`validate_graph` graph-union), so an adapter-side shape could never relax the
+existing `sh:in`; the fix had to live in the core standard. We chose to keep
+`asb:qualifier` pristine and route domain qualifiers to a new open slot
+(Reading 1) rather than dilute the published closed vocabulary.
+
+### Compatibility
+
+Additive. v1.6 serialisations always carry a core `asb:qualifier`, so they
+still satisfy `QualifierPresenceShape` and remain valid. Consumers gain the
+`domain_qualifier` slot; no existing slot changed its `slot_uri` or range.
+
+---
+
+## [1.6.1] - 2026-05-26
+
+### Fixed
+
+- **Package `context.jsonld` for downstream consumers.** Move
+  `docs/context.jsonld` into `src/indicium/schema/context.jsonld` (canonical
+  location) and symlink it back to `docs/` so mkdocs continues to publish it.
+  Wheels now ship the file, so consumers can load it via
+  `importlib.resources.files("indicium.schema") / "context.jsonld"`.
+
+---
+
+## [1.6.0] - 2026-05-24
+
+### Added
+
+- **Claim aliases:** `predicate` (alias for `relation`) and `super_pattern`
+  (alias for `qualifier`) — explicit names matching the ASB spec.
+- **Evidence aliases + new slots:** `quote_exact` (alias for `quote`),
+  `supports_claim` (alias for `for_claim`, mapped to `sepio:0000007`),
+  `quote_location` (string locator), `eco_code` (range:
+  `EcoCodeAsbSubset`).
+- **`EcoCodeAsbSubset` enum** — 8 ECO codes ASB emits (textual_quotation,
+  computational_evidence, expert_curation, inference_from_background_knowledge,
+  author_statement, experimental_evidence, combinatorial_evidence,
+  traceable_author_statement).
+- **Source slots:** `doi`, `paragraph_id`, `xpath_pointer` — explicit
+  forms of the InformationSource locators ASB targets.
+- **`SoftwareEntity` class** — new class for globally-identified tools
+  (`canonical_url`, `version`, `edam_operation`, `edam_topics`,
+  `bio_tools_id`). Added to `IndiciumDocument.software_entities`.
+- **JSON-LD `@context`** at `docs/context.jsonld` — stable mapping for
+  downstream consumers. To be served at `w3id.org/indicium/context.jsonld`
+  pending the w3id PR; currently published at
+  `holobiomicslab.github.io/indicium/context.jsonld`.
+- **`docs/sepio-assertion.md`** — reference for the SEPIO assertion
+  pattern (skill → claim).
+- **`docs/uri-scheme.md`** — reference for `indicium:claim/<uuid>` +
+  content-hash citation variant.
+- **`tests/fixtures/asb_skill_roundtrip/`** — canonical fixture consumed
+  by Plan 1c's round-trip CI test in indicium-adapters.
+
+### Compatibility
+
+All Wave 1 changes are **additive**: every new slot is non-required and
+shares its `slot_uri` with an existing slot (where one exists). v1.5
+serialisations remain valid; v1.6 consumers gain the spec-required
+names.
+
+---
+
+## [1.5.0] - 2026-05-23
+
+### Added
+- `extra_shapes` keyword argument to `validate_graph()` — callers (e.g. domain adapters via
+  `SHACLProvider`) can now inject additional SHACL shapes that are merged with the built-in
+  schema shapes before validation.
+
+### Fixed
+- `allow_warnings=True` now passed to pyshacl in `validate_graph()` so that `sh:Warning`-severity
+  shapes no longer set `conforms=False`; warnings are reported in the validation report text only.
+- Conditional SHACL constraint added: `superseded_by` is now required when `claim_status = superseded`.
+- Core types (`Claim`, `Evidence`, `Source`, and status enums) are now re-exported from the
+  top-level `indicium` package for ergonomic imports.
+
+### Deprecated
+- `indicium.adapters.astra.claim_to_insight` — use `astra_bridge` instead.
+
+---
+
+## [1.4.0] - 2026-05-20
+
+### Added
+- `IndiciumDocument` container type for grouping claims.
+- `superseded_by` field on `Claim`.
+- Fixed `ClaimLink` URI generation.
+
+---
+
+## [1.3.0] - 2026-05-15
+
+### Added
+- `ClaimLink`, `ClaimStatus` types.
+- OA (Web Annotation) selectors for evidence provenance.
+- ASTRA bridge adapter.
+
+---
+
+## [1.2.0] - 2026-05-10
+
+### Added
+- `Script` and `DataAsset` classes for code/data artefacts as evidence.
+
+---
+
+## [1.1.0] - 2026-05-05
+
+### Added
+- `Figure` class and `FigureType` enum for figure-as-evidence support.

indicium_standard-2.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Louis-Felix Nothias
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

indicium_standard-2.0.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: indicium-standard
+Version: 2.0.0
+Summary: Shared claim/evidence standard (ECO/CiTO/SEPIO/PROV-O + Bucur SuperPattern)
+Project-URL: Homepage, https://holobiomicslab.github.io/indicium
+Project-URL: Documentation, https://holobiomicslab.github.io/indicium/
+Project-URL: Repository, https://github.com/HolobiomicsLab/indicium
+Project-URL: Issues, https://github.com/HolobiomicsLab/indicium/issues
+Project-URL: Changelog, https://holobiomicslab.github.io/indicium/changelog/
+Author-email: Louis-Félix Nothias <louis-felix.nothias@cnrs.fr>
+License-Expression: MIT
+License-File: LICENSE
+Keywords: agentic-science,cito,claims,eco,evidence,linkml,prov-o,scientific-standard,sepio
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Requires-Python: >=3.11
+Requires-Dist: pydantic>=2.0
+Requires-Dist: pyshacl>=0.26
+Requires-Dist: rdflib>=7.0
+Provides-Extra: astra
+Requires-Dist: pyyaml>=6.0; extra == 'astra'
+Provides-Extra: codegen
+Requires-Dist: linkml-runtime>=1.8; extra == 'codegen'
+Requires-Dist: linkml>=1.8; extra == 'codegen'
+Requires-Dist: pyyaml>=6.0; extra == 'codegen'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.25; extra == 'docs'
+Description-Content-Type: text/markdown
+
+<p align="center">
+  <picture>
+    <source media="(prefers-color-scheme: dark)" srcset="docs/assets/brand/indicium-mark-dark.svg">
+    <source media="(prefers-color-scheme: light)" srcset="docs/assets/brand/indicium-mark.svg">
+    <img src="https://raw.githubusercontent.com/HolobiomicsLab/indicium/main/docs/assets/brand/indicium-mark.svg" width="120" alt="Indicium mark">
+  </picture>
+</p>
+
+<h1 align="center">Indicium</h1>
+
+<p align="center">A versioned standard for a typed scientific claim bound to the evidence that grounds it.</p>
+
+<p align="center">
+  <a href="https://github.com/HolobiomicsLab/indicium/blob/main/LICENSE"><img src="https://img.shields.io/badge/license-MIT-00284b" alt="License: MIT"></a>
+  <a href="https://github.com/HolobiomicsLab/indicium/blob/main/pyproject.toml"><img src="https://img.shields.io/badge/python-3.11%2B-00284b" alt="Python 3.11+"></a>
+  <a href="https://github.com/HolobiomicsLab/indicium/actions/workflows/ci.yml"><img src="https://github.com/HolobiomicsLab/indicium/actions/workflows/ci.yml/badge.svg" alt="Tests"></a>
+  <!-- Uncomment once indicium-standard is on PyPI (RELEASING.md, follow-ups):
+  <a href="https://pypi.org/project/indicium-standard/"><img src="https://img.shields.io/pypi/v/indicium-standard?color=00284b" alt="PyPI"></a>
+  -->
+</p>
+
+---
+
+## What it is
+
+Indicium is a small, standalone, versioned **standard for a typed scientific claim
+bound to the evidence that grounds it.** One LinkML source of truth generates pydantic
+models, JSON Schema, SHACL shapes and OWL. It reuses community ontologies rather than
+reinventing them:
+
+| Axis | Standard |
+|------|----------|
+| Evidence type | **ECO** (Evidence & Conclusion Ontology) |
+| Claim to citation relation | **CiTO** |
+| Source and document type | **DoCO** and **IAO** |
+| Article type | **FaBiO** |
+| Assertion and evidence structure | **SEPIO** |
+| Provenance | **PROV-O** |
+| Claim structure | **Bucur et al.** 5-slot SuperPattern (K-CAP 2021) |
+
+The one thing Indicium mints is the **binding**: a claim, its typed evidence, and the
+source that evidence points to, provenance-stamped. That binding is the load-bearing
+contribution. The claim structure is borrowed from Bucur; the value Indicium
+standardizes is the *typed grounding of claims in evidence.*
+
+Indicium is a vocabulary and a standard, not a tool and not a store. Every tool that
+mints claims imports it, so a claim minted by any of them is structurally identical to
+one minted by another, merges with it, and never travels without its evidence trace.
+
+| Part | Where |
+|------|-------|
+| LinkML schema, the source of truth | `src/indicium/schema/indicium.yaml` |
+| Pydantic models (`Claim`, `Evidence`, `Source`, `CitationLink`, `ClaimLink`, `IndiciumDocument`, ...) | `indicium.generated.model`, re-exported from `indicium` |
+| SHACL shapes, OWL ontology, JSON Schema | `src/indicium/generated/`, copied to `docs/schema-assets/`; the published SHACL file adds the supplemental shapes of `src/indicium/augmentation/` |
+| JSON-LD context | `src/indicium/schema/context.jsonld` |
+| SHACL validation | `indicium.validate_graph` |
+| Quote verification kernel | `indicium.verify_quote` |
+| Projections to ASB task cards, ASTRA and KGmemory | `indicium.adapters`, `indicium.astra_bridge` |
+
+### The name
+
+*Indicium* (Latin) is "a sign or mark that points to the truth"; in law, the
+evidentiary indication. The package is named for what it standardizes: every claim
+carries its **indicia**, the traces that justify believing it.
+
+- **`indicium`** (singular) is the standard and this package.
+- **indicia** (plural) is the body of evidence attached to a claim, and the term
+  consumer APIs use for the produced collection.
+
+## Install
+
+Requires Python 3.11 or newer.
+
+```bash
+pip install indicium-standard      # distribution name
+python -c "import indicium"        # import name
+```
+
+Optional extras:
+
+```bash
+pip install "indicium-standard[astra]"     # ASTRA bridge (PyYAML)
+pip install "indicium-standard[codegen]"   # regenerate the artefacts from the LinkML source
+```
+
+The 2.0.0 upload to PyPI is pending ([RELEASING.md](https://github.com/HolobiomicsLab/indicium/blob/main/RELEASING.md)). Until
+`pip install indicium-standard` finds it, install from the repository:
+
+```bash
+pip install "git+https://github.com/HolobiomicsLab/indicium"
+```
+
+> **The distribution is `indicium-standard`; the import package is `indicium`.**
+> The PyPI name `indicium` belongs to an unrelated, abandoned key-value-store
+> package that also ships a top-level `indicium` module. Installing both into the
+> same environment will clobber the import. Always depend on `indicium-standard`.
+
+## Quickstart
+
+Validate a claim against the SHACL shapes (adapted from `tests/test_validate.py`):
+
+```python
+import rdflib
+from indicium import ASB_BASE, validate_graph
+
+claim = f"""
+@prefix asb: <{ASB_BASE}> .
+<urn:claim:1> a asb:Claim ;
+    asb:context "in vitro" ;
+    asb:subject "compound A" ;
+    asb:qualifier "inhibits" ;
+    asb:relation "inhibits growth of" ;
+    asb:object "cell line B" .
+"""
+conforms, report = validate_graph(rdflib.Graph().parse(data=claim, format="turtle"))
+print(conforms)  # True
+
+incomplete = f"""
+@prefix asb: <{ASB_BASE}> .
+<urn:claim:2> a asb:Claim ; asb:context "in vitro" .
+"""
+conforms, report = validate_graph(rdflib.Graph().parse(data=incomplete, format="turtle"))
+print(conforms)  # False
+```
+
+`report` names each missing slot. The [quickstart](https://holobiomicslab.github.io/indicium/quickstart/) continues with
+the typed model and the adapters; every Python example in this README and on the Home,
+Quickstart and URI scheme pages runs in the test suite (`tests/test_docs_examples.py`).
+
+## Vocabulary and IRIs
+
+Import the namespace bases; never copy the IRI string into your own code. A
+hardcoded base keeps pointing at the old namespace when the standard moves, and
+the SHACL shapes then match nothing: every graph validates as `conforms=True`
+while no constraint is actually checked.
+
+```python
+from indicium import ASB_BASE, INDICIUM_BASE, asb_term
+
+asb_term("Claim")   # 'https://w3id.org/asb#Claim'
+```
+
+```python
+ASB = "https://w3id.org/asb#"   # don't: silently dead after a move
+```
+
+| Prefix | Namespace | Names | Resolves (measured 2026-10-30) |
+|--------|-----------|-------|------------------|
+| `asb:` | `https://w3id.org/asb#` | `asb:Claim` and its SuperPattern slots (`context`, `subject`, `qualifier`, `relation`, `object`), plus `domainQualifier`, `sourceTaskKind` and `workflowCoupling` | Yes. Registered on w3id.org on 29 October 2026; 303 to `holobiomicslab.eu/ns/asb`, which serves Turtle, JSON-LD and HTML |
+| `asbval:` | `https://w3id.org/asb/validation#` | Validation assertion terms used beside `asb:` by ASB | Yes. Same registration; 303 to `holobiomicslab.eu/ns/asbval` |
+| `indicium:` | `https://w3id.org/indicium/` | The schema id, the JSON-LD context prefix, and every class and slot without its own IRI binding: claim metadata, the evidence and source slots, `ClaimLink`, `CitationLink`, `IndiciumDocument` | No (404). Not registered yet; the request files are in [`docs/release/w3id-indicium/`](https://github.com/HolobiomicsLab/indicium/tree/main/docs/release/w3id-indicium) |
+
+[`docs/uri-scheme.md`](https://holobiomicslab.github.io/indicium/uri-scheme/) has the redirect chains, the identifier
+conventions for claims and evidence, and what the `/indicium` registration will point
+at. `tests/test_namespace_resolves.py` fetches each namespace when
+`INDICIUM_NETWORK_TESTS=1` is set.
+
+## Ecosystem
+
+Indicium is the shared layer; the projects below mint, store or consume its claims.
+
+| Project | What it is | Relation to Indicium |
+|---------|------------|----------------------|
+| [ASTRA](https://astra-spec.org) | A declarative YAML format for scientific analyses: inputs, outputs, decisions and evidence ([astra-spec](https://github.com/LightconeResearch/astra-spec)) | `indicium.astra_bridge` turns claims into ASTRA insights and reads ASTRA findings back as claims |
+| AgenticScienceBuilder (ASB) | Distils research articles into agent skills, task cards and capsules | Depends on `indicium-standard>=2.0.0,<3`; its claims use the `asb:` vocabulary |
+| [asb-skill-collections](https://github.com/HolobiomicsLab/asb-skill-collections) | Registry and release tooling of the ASB skill collections | The v1 trees carry Indicium documents written before 2.0.0 (earlier `asb:` base, not 2.0.0-conformant); later versions will carry 2.0.0 documents |
+| `asb-skills-<domain>` | The skill collections, one repository per domain | Built by ASB; same vocabulary |
+| [Perspicacité](https://github.com/HolobiomicsLab/Perspicacite-AI) | Local-first retrieval-augmented system for searching and organizing the scientific literature | Uses the Indicium stack, when installed, for claim validation, the claim graph and the ASTRA export |
+| Scriptorium | Manuscript authoring | Depends on `indicium-standard>=2.0.0,<3` and the adapters |
+| KGmemory | Where claims are stored and reasoned over | `indicium.adapters.kgmemory` emits a JSON-LD node typed `mem:SemanticMemory` |
+| `indicium-adapters` | The `DomainAdapter` and `SHACLProvider` protocols and entry-point discovery | Domain shapes reach `validate_graph(..., extra_shapes=...)` |
+| `indicium-adapters-<domain>` | Domain bundles: agentic-ai, astronomy, epigenomics, genomics, metabarcoding, metabolomics, metagenomics, multi-omics, proteomics, transcriptomics | Ontology terms and SHACL shapes per domain |
+
+AgenticScienceBuilder, Scriptorium, KGmemory, the `asb-skills-<domain>` collections
+and the `indicium-adapters` family are not public yet.
+
+## Development
+
+```bash
+uv sync --frozen --extra codegen --extra docs
+uv run pytest -q              # includes the conformance suite (parity with the Scriptorium SHACL)
+make lint                     # ruff over src/ and scripts/
+make gen                      # regenerate model.py, shapes.ttl, ontology.ttl, schema.json
+make context                  # regenerate the packaged JSON-LD context from the LinkML URI bindings
+make schema-assets            # make gen and make context, then copy the artefacts and the changelog into docs/
+uv run mkdocs build --strict  # the documentation site, as docs.yml deploys it
+```
+
+`docs/changelog.md` is a copy of `CHANGELOG.md` (`make docs-changelog`); edit only the
+latter. `make gen` writes canonical Turtle, so a second run is byte-identical to the
+committed files; `release.yml` fails when it is not.
+
+Namespace bases are stable identifiers. Their registration and the vocabulary site are
+prepared separately from the Python release; they do not provide an instance store.
+Read the [URI scheme](https://holobiomicslab.github.io/indicium/uri-scheme/) and the
+[SEPIO compatibility notes](https://holobiomicslab.github.io/indicium/sepio-assertion/)
+before exporting RDF.
+
+## Release and versioning policy
+
+Indicium follows [Semantic Versioning](https://semver.org/), read for a vocabulary:
+
+- **Term IRIs are immutable after a tagged release.** Published data embeds them.
+- **Additive changes are minor:** a new class, slot or enum value.
+- **An IRI change or a slot removal is major,** as is a tighter cardinality. This is
+  why the move of the `asb:` base to `https://w3id.org/asb#` is 2.0.0.
+
+A tag `v<version>` that matches `pyproject.toml` and a dated `CHANGELOG.md` section
+runs the release (`.github/workflows/release.yml`): the checks, tests, documentation
+build and installed-wheel check first, then the upload of the wheel and the sdist to
+PyPI through Trusted Publishing, then the GitHub release with the same files and the
+three schema artefacts.
+[RELEASING.md](https://github.com/HolobiomicsLab/indicium/blob/main/RELEASING.md) is the maintainer checklist. Changes are listed in
+[CHANGELOG.md](https://github.com/HolobiomicsLab/indicium/blob/main/CHANGELOG.md).
+
+## Citation
+
+[CITATION.cff](https://github.com/HolobiomicsLab/indicium/blob/main/CITATION.cff) holds the citation metadata, which GitHub offers as
+"Cite this repository". No DOI exists yet. BibTeX, derived from that file with
+`cffconvert -f bibtex` (citation key renamed):
+
+```bibtex
+@misc{nothias_indicium,
+  author = {Nothias, Louis-Félix},
+  title  = {Indicium: a standard for typed scientific claims bound to their evidence},
+  url    = {https://github.com/HolobiomicsLab/indicium}
+}
+```
+
+## License
+
+MIT, see [LICENSE](https://github.com/HolobiomicsLab/indicium/blob/main/LICENSE). Developed at the Holobiomics Lab, CNRS / Université Côte
+d'Azur.