bioai-evidence-validator 0.4.1__tar.gz

bioai_evidence_validator-0.4.1/.gitattributes

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+* text=auto eol=lf

bioai_evidence_validator-0.4.1/.github/workflows/ci.yml

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+name: Repository checks
+on:
+  push:
+    branches: [main]
+  pull_request:
+permissions:
+  contents: read
+jobs:
+  verify:
+    timeout-minutes: 15
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: '3.11'
+          - os: ubuntu-latest
+            python: '3.12'
+          - os: ubuntu-latest
+            python: '3.13'
+          - os: windows-latest
+            python: '3.13'
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+      - name: Install locked tooling
+        run: python -m pip install uv==0.12.17
+      - name: Install locked project
+        run: uv sync --frozen --extra dev --python ${{ matrix.python }}
+      - name: Run tests
+        run: uv run --frozen pytest
+      - name: Build distributable
+        run: uv build
+      - name: Verify installed wheel and CLI outside editable source
+        shell: bash
+        run: uv run --isolated --no-project --python ${{ matrix.python }} --with ./dist/*.whl python tools/check_distribution.py

bioai_evidence_validator-0.4.1/.github/workflows/release.yml

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+name: Release
+on:
+  push:
+    tags: ['v*']
+permissions:
+  contents: read
+jobs:
+  build:
+    timeout-minutes: 15
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+      - name: Install locked tooling
+        run: python -m pip install uv==0.12.17
+      - name: Check tag matches package version
+        run: |
+          version=$(python -c "import tomllib; print(tomllib.load(open('pyproject.toml', 'rb'))['project']['version'])")
+          if [ "v$version" != "$GITHUB_REF_NAME" ]; then
+            echo "Tag $GITHUB_REF_NAME does not match pyproject version $version" >&2
+            exit 1
+          fi
+      - name: Install locked project
+        run: uv sync --frozen --extra dev
+      - name: Run tests
+        run: uv run --frozen pytest
+      - name: Build distributable
+        run: uv build
+      - name: Verify installed wheel and CLI outside editable source
+        run: uv run --isolated --no-project --with ./dist/*.whl python tools/check_distribution.py
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish-pypi:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/bioai-evidence-validator/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    needs: publish-pypi
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+      - name: Create GitHub release from the CHANGELOG section
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          version="${GITHUB_REF_NAME#v}"
+          awk -v v="$version" '
+            /^## / { if (found) exit; if (index($0, "## " v " ") == 1) { found = 1; next } }
+            found' CHANGELOG.md > release-notes.md
+          test -s release-notes.md
+          gh release create "$GITHUB_REF_NAME" dist/* --verify-tag \
+            --title "$GITHUB_REF_NAME" --notes-file release-notes.md

bioai_evidence_validator-0.4.1/.gitignore

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+.venv/
+__pycache__/
+*.py[cod]
+.pytest_cache/
+*.egg-info/
+dist/
+build/
+artifacts/
+validation_report.json

bioai_evidence_validator-0.4.1/CHANGELOG.md

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+# Changelog
+
+## 0.4.1 — Required-evidence quality and real-source evaluation
+
+- Apply extraction-method quality gates to each required evidence type independently.
+- Prevent unrelated manual/parser evidence from admitting an LLM-only required result.
+- Add an attributed, frozen VBO canine name-mapping case and source rebuild script.
+- Evaluate 72 real-source names, 160 controlled faults, and 16 explicit trust-boundary cases separately.
+- Preserve generic main and the legacy canine-breed branch.
+- Publish to PyPI from version tags; add package metadata and citation file.
+- Reject CLI input nested deeper than 100 levels (exit 3) on every platform and Python version.
+
+## 0.4.0 — Domain-neutral main
+
+- Preserve canine 0.3 functionality on the `canine-breed` branch.
+- Replace canine defaults with a generic entity/relation/evidence schema and strict YAML profiles.
+- Add general, literature-claim, dataset-label, and custom assay examples.
+- Bind human adjudications to statements and uses; enforce evidence scope and reference integrity.
+- Replace `--policy` with `--profile`; add profile discovery and generic audit fields.
+- Remove the canine SQLite command from main. See `docs/MIGRATION-0.4.md` for breaking changes.
+
+## 0.3.0 — Evidence and snapshot contract hardening
+
+- Require resolved supporting evidence, selected-candidate consistency and
+  compatible claim predicates; block relationship claims from sample/frequency label use.
+- Enforce scope exclusions from concept scope, use only supporting scope evidence,
+  reject blank provenance and unresolved references in unused evidence.
+- Reject incomplete/duplicate/unknown policy configuration; custom schemas cannot
+  relax the packaged structural baseline. Snapshot validation context per batch.
+- Reject duplicate database IDs, WAL/SHM/journal sidecars, malformed manifests
+  and unrecognized boolean evidence. Include resolution-row provenance,
+  limits/accounting and batch hashes; publish the completion summary last.
+- Preserve earlier policy files, synthetic examples and operational CLI exit codes.
+
+## 0.2.0 — Evidence admission contracts and reproducible CLI
+
+- Version schema/policy 0.2; preserve policy 0.1 and record generated-schema hashes.
+- Prevent withdrawn statements or conflicting human judgments from silently being admitted.
+- Reject missing, empty, malformed, duplicated or unknown requested uses.
+- Make structural and identity errors block the entire record, including unknown uses.
+- Require evidence collections and reject duplicate IDs before dictionary lookup.
+- Return structured operational CLI errors; parse UTF-8 strictly and write reports atomically.
+- Add regression tests, a Linux/Windows CI workflow and an installed-wheel smoke check.
+- Include the Apache-2.0 license already declared in project metadata.

bioai_evidence_validator-0.4.1/CITATION.cff

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+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "BioAI Evidence Validator"
+abstract: >-
+  Evidence validation and policy engine for AI-assisted biological curation.
+  It checks evidence structure, provenance consistency, scope and review
+  requirements, then reports an admission decision for each requested use.
+authors:
+  - family-names: Sun
+    given-names: Ningyu
+version: 0.4.1
+license: Apache-2.0
+repository-code: "https://github.com/NingyuSUN/bioai-evidence-validator"
+keywords:
+  - bioinformatics
+  - biocuration
+  - evidence
+  - provenance
+  - LLM
+  - LinkML

bioai_evidence_validator-0.4.1/LICENSE

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bioai_evidence_validator-0.4.1/PKG-INFO

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+Metadata-Version: 2.5
+Name: bioai-evidence-validator
+Version: 0.4.1
+Summary: Standards-aligned evidence policy validation for AI-assisted biological curation
+Project-URL: Homepage, https://github.com/NingyuSUN/bioai-evidence-validator
+Project-URL: Documentation, https://github.com/NingyuSUN/bioai-evidence-validator/tree/main/docs
+Project-URL: Changelog, https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/CHANGELOG.md
+Project-URL: Issues, https://github.com/NingyuSUN/bioai-evidence-validator/issues
+Author: Ningyu Sun
+License: Apache-2.0
+License-File: LICENSE
+Keywords: ai-safety,biocuration,bioinformatics,evidence,knowledge-graph,linkml,llm,ontology,provenance,validation
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.11
+Requires-Dist: jsonschema<5,>=4.23
+Requires-Dist: linkml<2,>=1.8
+Requires-Dist: pyyaml<7,>=6.0
+Provides-Extra: dev
+Requires-Dist: pytest<9,>=8; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# BioAI Evidence Validator
+
+[![CI](https://github.com/NingyuSUN/bioai-evidence-validator/actions/workflows/ci.yml/badge.svg)](https://github.com/NingyuSUN/bioai-evidence-validator/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/bioai-evidence-validator)](https://pypi.org/project/bioai-evidence-validator/)
+[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-blue)](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/pyproject.toml)
+[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue)](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/LICENSE)
+
+**Stop AI-extracted biological claims from entering your knowledge base or
+training set before their evidence is good enough for that use.**
+
+An LLM can turn a paper into a tidy `gene → associated_with → phenotype` record
+that passes every schema check. This toolkit asks the next question: *is the
+evidence behind it sufficient for the specific use you have in mind?* It checks
+evidence structure, provenance consistency, scope and human-review requirements,
+then returns an auditable **admitted / review_required / rejected** decision for
+each requested use.
+
+```bash
+pip install bioai-evidence-validator
+```
+
+## 30-second example
+
+The two records below are identical except for one field: how the supporting
+evidence was extracted.
+
+```diff
+   "evidence_type": "publication_result",
+-  "extraction_method": "llm_extraction",
++  "extraction_method": "manual_curation",
+```
+
+```console
+$ bioevidence validate examples/literature_claim/llm_only.json --profile literature-claim
+```
+
+```json
+{
+  "overall_status": "review_required",
+  "findings": [
+    {
+      "rule_id": "BEV008",
+      "severity": "review",
+      "message": "Required evidence type 'publication_result' comes only from LLM extraction.",
+      "blocking_uses": ["research_summary"]
+    }
+  ],
+  "use_decisions": [
+    { "use": "research_summary", "admission_status": "review_required", "reason_codes": ["BEV008"] }
+  ]
+}
+```
+
+The command exits with **2**, so a pipeline can route the record to a reviewer.
+The manually curated version (`examples/literature_claim/curated_association.json`)
+is `admitted` with exit code **0**. Every full report also records the input,
+schema and profile SHA-256 hashes and versions for audit.
+
+## Why not just JSON Schema or Pydantic?
+
+A schema tells you a record is well formed. It cannot tell you whether the
+record is trustworthy enough for a particular purpose.
+
+| | Schema validation | This validator |
+|---|:---:|:---:|
+| Record shape and types | ✅ | ✅ (LinkML) |
+| Different evidence rules per intended use (summary vs. KB vs. training) | — | ✅ |
+| Quality gate per required evidence type (LLM-only evidence cannot ride on unrelated manual evidence) | — | ✅ |
+| Provenance consistency (source hashes, resolved references, scope) | — | ✅ |
+| Human adjudications bound to a specific statement and use | — | ✅ |
+| Machine-readable audit report with hashes of input, schema and profile | — | ✅ |
+
+On the real-data benchmark below, schema-only checks admitted **160/160**
+injected faults; the full validator admitted **0/160**.
+
+## Use it
+
+### Command line
+
+```bash
+bioevidence profiles                                   # list built-in profiles and their use contracts
+bioevidence validate record.json --profile literature-claim
+bioevidence validate record.json --profile my_profile.yaml --output report.json
+bioevidence generate-schema --output record.schema.json  # JSON Schema for the input format
+```
+
+Exit codes: **0** admitted, **1** rejected, **2** review required, **3** input or configuration error.
+
+### Python
+
+```python
+import json
+from pathlib import Path
+
+from bioevidence_validator.engine import validate_record
+
+record = json.loads(Path("record.json").read_text(encoding="utf-8"))
+report = validate_record(record, profile="literature-claim")
+
+for decision in report["use_decisions"]:
+    print(decision["use"], decision["admission_status"], decision["reason_codes"])
+```
+
+`profile` accepts a built-in name or a path to your own YAML profile.
+
+## How it works
+
+```mermaid
+flowchart TD
+    A["Structured evidence JSON"] --> B["LinkML structure checks"]
+    B --> C["Reference and scope checks"]
+    P["Selected YAML profile"] --> C
+    C --> D["Evidence and human review requirements"]
+    D --> E["Decision for each requested use"]
+    E --> F["Audit report: findings, versions and hashes"]
+    S["Frozen source evidence + intended use"] --> R["Independent human annotation"]
+    R --> J["Resolve disagreements and record uncertainty"]
+    J --> G["Freeze gold-standard test set"]
+    G --> V["Compare held-out decisions with gold standard"]
+    F --> V
+    V --> M["False admission, false block and review rates"]
+```
+
+This diagram defines the complete project workflow. Each project supplies its own
+reviewed reference labels; the validator's decisions are evaluated against them.
+Gold labels stay separate from runtime evidence and rule development.
+
+Domain rules are YAML profiles: new entity types, relations, evidence types and
+uses do not require engine edits.
+
+| Example profile | Assertion | Use contract |
+|---|---|---|
+| `general` | Any typed entity–relation–entity statement | Provenance, scoped support, optional human review by use |
+| `literature-claim` | Gene/variant associated with phenotype/disease | Publication evidence; human acceptance for knowledge-base admission |
+| `dataset-label` | Sample assigned a label | Curated label plus sample link; human acceptance for training |
+| Custom YAML | Compound measured response in an assay | Assay evidence; defined without changing Python code |
+
+See [Create a profile](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/docs/PROFILES.md).
+
+## Run the examples from source
+
+Python 3.11+ and [uv](https://docs.astral.sh/uv/), from the repository root:
+
+```bash
+uv sync --frozen --extra dev
+uv run bioevidence profiles
+uv run bioevidence validate examples/general/curated_assertion.json
+uv run bioevidence validate examples/literature_claim/llm_only.json --profile literature-claim
+uv run bioevidence validate examples/custom_profile/assay_record.json --profile examples/custom_profile/assay.yaml
+uv run pytest
+```
+
+## Build a gold standard for your project
+
+1. **Define the task:** specify the domain, intended uses, label definitions and evidence requirements in a written rubric.
+2. **Select and freeze cases:** retain source versions and record hashes; group related entities and aliases into the same development/test split.
+3. **Review independently:** domain reviewers label mapping correctness and use-specific admission without seeing validator predictions; record evidence and uncertainty.
+4. **Resolve and version:** preserve original reviews, document disagreements and adjudication, then freeze the labels and provenance manifest.
+5. **Evaluate:** compare held-out decisions with that reference; report false admissions, false blocks and review rates with counts and denominators.
+
+Use the [annotation templates](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/evaluation/gold_standard/README.md) and
+[detailed protocol](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/docs/GOLD_STANDARD.md). Each gold standard is specific to a task,
+source version and intended use. Document reviewer roles and whether labels are
+single-reviewed or independently reviewed by multiple people.
+
+## Real-data case
+
+[VBO canine name mapping](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/examples/vbo_canine/README.md) uses a frozen public ontology:
+72 real-name cases, 160 controlled errors, and 16 separately reported trust-boundary
+cases. It compares schema-only checks, the previous aggregate quality gate, and
+per-required-evidence-type validation. Source-derived labels are not expert annotations.
+
+```bash
+uv run python examples/vbo_canine/run.py --output artifacts/vbo-canine
+```
+
+### Benchmark results (v0.4.1)
+
+![VBO canine benchmark comparing false admissions across three validation methods](https://raw.githubusercontent.com/NingyuSUN/bioai-evidence-validator/main/docs/assets/vbo_canine_benchmark.svg)
+
+On 72 real-source name mappings, the full validator admitted all 48 unambiguous cases and blocked automatic admission of all 24 ambiguous names (0/48 false blocks; 0/24 false admissions). Across 160 deliberately injected faults, false admissions were 160/160 for schema-only, 64/160 for the aggregate-quality ablation, and 0/160 for the full validator; the full validator sent 80 cases to review and rejected 80. All three methods admitted 16/16 falsified-target trust-boundary cases, showing the need for trustworthy source ingestion and supplied metadata.
+
+**Interpretation limits:** Reference labels are derived from the pinned VBO source and authored fault specifications, not independent expert annotations. The 160 mutations share 16 seed cases and are correlated. This benchmark tests the mapping contract and controlled fault detection; it does not estimate biological accuracy or production error rates. See the [protocol and full results](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/examples/vbo_canine/README.md) and [machine-readable summary](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/examples/vbo_canine/results/summary.json).
+
+## Scope
+
+The VBO case uses attributed public data; other fixtures are synthetic.
+Admission means **the supplied record meets the selected
+profile**, not that a biological claim is true. The toolkit does not retrieve papers,
+verify reviewer identities, train models, or measure prediction accuracy. The generic core compares supplied hashes; the VBO importer also hashes its local source
+projection. External source truth and cohort independence require upstream verification.
+
+## Versions and branches
+
+`main` is the domain-neutral framework (0.4.1). The complete canine implementation
+and SQLite adapter from 0.3 live on the
+[`canine-breed` branch](https://github.com/NingyuSUN/bioai-evidence-validator/tree/canine-breed);
+see the [0.4 migration guide](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/docs/MIGRATION-0.4.md) and
+[changelog](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/CHANGELOG.md).
+
+## Citing
+
+If you use this toolkit in research, please cite it using the metadata in
+[`CITATION.cff`](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/CITATION.cff)
+(GitHub's "Cite this repository" button generates APA and BibTeX).
+
+[Create a profile](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/docs/PROFILES.md) ·
+[Engineering contract](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/docs/ENGINEERING.md) ·
+[Design case study](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/docs/CASE_STUDY.md) ·
+[Architecture decision](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/docs/ADR-002-domain-neutral-main.md) ·
+[Apache-2.0](https://github.com/NingyuSUN/bioai-evidence-validator/blob/main/LICENSE)