digital-registrar 0.2.0b3

The Digital Registrar — a schema-first framework for multi-cancer, privacy-preserving pathology abstraction via local LLMs.

Digital Registrar

A schema-first framework for multi-cancer, privacy-preserving pathology abstraction via local LLMs.

TL;DR — pip install digital-registrar-gui && registrar-infer-gui → paste a pathology report → get structured JSON. Requires either a local Ollama server with one of gpt-oss:20b / qwen3:30b / gemma3:27b pulled, or an OPENAI_API_KEY. See Quickstart.

Digital Registrar transforms free-text surgical pathology reports into machine-readable registry records using a College of American Pathologists (CAP)-aligned clinical ontology, encoded as strictly-typed DSPy signatures. The system covers 10 major cancer types across 192 per-organ registry field cells (60 unique field names) — including complex variable-length structures like lymph-node groups and surgical margins — and is model-agnostic: any local LLM can serve as the inference engine. Designed for on-premise deployment on a single 48 GB GPU, it keeps sensitive clinical text inside the institution.

Highlights

• Schema-first architecture — the clinical ontology is the durable contribution; LLMs are interchangeable engines.
• CAP-aligned, registry-grade — 10 cancer types, 192 per-organ field cells (60 unique), validated against gold-standard human annotations.
• Privacy-preserving by design — local LLMs only, single 48 GB GPU, no cloud round-trip required.
• Validated generalizability — 92.0 % macro-mean exact-match on 893 internal reports (10 organs); 77.5 % on the external TCGA cohort of 242 reports — 88.0 % after excluding structurally-silent fields (paper).

Quickstart (end users)

Prerequisites — pick one LLM backend

The toolkit is BYO-LLM. You need either:

• Local Ollama with one of the three paper-benchmarked models pulled:

  ollama pull gpt-oss:20b      # default — best accuracy on internal validation
  ollama pull qwen3:30b        # alt MoE (Qwen3-30B-A3B)
  ollama pull gemma3:27b       # alt dense
  

  Sized for a single ~48 GB GPU. Smaller VRAM works with quantised tags but is unbenchmarked.

• OpenAI: set OPENAI_API_KEY in your env (or in ~/.config/digital-registrar/.env), then pick gpt5_4_mini in the GUI's model dropdown.

Run the GUI in 30 seconds

# Path A — local Ollama (default)
pip install digital-registrar-gui
registrar-infer-gui                 # opens http://localhost:8502 with gpt-oss:20b

# Path B — OpenAI
export OPENAI_API_KEY=sk-...
pip install digital-registrar-gui
registrar-infer-gui                 # then change the model selector to gpt5_4_mini

Paste a report (or point at a folder of .txt files) and the structured JSON appears on the right. The expander shows the full DSPy LM trace (router + group extractors).

Other packages

The toolkit ships as four pip-installable packages. Pick the apps you need:

# Inference GUI — paste a report, see the structured extraction
pip install digital-registrar-gui
registrar-infer-gui                 # opens http://localhost:8502

# Annotation tool — review pipeline output against gold
pip install digital-registrar-annotator
registrar-annotate-workspace

# Schema editor — curate the CAP-aligned per-organ schema
pip install digital-registrar-schema-editor
registrar-schema-gui

# Core only (CLI + Python API) — for pipelines, scripts, and downstream tools
pip install digital-registrar
registrar-pipeline --input <folder>

Each app depends on digital-registrar (the core), so installing any of the apps brings the pipeline along automatically.

Audience

Built for cancer registrars, pathology informatics teams, and clinical researchers who need registry-grade structured extraction from narrative pathology reports without sending PHI off-premise.

Repository layout

drr-next/
├── src/digital_registrar/      ← THE core (pipeline, schemas, signatures, eval, paths)
├── apps/
│   ├── infer-gui/              ← digital-registrar-gui (Streamlit inference)
│   ├── schema-editor/          ← digital-registrar-schema-editor
│   └── annotator/              ← digital-registrar-annotator
├── attic/                      ← research scaffolding (benchmarks, ablations, baselines, obfuscator)
├── packaging/                  ← release pipeline (PyInstaller, Docker, hosted demo)
├── workspace/                  ← gitignored runtime data (data, results, runs)
├── examples/                   ← small read-only fixtures
├── tests/                      ← core tests
└── docs/                       ← architecture, API, eval, release

Dev install (cloners)

git clone https://github.com/kblab2024/digitalregistrar.git digitalregistrar 
cd digitalregistrar 
make install-dev      # installs core + 3 apps + dev tooling
make test             # core + app test suites
make lint             # ruff

make install-dev installs the vendored tnmhelper wheel first, then pip install -e . (core), then pip install -e apps/<each> for the three downstream apps. Anyone with pip can clone and install in one command — no uv required.

Public Python API

from digital_registrar import (
    run_pipeline, setup_pipeline,                  # extraction
    load_pydantic_model, load_json_schema,         # schemas
    list_organs, CASE_MODELS, build_case_model,
    build_extraction_signatures, ExtractionStep,   # signatures
    field_metrics, nested_field_metrics,           # eval
    pairwise_compare, completeness, score_case,
    WORKSPACE_ROOT, workspace_root, results_root,  # paths
)

See docs/api.md for the full reference.

Documentation

Topic	Where
Pipeline architecture (v1 legacy, v2 factory)	docs/architecture/pipeline.md
Three-layer schema architecture	docs/architecture/schemas.md
AJCC TNM staging via tnmhelper	docs/architecture/staging.md
DSPy deep dive	docs/architecture/dspy_deep_dive.md
Annotation workflow	docs/workflows/annotation.md
Eval (prediction vs annotation)	docs/eval/index.md
Public Python API	docs/api.md
Release pipeline (PyPI / hosted demo / bundles / Docker)	docs/release.md
Research scaffolding (benchmarks, ablations, obfuscator)	attic/README.md

Releasing

The project supports three distribution paths for layman users (see docs/release.md):

• PyPI — pip install digital-registrar-gui for Python users.
• Hosted Streamlit demo — public URL for paper reviewers / casual visitors. Safety checklist in docs/release.md.
• Native bundles + Docker — .dmg / .exe / Docker images for non-technical end users, built via make bundle and make docker-build.

Citation

If you use the Digital Registrar in your research, please cite:

Chow N-H, Chang H, Chen H-K, et al. Digital Registrar: A Schema-First Framework for Multi-Cancer Privacy-Preserving Pathology Abstraction via Local LLMs. Diagnostics. 2026;16(11):1644. doi: 10.3390/diagnostics16111644

Machine-readable metadata in CITATION.cff.

License

MIT — see LICENSE.