Opengate MCP Server

OpenGATE

Evidence over plausibility.

OpenGATE is an open-source framework for evaluating evidence-grounded AI systems — systems that must justify every answer from underlying source documents. It measures one thing above all: can the system prove its answer from the source material?

As AI moves into high-stakes domains — healthcare, scientific publishing, regulatory, legal, finance — evaluation is becoming as fundamental as automated testing is in traditional software engineering. OpenGATE turns grounding failures into numbers you can track, and gates every prompt, model, or workflow change against a baseline so reliability can't quietly regress.

Originally developed to power RefCheckr. Designed to evaluate any AI system built on retrieved documents or reference material.

Evaluating your own RAG, doc-QA, or legal/scientific assistant? Scaffold a working setup in one command:

npx @pharmatools/opengate init      # gold cases + HTTP config + GitHub Action

Then point opengate.http.json at your endpoint and run. Full walkthrough in the Getting Started guide.

Why not DeepEval?

Use both. General-purpose frameworks such as DeepEval and OpenAI Evals evaluate AI systems in general. OpenGATE specialises in systems that must justify every answer from evidence:

• Provenance is first-class — does the cited passage actually exist, verbatim, in the source?
• Citation fidelity is first-class — are the right citations detected and mapped to the right references?
• Regression detection is first-class — every run is diffed against a baseline; drops fail the build.

If your system's core promise is grounded answers, these aren't plugins — they're the whole evaluation. That's the niche OpenGATE fills.

First evaluation in 60 seconds

No API key needed — the offline suite tests deterministic logic against the bundled gold set:

npx @pharmatools/opengate

Or from a clone:

git clone https://github.com/nickjlamb/opengate.git
cd opengate
npm run eval

For programmatic use, the metric and citation primitives are importable directly:

import { detectCitations, verdictAccuracy, precisionRecallF1 } from '@pharmatools/opengate';

OpenGATE — 25 case(s), online=false, sha=eff971b

  ✓ citation-detection   PASS
      perClaim_exactSetRate      100.0%
      perClaim_jaccardMean       100.0%
      supportedStyle_accuracy    100.0%
  ⊘ claim-extraction     SKIPPED — online scorer (pass --online)
  ⊘ verdict-accuracy     SKIPPED — online scorer (pass --online)

To run the online scorers against a live system (bundled RefCheckr adapter):

export REFCHECKR_BASE_URL=http://localhost:3848
export REFCHECKR_TOKEN=<a valid auth token>
export OPENGATE_EVAL_REPEATS=3        # optional: measure verdict consistency
export OPENGATE_EVAL_MODEL=sonar-pro  # optional: label the model in the scorecard

npm run eval:online
npm run eval:baseline   # save current run as the regression reference
npm run eval:ci         # exit non-zero on any failure or metric regression

Architecture

                        ┌─────────────────────────────────┐
                        │            OpenGATE             │
                        │                                 │
                        │  benchmark datasets (gold sets) │
                        │  scorers (one per metric family)│
                        │  scorecards (versioned, on disk)│
                        │  regression gate (CI)           │
                        └───────────────┬─────────────────┘
                                        │ adapters
                 ┌──────────────┬───────┴──────┬──────────────┐
                 ▼              ▼              ▼              ▼
          RefCheckr    Redacta    Patiently AI   PubCrawl    your system
         (QA, first) (redaction)  (simplify)   (retrieval)  (write one)

Where it sits in the development loop:

change a prompt, model, or pipeline
              ↓
        run OpenGATE
              ↓
     metrics vs baseline?
        ↙          ↘
  ▲ improved      ▼ regressed
    deploy         investigate (build fails in CI)

Core concepts

Gold cases — hand-labelled benchmark cases (datasets/cases/): source text, the claims that should be extracted, the sentences that should not be, and reference snippets with known-correct verdicts. Copy _template.json to add one; format spec in datasets/SCHEMA.md, labelling rules in datasets/LABELING-GUIDE.md.

Scorers — one module per metric family (src/scorers/):

Offline scorers run with no API key — fast enough for every commit. Online scorers exercise a live system through an adapter.

Scorecards — every run writes results/<timestamp>.json stamped with the git SHA, so any result is reproducible and auditable. Per-model runs carry a run_model label, turning the results directory into a measured model comparison (accuracy × hallucination × latency × cost).

Regression gate — --baseline saves a reference; subsequent runs print per-metric deltas (▲/▼ in percentage points) and --ci fails the build on any drop. Baselines are per-adapter (baseline.<adapter>.json), so a PubCrawl retrieval scorecard can't clobber a RefCheckr QA one — each adapter keeps its own reference. No change ships without proving it didn't make the system less reliable.

HTML report — add --report to any run (or opengate report to render the latest snapshot) for a self-contained HTML dashboard: pass/fail per scorer, metric deltas vs baseline, and every named failure. One file — open it, email it, or attach it to a CI run. No dependencies, no server.

Adapters: evaluating your own system

Scorers never talk to a system directly — they go through an adapter, injected by the runner. The bundled src/adapters/refcheckr.mjs is the reference implementation; select your own with:

OPENGATE_ADAPTER=./adapters/my-system.mjs npm run eval:online

--adapter (and OPENGATE_ADAPTER) accept a path, or a bare bundled-adapter name — http, refcheckr, redacta, patiently, pubcrawl — which resolves regardless of the current directory. That's what lets the GitHub Action reference the bundled HTTP adapter with just adapter: http.

An adapter is one file: two base exports — onlineAvailable(), onlineConfigHint() — plus at least one complete capability: qa (splitClaims + analyzeBatch) or redaction (redact). Scorers check adapter.capabilities and skip cleanly across the boundary. Optional timing/token/model-label hooks unlock latency and cost columns in the scorecard. Adapters are validated at load: a malformed one fails fast with a message naming every missing export and incomplete capability.

For REST-backed systems there's a no-code path: the bundled generic HTTP adapter (src/adapters/http.mjs) reads endpoint paths and headers from opengate.http.json (see opengate.http.example.json), with ${ENV} interpolation and built-in latency/token capture.

Full contract, minimal skeleton, and verdict-mapping notes: ADAPTERS.md. New to OpenGATE? The Getting Started guide walks a generic RAG system from zero to a CI gate.

The methodology travels; only the gold set changes.

MCP server: agents that check their own grounding

Beyond CI, OpenGATE's grounding check is available as an MCP server (@pharmatools/opengate-mcp), so an AI agent can verify its own answers before returning them — "here's my answer and the context I based it on, is it grounded?" One tool, check_grounding; deterministic, no judge model. Add it to Claude Desktop or any MCP client:

{ "mcpServers": { "opengate": { "command": "npx", "args": ["-y", "@pharmatools/opengate-mcp"] } } }

The same check is importable programmatically: import { checkGrounding } from '@pharmatools/opengate/grounding'.

CI: the GitHub Action

Use OpenGATE as a drop-in regression gate in any repository. Keep your gold set and committed baseline (baseline.<adapter>.json) in your own tree; any metric that drops fails the build:

- uses: nickjlamb/opengate@v0
  with:
    datasets: ./evals/datasets      # your cases/ + fixtures/
    results: ./evals/results        # where baseline.<adapter>.json lives
    adapter: ./evals/my-adapter.mjs # or the bundled HTTP adapter
    online: 'true'
  env:
    MY_SYSTEM_URL: ${{ vars.MY_SYSTEM_URL }}
    MY_SYSTEM_TOKEN: ${{ secrets.MY_SYSTEM_TOKEN }}

All inputs are optional — with none, it runs the offline suite against the bundled gold set. The same overrides work locally: --datasets <dir> and --results <dir> (or OPENGATE_DATASETS / OPENGATE_RESULTS).

Proven in production

Run against RefCheckr's gold set, OpenGATE:

• surfaced a silent parse-failure mode affecting ~50% of multi-claim verdicts, eliminated with enforced structured output (→ 0);
• halved passage hallucination (5.8% → 2.4%) by driving a measured production model change — a decision made on numbers, not reputation;
• holds claim extraction at ~0.95 F1 with near-full recall.

Full methodology and the model comparison: how RefCheckr is evaluated.

Second implementation: Redacta

Redacta exercises the framework's redaction capability — proof the methodology isn't QA-shaped. The bundled adapter wraps the @pharmatools/redacta engine, scored against synthetic UK clinical notes with gold-labelled identifiers:

npm install --no-save @pharmatools/redacta
node src/runner.mjs --online --adapter ./src/adapters/redacta.mjs

On its first run against the new gold set, the eval found two real engine bugs — relation phrases like "Next of kin:" swallowed nested name matches, and apostrophe surnames (O'Brien) were dropped from name capture. Both were fixed in @pharmatools/redacta 1.2.1 and confirmed by the eval (knownGap_closed: 2), then promoted to gold. Street-line address detection followed in 1.3.0, closing the last tracked gap. Current scorecard: 100% recall on 25 gold identifiers, 0 leaks, no open gaps.

Third implementation: Patiently AI

Patiently AI exercises the simplify capability — faithfulness scoring for text that is paraphrase by design. On its first production run, the eval found the simplifier dropping safety-critical specifics: an antibiotic dose vanished from a Brief discharge summary and a haemoglobin value from a lab letter (anchor recall 86%). Root cause: the composed prompt had no faithfulness rule. A preservation rule added to Patiently's tone prompts (additively — the backend is shared with another product) took the next run to 100% anchor recall, 0 dropped facts, 0 fabricated numbers, 0 contract violations — with the readability grade slightly better than before the fix.

node src/runner.mjs --online --adapter ./src/adapters/patiently.mjs

Fourth implementation: PubCrawl

PubCrawl is the odd one out — an MCP server wrapping PubMed and ClinicalTrials.gov, with no model. It exercises the retrieval capability: the deterministic layer everything else grounds on. A silent XML-parser regression (a collapsed author array, a merged abstract) would poison every citation built on the record, so the scorer checks retrieval fidelity against hand-verified anchors and structural invariants. The adapter drives PubCrawl through its real MCP interface, so the full production parse path is under test — and scripts/capture-retrieval-case.mjs bootstraps gold cases from live records for you to verify against the source.

npm install --no-save @modelcontextprotocol/sdk
node scripts/capture-retrieval-case.mjs 31904519 > datasets/cases/retrieval-example.json  # then verify anchors
node src/runner.mjs --online --adapter ./src/adapters/pubcrawl.mjs

That OpenGATE scores a non-AI system at all is the point: evidence-grounded AI is only as trustworthy as the retrieval beneath it, so the retrieval belongs in the same regression gate.

Layout

opengate/
  datasets/
    cases/        gold-labelled source sections (copy _template.json to add)
    fixtures/     citation-style coverage fixture
    SCHEMA.md     case format spec
    LABELING-GUIDE.md
  src/
    lib/          metrics.mjs (PRF1, Jaccard, verdict accuracy, confusion matrix)
                  citations.mjs (reference impl of deterministic citation logic)
    scorers/      one file per metric family
    adapters/     system-under-test boundary (refcheckr.mjs is the reference)
    runner.mjs    CLI: discover cases → run scorers → report → snapshot → regression-check
  results/        timestamped run snapshots + baseline.<adapter>.json

Roadmap

• Grounding depth — the grounding scorer checks anchor recall, fabrication, and abstention deterministically; contextual-precision/recall of the retrieved passages themselves is a natural next metric
• Retrieval breadth — retrieval currently scores one PubMed record type; extend to full-text, citation formatting, and trial detail across PubCrawl's other tools
• Retrieval coverage — the retrieval gold set is one case; add a single-author paper (the exact array-collapse risk the capability exists to catch), a trial (NCT) record, and a full-text/citation case across PubCrawl's other tools
• Number-adjacent superscript — week 24.1 is genuinely ambiguous with decimals; remains a tracked known gap
• Growing gold set — more domains, all six verdict types, real-world reference material
• Stable adapter surface — the contract may still shift pre-1.0; semver will signal breaking changes

Contributing

Contributions are welcome, particularly:

• Gold cases — new domains and citation styles (see datasets/LABELING-GUIDE.md)
• Adapters — connect OpenGATE to your evidence-grounded system
• Scorers — new metric families that fit the gold-case format

Open an issue to discuss before large changes. Interfaces — particularly the adapter surface — may still shift pre-1.0.

License

MIT — because evaluation frameworks shouldn't be black boxes. If an evaluation influences deployment decisions, engineers should be able to inspect every scorer, metric, and benchmark.