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Agent Annotate — Standalone

Publication-grade clinical-trial annotation with a local multi-agent LLM pipeline.

Agent Annotate takes a list of ClinicalTrials.gov NCT IDs and produces structured, evidence-backed annotations for each trial — running entirely on your own machine against models served by Ollama. No data leaves your host except read-only queries to public research APIs.

This is the standalone repackaging: a single self-contained FastAPI service with no external auth, no sibling services, and a one-command installer. It runs on any machine that can run the models (macOS, Linux, or Windows).

What it does

For each trial it answers six fields, each backed by cited evidence:

Field Question
classification Is the intervention an antimicrobial peptide (AMP) or not?
peptide Is the drug a peptide, and what is its sequence/identity?
sequence The amino-acid sequence, when identifiable.
delivery_mode How is it administered (IV, topical, oral, …)?
outcome Did the trial succeed, fail, or is the outcome unknown?
reason_for_failure If it failed, why?

The pipeline works in three stages:

  1. Research — ~25 parallel agents query public databases (ClinicalTrials.gov, PubMed/PMC, FDA, UniProt, ChEMBL, RCSB PDB, DRAMP, DBAASP, SEC EDGAR, NIH RePORTER, and more) and collect evidence.
  2. Annotation — a primary LLM proposes each field from the evidence.
  3. Blind multi-model verification — three different model families independently verify each annotation from distinct adversarial personas (conservative / evidence-strict / adversarial), and a reconciler resolves disagreements. This cognitive diversity is what makes the output publication-grade.

Deep technical detail lives in docs/METHODOLOGY.md and the end-user walkthrough in docs/USER_GUIDE.md.

Requirements

  • OS: macOS, Linux, or Windows 10/11 (PowerShell).
  • Python: 3.10 or newer (3.11 / 3.12 recommended for the widest wheel support).
  • Ollama: installed automatically by the installer.
  • RAM: the default mac_mini model profile fits comfortably in 16–24 GB. The optional server profile needs 240 GB+.
  • Disk: ~25–30 GB for the default models.
  • Network: outbound HTTPS to public research APIs (see Network egress). The API boots fine offline, but annotation jobs need internet.

Quick start

macOS / Linux

git clone <this-repo-url> agent-annotate
cd agent-annotate
git checkout birollabs-migration

./install.sh        # installs Ollama + models + Python deps  (use --server for big models)
./run.sh            # starts the API; auto-selects a free port and prints the URL

Windows (PowerShell)

git clone <this-repo-url> agent-annotate
cd agent-annotate
git checkout birollabs-migration

.\install.ps1       # installs Ollama + models + Python deps  (-Server for big models)
.\run.ps1           # starts the API; auto-selects a free port and prints the URL

run.sh / run.ps1 pick the first free port starting at 9005 and print the exact URL (e.g. http://127.0.0.1:9005). Pin one with PORT=8080 ./run.sh. The examples below use 9005 — substitute whatever port it printed.

Verify it's up (use the printed port):

curl http://127.0.0.1:9005/api/health
# {"status":"ok","version":"0.1.0"}

Open the same URL in a browser for the bundled web UI.

What the installer does

install.sh / install.ps1 is idempotent — safe to re-run. It runs a full preflight and warns (without aborting) on anything that could bite you:

  1. Preflight checks — verifies Python 3.10+, venv/pip, git, curl, and network reachability; measures RAM and free disk and warns if either is below what the chosen model profile needs, so you find out before a multi-GB pull fails.
  2. Installs Ollama if absent, starts its server, and waits for it.
  3. Pulls the LLM models for the chosen profile (cached models verify instantly).
  4. Creates a .venv virtualenv and installs requirements.txt.
  5. Creates the runtime directories (results/…, logs/) and copies .env.example → .env.

It prints a summary with a warning count at the end. Flags: --server (large profile) and --skip-models (set everything up but skip the pulls). Re-pull a single model anytime with ollama pull <model>.

Models & hardware profiles

The pipeline's model selection lives in config/default_config.yaml under orchestrator.hardware_profile. Two profiles ship:

mac_mini (default — 16–24 GB RAM)

Role Model
Primary annotator + reconciler (all 6 fields) qwen3:14b
Annotator / verifier (adversarial) llama3.1:8b
Verifier (conservative) gemma3:12b
Verifier (evidence-strict) qwen3:8b

./install.sh pulls exactly these four.

server (optional — 240 GB+ RAM)

Premium reasoning model (kimi-k2-thinking) for the hardest fields plus larger verifiers (gemma2:27b, qwen2.5:32b, phi4:14b). Install with ./install.sh --server and set hardware_profile: "server" in the config.

Missing models are also auto-pulled by the app on first use, but a cold pull mid-job can be slow — pre-pulling via the installer avoids first-job timeouts.

Using the API

The API is open (no authentication). By default it accepts any valid NCT ID (NCT followed by 8 digits). Jobs are queued and processed one at a time.

1. Submit a job

curl -s -X POST http://127.0.0.1:9005/api/jobs \
  -H 'Content-Type: application/json' \
  -d '{"nct_ids": ["NCT12345678", "NCT87654321"]}'   # replace with real NCT IDs
{ "job_id": "a1b2c3d4e5f6", "status": "queued", "total_trials": 2, "queue_position": 0 }

2. Poll job status

curl -s http://127.0.0.1:9005/api/jobs/a1b2c3d4e5f6
# full job record incl. status: queued → running → completed (per-trial progress)

# live pipeline view (which agent is running on which trial):
curl -s http://127.0.0.1:9005/api/status/pipeline/a1b2c3d4e5f6

3. Fetch results

curl -s http://127.0.0.1:9005/api/results/a1b2c3d4e5f6              # full JSON
curl -s http://127.0.0.1:9005/api/results/a1b2c3d4e5f6/summary     # summary
curl -sOJ http://127.0.0.1:9005/api/results/a1b2c3d4e5f6/csv       # download CSV

Common endpoints

Method & path Purpose
GET /api/health Liveness probe.
POST /api/jobs Create/queue a job ({"nct_ids": [...]}).
GET /api/jobs · GET /api/jobs/{id} List jobs · job detail.
POST /api/jobs/{id}/cancel · /resume Cancel · resume a job.
GET /api/status/pipeline/{id} Live per-trial pipeline status.
GET /api/results/{id} · /csv · /summary Results JSON · CSV · summary.
GET /api/status/models Models available in Ollama.
GET/PUT /api/settings · POST /api/settings/reload Runtime config.
GET /api/review · POST /api/review/{job}/{nct}/{field} Human review queue / corrections.

Interactive API docs are always available at http://127.0.0.1:9005/docs (Swagger UI).

Configuration

Environment (.env)

Copy .env.example to .env. Everything is optional:

Variable Default Purpose
AGENT_ANNOTATE_PORT 9005 App's self-reported port (diagnostics).
OLLAMA_HOST / OLLAMA_PORT localhost / 11434 Where Ollama is served.
OLLAMA_TIMEOUT 600 Max seconds per LLM call.
PUBMED_API_KEY — NCBI key → 10 req/s (vs 3).
OPENALEX_EMAIL / CROSSREF_EMAIL — "Polite pool" contact emails.
CORS_ORIGINS localhost:5173,9005 Browser origins allowed to call the API.

Pipeline (config/default_config.yaml)

Models, the research/annotation agent graph, evidence thresholds, verifier personas, per-model timeouts, and hardware_profile. Edit and call POST /api/settings/reload (or restart) to apply.

Binding host/port

HOST=0.0.0.0 PORT=8080 ./run.sh        # listen on all interfaces, port 8080

Optional: bring your own annotations

Agent Annotate is annotation-only: it accepts any valid NCT ID and runs entirely on its own. There is no concordance / inter-rater-agreement (AC1, Cohen's κ) analysis in the product — it just annotates.

If you have your own human annotations and want to score the agent against them, drop a ground-truth CSV at docs/human_ground_truth_train_df.csv (the column layout expected by scripts/score_full_corpus.py). That enables the optional dev scoring scripts under scripts/ (e.g. compare_jobs.py, score_full_corpus.py) and lets the EDAM memory learn from your labels. It is never required — the annotator works fully without it, and job submission is not restricted by it.

Project layout

.
├── app/                  # FastAPI service: routers, services, models, prebuilt SPA
│   ├── main.py           #   ASGI entrypoint (app.main:app)
│   ├── config.py         #   env + path configuration
│   ├── routers/          #   /api/* endpoints
│   └── services/         #   orchestrator, ollama client, persistence, memory (EDAM)
├── agents/               # research + annotation + verification agents
├── config/               # default_config.yaml (the pipeline definition)
├── frontend/             # React/Vite source for the web UI (prebuilt copy in app/static/spa)
├── scripts/              # dev/eval tooling (scoring, slice-builders, regression tests)
├── docs/                 # methodology, paper, strategy, user guide, business docs
├── install.sh / .ps1     # dependency installers
├── run.sh / .ps1         # start the API
├── requirements.txt
└── .env.example

Generated at runtime (git-ignored): results/, logs/, .venv/.

Where everything is saved

Everything the app writes lives under the repo root and is git-ignored. Nothing is uploaded anywhere — only read-only queries go out to the public research APIs (see Network egress); annotation results never leave your machine.

Path What's stored
results/json/<job_id>.json Final annotation result for a job — every field + its supporting evidence.
results/csv/<job_id>_*.csv Exported CSV of a job's annotations (one row per trial).
results/jobs/<job_id>.json Job/queue state record — used to restore queued jobs after a restart.
results/research/<job_id>/ Per-trial raw research evidence + _meta.json. Written incrementally so a crashed job can resume.
results/annotations/<job_id>/ Per-trial annotation output as it's produced (mid-run progress).
results/atomic_pub_cache/ Cached per-publication assessments (re-used across trials).
results/edam.db SQLite "EDAM" memory store (self-learning corrections). -wal/-shm are transient.
results/review_queue.json Human review-queue corrections submitted via the review API.
logs/agent_annotate.log Rotating application log (10 MB × 10 backups).
.env Your local config (copied from .env.example).

Outside the repo:

Path What's stored
~/.ollama/models/ Downloaded LLM weights — the bulk of the disk footprint (~30 GB for the default profile). Relocate by setting OLLAMA_MODELS.
.venv/ The Python virtualenv (lives in-repo but is git-ignored).

How a job flows through storage: submit → the job record lands in results/jobs/ and the queue → research agents write evidence into results/research/<job_id>/ → annotation + verification write into results/annotations/<job_id>/ → on completion the merged result is written to results/json/<job_id>.json (and CSV on export). Because each stage persists to disk, an interrupted job resumes from where it stopped via POST /api/jobs/{id}/resume.

Cleaning up: delete results/<*>/<job_id>* to remove a single job, or wipe the whole results/ tree to reset all output — the app recreates the directory structure on the next start. Model weights are managed separately with ollama rm <model>.

Development

  • Run the test suite: bash scripts/run_full_regression.sh (source-level trip-wires + versioned regression tests + live API integration tests).
  • Score a job vs ground truth: python scripts/score_full_corpus.py / python scripts/compare_jobs.py (require the GT CSV in docs/).
  • Build NCT slices: the scripts/pick_*.py utilities.
  • The living development docs are CONTINUATION_PLAN.md, LEARNING_RUN_PLAN.md, and docs/AGENT_STRATEGY_ROADMAP.md.

Troubleshooting

Symptom Fix
503 Ollama is unreachable on job submit Start Ollama: ollama serve. Confirm curl localhost:11434/api/tags.
Job stuck at "running" / very slow First call cold-loads the model. Big models (qwen3:14b) take time; raise OLLAMA_TIMEOUT.
ollama pull fails / times out Re-run ollama pull <model>; check disk space and network.
Annotation fields all "Unknown" Likely no internet egress to the research APIs — see below.
Address already in use Another process holds the port — PORT=9006 ./run.sh.
pip install fails on Python 3.13/3.14 Use Python 3.11 or 3.12: PYTHON_BIN=$(which python3.12) ./install.sh.
Web UI 404s but /api/health works The prebuilt SPA at app/static/spa/ is missing; the API still works headless.

Network egress

Real annotation queries these public hosts (read-only): clinicaltrials.gov, api.fda.gov, accessdata.fda.gov, eutils.ncbi.nlm.nih.gov / pubmed.ncbi.nlm.nih.gov, europepmc.org, api.openalex.org, api.semanticscholar.org, api.crossref.org, doi.org, rest.uniprot.org, dramp.cpu-bioinfor.org, dbaasp.org, www.ebi.ac.uk, *.rcsb.org, aps.unmc.edu, guidetopharmacology.org, trialsearch.who.int, api.reporter.nih.gov, efts.sec.gov / www.sec.gov, lite.duckduckgo.com. The app boots and health-checks fine without them; only annotation degrades.

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An LLM-based peptide clinical trial annotation tool/workflow.

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