Clinical NLP with
John Snow Labs

We build John Snow Labs clinical NLP pipelines that de-identify, extract, and structure healthcare data at scale, turning free-text records into HIPAA-safe, analytics-ready clinical insight.

Trusted by Fortune-500 brands and ambitious startups across 36 countries
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What changes for you

HIPAA-Safe clinical
NLP at scale

Free-text records de-identified and structured into analytics-ready data, safely.

  • HIPAA-safe de-identification at scale

    JSL de-identification achieves >99% precision and recall on PHI across clinical note types. Every de-identified record has an audit log. The output meets HIPAA Safe Harbour de-identification standards and is suitable for research partnerships, AI training pipelines and population health analytics.

  • Clinical entity extraction at EHR scale

    JSL NER models extract: diseases, medications, dosages, procedures, anatomical sites, clinical findings, temporal expressions - linked to SNOMED CT, RxNorm, LOINC and ICD-10. Free text becomes queryable structured data. Your analytics team can finally query what's in the notes.

  • Coding assistance that doubles throughput

    ICD-10 and CPT code suggestions with confidence scores and supporting text extracts from the clinical note. Coders review and confirm - they don't code from scratch. On complex multi-code records, this typically doubles coder throughput and improves accuracy on missed secondary diagnoses.

Where most integrations break

Why generic NLP misses clinical text

General NLP misreads clinical language; John Snow Labs is built for medical context.

Who we work with

Built for the clinical data owner

Whoever owns research or coding data: we deliver accuracy on real clinical text.

Chief Research Officer · VP Research

Our research partnership is blocked because we can't de-identify 500,000 records.

JSL de-identification pipeline runs your backlog in hours, with an audit log per record your IRB can review.
  • De-ID in hours not months · >99% PHI detection
  • Audit log per record for IRB review
  • HIPAA Safe Harbour compliance on the output
CMIO · Clinical Informatics Lead

80% of our clinical data is unstructured. Analytics can only query structured fields.

JSL NER extracts diseases, medications, procedures, findings from free text linked to SNOMED/RxNorm/LOINC. Your data lake gains the free-text layer.
  • Clinical NER → structured entities linked to SNOMED/RxNorm/LOINC
  • Free text → queryable structured data at EHR scale
  • ↑ 400% queryable clinical data coverage
VP Revenue Cycle · Coding Manager

Our coders are backlogged. Complex multi-diagnosis records take longest and have the most missed codes.

ICD-10/CPT suggestions with supporting text from the clinical note. Coders review - they don't code from scratch.
  • ↑ 2.1× coder throughput on complex records
  • Supporting text shows coders where the code evidence is
  • Coder override logging · accuracy trending over time
CISO · DPO

We need to know every piece of PHI in our unstructured data estate.

JSL PHI detection across your clinical free text: names, dates, locations, identifiers, context-dependent PHI. Full data map.
  • PHI detection across all clinical note types
  • Data map: where PHI exists in your unstructured estate
  • Audit trail for compliance and data governance
Data Scientist · Head of Analytics

I want to run population health queries over clinical notes. I can't because the data isn't structured.

JSL NER + annotation pipeline turns your free-text notes into a structured, queryable layer alongside your EHR structured data.
  • Clinical NER → queryable entities
  • Annotation pipeline: automated + human-in-the-loop review
  • Integration with Databricks / Snowflake / BigQuery
Head of Pharmacovigilance

We need to detect adverse drug events from free-text clinical notes at population scale.

JSL adverse drug event extraction models run across your clinical note population detecting, classifying and causality-attributing ADEs your structured data misses.
  • ADE extraction across clinical note population
  • Causality and severity classification included
  • Population-scale surveillance without manual review
Production workflows we've shipped

Clinical NLP workflows in daily use

De-identification, entity extraction, and ICD/CPT coding running live.

Ecommerce
Research

De-identification for research datasets

500k clinical records de-identified at >99% precision/recall with audit log per record. IRB-compatible.

↓ 9mo backlog → 19hr runtime
B2B SaaS
Revenue cycle

ICD coding assistance

Clinical notes → ICD-10/CPT suggestions with supporting text. Coders review.

↑ 2.1× coder throughput
Healthcare
Analytics

Free-text → structured data

NER over clinical notes → structured disease, medication, procedure entities linked to SNOMED/RxNorm.

↑ 400% queryable clinical data coverage
Finance
Pharmacovigilance

Adverse event extraction

Clinical notes → adverse drug event extraction with causality and severity. Population-scale surveillance.

↓ 87% manual review time
Legal
Quality

Quality measure extraction

NLP over clinical notes → HEDIS/PQRS quality measure evidence extraction. Automated quality scoring.

↑ HEDIS measure capture rate 28pts
Logistics
Population health

Disease cohort identification

Identify patients with conditions buried in free text not just ICD codes.

↑ 3.1x cohort identification precision
services
AI training

Clinical AI training data

De-identified, entity-annotated clinical text for fine-tuning clinical language models.

Raw EHR to Labelled Data
Education
Compliance

PHI audit and data mapping

Identify where PHI exists across your unstructured data estate for compliance and data mapping.

PHI data map across EHR free text
Cross
Drug discovery

Literature mining

Systematic extraction of clinical findings from published literature + EHR data for research.

↓ 6wks → 2d per literature review
The delivery sprint

Clinical text to coded Pipeline

Week 1-2 · Clinical NLP audit

Sample your clinical text

Sample 1,000 clinical notes across your note types. Benchmark JSL de-identification and NER on your actual text. Accuracy report on your sample before we propose the full pipeline.

DeliverableClinical text sample · JSL accuracy report · pipeline architecture
Week 2-5 · Pipeline build

De-ID + NER + coding pipeline

De-identification pipeline. Clinical NER with SNOMED/RxNorm/LOINC linking. ICD/CPT coding assistance (if in scope). Audit log per record.

DeliverablePipeline in staging · accuracy on held-out sample · audit log live
Week 5-7 · Scale & integrate

Spark cluster + EHR integration

Spark cluster configuration for your record volume. EHR integration (HL7 FHIR, Epic, Cerner, or batch export). Backlog run at scale. Integration with your data lake.

DeliverableProduction pipeline · backlog clearing · data lake integration
Week 7-8 · Hand-off

Runbooks + pipeline ownership

Runbooks, pipeline maintenance docs, re-run procedures, accuracy monitoring. Optional 3-month SLA.

DeliverableFull pipeline ownership · accuracy monitoring · runbooks
STACK-SPECIALIZED

The stack behind clinical NLP

The John Snow Labs, pipeline, and validation stack tuned for clinical accuracy.

AI & Frontend
Deep integrations.
Maximum performance.
React / Next.js
Angular / Vue.js
HTML5 / CSS3
JavaScript
React Native
Swift / Kotlin
Intelligent interfaces built for modern user interactions.
Backend & AI Systems
Scalable. Secure.
Production-ready.
Node.js / Laravel
Python / FastAPI
Azure DevOps
Docker / Jenkins
AWS / Google Cloud
Microsoft Azure
Secure, scalable architectures powering intelligent systems.
Data & Enterprise Systems
One codebase.
Many platforms.
MongoDB / MySQL
SQLite / SQL Server
WordPress / Magento
Shopify
Vector Databases
AI Retrieval Systems
Reliable data foundations for automation and intelligence.
No vendor lock-in Pause, pivot or stop anytime.
Tailored to your goals Tech that fits your roadmap.
Built for speed & scale Deliver value, faster.
Secure by default Best practices, every time.
AI PRODUCTS, IN PRODUCTION

NLP systems structuring healthcare data

Live pipelines turning free-text records into coded, analytics-ready data.

Industry expertise

We've shipped here. Many times over

Deep teams with industry context - not generalists googling compliance acronyms. Each industry below has 30+ shipped projects and a partner who knows the regulator.

Word of mouth

What clients tell their peers.

Real names, real companies, real numbers. Video on the left, written notes on the right - choose whichever feels more honest.

trieval

"They feel like our team — not a vendor."

RH
Ismail Abualsmah
CEO, Trieval
01:18
Repeat client
Although regulations prevented the site's launch, it met all requirements in terms of form and function. Fullestop's project plan charted a clear course to completion. The team's flexible, diverse talent pool enabled them to manage each stage of the project with consistent levels of skill.
Fast turnaround
Weekly demos, no surprises, and they push back when we're wrong. That last part is rare. Cut our cloud bill 47% in the first audit.

News & insights

Check Out the Latest Trends and Tech Discussions

We constantly come up with top-tier resources and breathtaking ideas that would help you stay informed about
the latest happenings in the tech world.

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Frequently Asked Questions

The questions every founder asks us.

  1. John Snow Labs NLP processes diverse formats, including physician notes, pathology reports, discharge summaries, and clinical trial documents, reliably.

  2. Yes, it has certified PHI de-identification models that remove personal identifiers while preserving data utility for research and analytics.

  3. Models are fine-tuned with domain-specific context, leveraging negation detection and disambiguation algorithms to clarify shorthand effectively.

  4. Fullestop offers fine-tuning on client-specific data, integration with custom workflows, and tailored dashboards for actionable insights.

  5. Yes, its fast processing allows extraction of timely insights from incoming clinical text to assist immediate point-of-care decisions.

Pick your starting line

Three ways to get clinical NLP working on your data.

Health system needing HIPAA-safe text extraction or a clinical research team building NLP pipelines from EHR data we have a low-risk first step for both.