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Transform Healthcare Research with Enterprise-Grade OMOP

A complete platform for turning your healthcare data into research-ready OMOP, with tools that go far beyond Atlas.

 

Is Your Data Stuck in the 20th Century?

The OHDSI ecosystem offers powerful possibilities, but most organizations struggle to unlock them.

Rigid Data Architectures

Researchers work on stale snapshots, without common data model, and no way to do collaborative research across institutions

Limited Toolboxes and Restricted Use Cases

No data upload, Not IRB integration, No private workspaces, No ID/DeID, No lineage, auditability or tracking of mapping and data elements

Half-baked OMOP Transforms

Limited to single departments or incomplete mapping, multiple DBs for PHI and de-identified data, batched based, brittle and/or poorly document. Most vendors deliver one-time ETL which you then use every month or quarter to rip and replace your data. Researchers wait weeks or months. Changes in the underlying data go un-noticed and undocumented. All of this makes research difficult to replicate across multiple sites.

Cognome's Comprehensive OMOP Solution

Service + Product Bundle: A complete ecosystem for transforming healthcare data into actionable research insights. All running in your environment. Your data. Your way. All the time.

Data Transformation Services

We transform your source data (EHR, claims, bio repositories, etc.) into an OMOP Common Data Model (CDM) with proven methodology and AI-powered concept mapping.

Cognome I/O

Enterprise data transformation platform that you can run (or we can manage for you). Takes real world multi-modal data from your EHR (and more), maps to your OMOP instance with real-time updates, provenance tracking, lineage and reproducibility. As well as regulatory grade compliance and governance with audit tracking & traceability.

Cognome Search

Self-service research platform that sits on top of any OMOP instance and makes your data accessible to researchers with capabilities far beyond OHDSI's Atlas.

PART 1:

Data Transformation Services

Most OMOP transformations fail or stall on concept mapping – the tedious, error-prone work of mapping thousands of always changing local EHR terms to standardized OMOP vocabulary. Our AI-powered approach changes everything.

LLM-Powered Concept Mapper

The OMOP Concept Mapper is a four-stage, LLM powered pipeline designed to automatically translate proprietary EHR terms into standardized concepts within the OMOP Common Data Model (CDM). The pipeline works by first expanding the input term, then retrieving candidate concepts from a knowledge graph, filtering out irrelevant matches, and finally selecting the best concept with a confidence score and justification for a human to approve. Accuracy is currently running at high 90th percentile.

Argos Interrogator

Argos Interrogator is a core component of Cognome I/O. It is the metadata intelligence layer. Its job is to automatically understand, document, and govern the source data as it gets transformed into OMOP. Specifically, it does four things:

1. Source Schema Interrogation: Automatically reads and understands the structure of a your source data systems (like Epic CLARITY), so you don't have to manually map it out.

2. Document Change Management: Tracks all schema changes over time, so if something upstream changes in the source system, Argos catches it and documents it.

3. Metadata Management & Concept Mapping: Links source concepts to OMOP vocabulary, and the OMOP Concept Mapper (the LLM-powered auto-mapping tool) sits here as well.

4. Data Quality Governance: Enforces quality rules on the underlying data and alerts on violations. This is distinct from the data quality reports in Search, which are about the quality of data within a cohort.

Multi-Modal Data Support

We bring all your data into your OMOP CDM - and expand the OMOP ontology to allow for it. This includes biological, clinical, health system community and societal data as well as structured EHR data, notes, images and data from devices. Everything is FAIR: Findable, Accessible, Interoperable & Reusable. Which makes it machine interpretable. We store the data in our semantic knowledge graph.

Supported Data Sources

EHR Systems
Epic
Oracle Health (Cerner)
MediTech
Extensible to any other EHR
 
Additional Sources
Notes of all types
Disease registries
Genomics
Claims
Imaging
Waveform

PART 2:

Cognome I/O

Enterprise data transformation engine with real-time capabilities, complete lineage, and platform-agnostic architecture.

Platform Agnostic

Works with Snowflake, Databricks, Oracle, InterSystems IRIS, PostgreSQL, SQL Server, and more

Complete Audit Trail

Machine-readable documentation of all transformations and access for reproducibility

Version Control

Complete version control and rollback capabilities for all mappings and transformations

Real-Time Updates

Continuous incremental updates (daily or real-time) built on Apache Spark for massive parallelization

Dynamic De-identification

Master Entity Index enables bidirectional transformation of patient identifiers based on IRB approval

Privacy-Preserving Linkage

Master Entity Index provides crosswalk matching for patients across systems without exposing PHI

PART 3:

Cognome Search

Cognome Search takes all the features that are available in OHDSI's Atlas and expands them and makes the features easier to use.

 

Cohort Upload

Because we support the ability to de-identify and re-identify data based on your IRB approval. You can import existing MRN lists directly into Search for analysis. Integrate external cohorts from registries, clinical trials, or collaborative studies.

Enable research on pre-identified patient populations without manual chart review.

Private Workspaces

Create secured analytic enclaves for specific research teams. Sometimes you don't want to give access to your entire data set to all researchers. Extract focused 'mini-OMOP' datasets around specific cohorts for focused studies.

Enable secure collaboration without exposing entire database.

IRB Integration

Real-time integration with institutional IRB systems. IRB protocol approval automatically grants appropriate data access. 

Eliminate manual IRB compliance workflows and reduce risk while maintaining only one database as your source of truth.

Unified Honest Brokering

Democratized access: Single database handles de-identified, coded limited and PHI data. Automated honest brokering based on IRB approval levels.

Simplified architecture reduces IT burden and eliminates data sync issues.

Dynamic De-identification

Automatic de-identification based on IRB protocol permissions. Researchers see only the data their protocol allows.

Reduces compliance burden and risk automatically.

ElasTex: Integrated NLP

Query clinical notes text directly, not just structured data. Build cohorts using concepts from unstructured clinical documentation.

Access the 80% of clinical data trapped in free text.

Cognome’s platform creates a unified ecosystem where you don’t just store data, you learn from it. Combine a real-time Learning Health System + embedded predictive analytics + secure, governed data collaboration and turn insights into action.

Governance, Privacy, and Honest Brokering

Built-in compliance infrastructure that protects patient privacy while enabling powerful research capabilities.

  • Complete audit trail: patients → data → users → IRBs and reverse

  • Dynamic de-identification AND re-identification based on IRB approval

  • Automated honest brokering workflows

  • Privacy-preserving record linkage across institutions

  • Governance rules determine what each user sees

  • Supports reproducibility standards for publication and regulatory compliance

IRB Compliant

Automated access controls

HIPAA Ready

Enterprise security

Full Audit Trail

Complete traceability

Role-Based Access

Granular permissions

Flexible Engagement Models

Choose the approach that fits your organization's resources and objectives.

 

Full-Service Model

Cognome handles all data transformation work

  • We maintain and update your OMOP instance

  • Ongoing support and optimization

  • Client gets finished product + tools

Train-and-Enable

Cognome performs initial transformation

  • We train your team to manage updates

  • Client manages the entire end-to-end process

  • Ability to license and extend source code if needed for custom solutions

  • Cognome provided support as needed

Hybrid Model

Mix based on your resources and preferences

  • Cognome handles complex initial build

  • Client maintains routine updates

  • Customized partnership based on your capabilities and budget

Why Cognome

World-class team with proven implementation experience.

15+ Years Experience

Building OMOP data lakes with blue-chip academic medical centers: UT Health, Montefiore, Einstein, NYU Langone, Johns Hopkins, Ohio State.

OHDSI Community Leadership

Active contributors with symposium presentations, published research, and development of advanced tools like LLM-powered concept mapping.

Grant Collaboration Support

Experienced team supporting grant applications and co-authoring research proposals. We understand academic funding requirements.

Embedded Academic Partnership

Team members currently working inside academic institutions who understand research workflows firsthand.

Multidisciplinary Team

Fellow researchers, data scientists, software engineers, product managers who understand the full research lifecycle.

Cost-Flexible Resources

Wholly owned subsidiary enables flexible onshore/offshore resource models, delivering significant cost savings without sacrificing quality. (Note: all work is performed in the USA unless explicit permission is granted)

Ready to Transform Your Research Data Infrastructure?

From first call to contract, typically 1-3 months.

1
Discovery Call
Assess current state and objectives

 

2
Gap Analysis
Often free for qualified prospects

 

3
Customized Proposal
Scope, timeline, and pricing

 


 Contact us to get started