Healthcare ETL Pipelines Your Dashboards Can Trust
Your EHR, clearinghouse, billing system, and books all report last month differently. We extract from every one of them into a single warehouse, with one definition of production, denials, and days in AR — applied identically across every location.
Book a Discovery CallEvery Argument About Last Month's Numbers Starts in the Pipeline
Four systems, four answers
Charges in the EHR, claim status at the clearinghouse, payments posted in billing, deposits in the bank. Manual exports, three locations on three different report formats, and provider IDs that don't match across systems. Month-end close becomes an argument instead of a review.
The pipeline is the invisible part
Done right, refreshes run automatically before your team arrives, definitions match across locations, and the close takes days instead of weeks. Done wrong, someone rebuilds the same spreadsheet every month and leadership spends the meeting deciding whose number is correct.
Open-source — and your choice of hosting
We build on dbt, Airflow, and n8n on infrastructure you choose: your own cloud account so PHI never leaves your boundary, or hosted and operated by us under a Business Associate Agreement. No per-row pricing, no vendor lock-in, and the pipelines carry over if you ever migrate.
What We Build
EHR-to-Warehouse Pipelines
Extraction from Epic, Oracle Health, athenahealth, eClinicalWorks, DrChrono, NextGen, Open Dental, and Dentrix — plus clearinghouse claim and remittance files, 835/837 data, billing platforms, payroll, and QuickBooks — into ClickHouse, PostgreSQL, BigQuery, or Azure SQL. Where a system only produces scheduled exports, we build the custom extractor.
Transformation & Metric Consistency
We use dbt to turn raw extracts into analytics-ready models — one definition of production, denial rate, net collection rate, and days in AR, with provider and location dimensions normalized so every site is genuinely comparable. Documented lineage, version-controlled, and tested for accuracy before any dashboard touches it.
Orchestration & Scheduling
Pipelines that run manually aren't pipelines. We set up scheduling and orchestration (Airflow, n8n, or Windmill) so your data syncs happen automatically, failures are alerted and logged, and your warehouse is always current without anyone babysitting it.
How an ETL Engagement Works
Discovery & Audit
We audit every system holding a piece of the revenue picture — EHR, practice management, clearinghouse, billing, payroll, scheduling — and document how each location is configured, what it can export, and at what frequency.
Architecture Design
We design the pipeline architecture: which extraction tool fits your sources, what the data model looks like in the warehouse, and how orchestration will be handled. You review and approve before we write a line of code.
Pipeline Build
We build the extraction connections, write the dbt transformation models, and configure orchestration. Every component is version-controlled and documented.
Testing & Validation
We validate data accuracy against source systems, run dbt tests for null checks and referential integrity, and verify pipeline performance under realistic load.
Deployment & Ongoing Management
We deploy to your infrastructure, configure monitoring and alerting, and stay on retainer to handle maintenance, source system changes, and new connectors as your data needs grow. No data engineer required on your end.
Why Work With iKemo for Healthcare Data Integration
Open-source, zero vendor lock-in
We build on open-source tools your team can inspect, fork, and run forever — no per-row pricing, no vendor who can revoke access to your own pipeline. You own the stack regardless of whether you keep us on retainer.
Your infrastructure, or ours — your call
Run pipelines in your own cloud account so PHI never leaves your boundary and credentials stay yours, or have us host and operate them under a Business Associate Agreement. You own the stack either way, and you can switch models later as compliance requirements change.
We manage it — you use it
Most clients don't have a data engineer in-house. That's fine — we monitor the pipelines, handle source system changes, and add new connectors on retainer. Your team focuses on using the data, not maintaining the plumbing.
Scales with your data volume
Encounter and claim data compounds fast as a group grows — every location, every payer, every day. ClickHouse handles billions of rows and Airflow handles thousands of tasks, so acquisitions and new sites don't require a rebuild.
Healthcare ETL & Data Integration — Frequently Asked Questions
Which healthcare systems can you extract data from?
EHR and practice management systems including Epic (Clarity and Caboodle), Oracle Health CDR, athenahealth, eClinicalWorks, DrChrono, NextGen, Open Dental, and Dentrix — via API, FHIR endpoints, scheduled report exports, or direct database read depending on what the system supports. We also ingest clearinghouse claim and remittance files, payer 835/837 data, billing platforms, payroll systems, scheduling tools, and QuickBooks. Where a system only produces file exports, we build a custom extractor.
Is healthcare ETL HIPAA-compliant?
Yes, when the architecture is designed for it. We sign a Business Associate Agreement covering any PHI access, apply role and row-level access controls, log access and export events, and keep PHI inside the deployment boundary you choose. Because these pipelines move PHI daily, compliance is an architecture constraint from day one rather than a review step at the end.
Does our PHI have to leave our infrastructure?
No. Deployment is your choice. Pipelines and the warehouse can run in your own cloud account or on servers you control, so PHI never leaves infrastructure you own and credentials stay yours. Alternatively we host and operate the environment under a Business Associate Agreement. You can migrate between models later, since everything is built on open components that carry over.
Do we need a data warehouse first?
Not necessarily. We can set up your warehouse as part of the engagement. For most healthcare clients we recommend PostgreSQL for mixed transactional and analytics use, or ClickHouse for high-volume claim and encounter data across many locations. BigQuery works well if you're already in Google Cloud, and Azure SQL or Fabric fits Microsoft-centric groups.
Do you manage the pipelines after launch?
Yes — and most clients prefer this. Healthcare pipelines need ongoing attention: EHR vendors change APIs, export formats shift, clearinghouse files get restructured, and acquired locations arrive on different systems. Managed retainers cover monitoring, maintenance, source-system change handling, and new connectors. You focus on using the data; we keep it flowing.
How is this different from using Fivetran or Stitch?
Fivetran and Stitch are solid managed services — if you're already using them, we can build on top. Two practical differences for healthcare: consumption pricing gets expensive on claim and encounter volumes, and connector coverage for EHR and practice management systems is thin, so the hard part still needs custom work. An open-source stack avoids per-row pricing, keeps PHI inside your chosen boundary, and allows custom extraction logic. We're tool-agnostic.
Also Explore
Healthcare Revenue Dashboards →
Turn clean pipeline data into dashboards your billing leads and practice managers act on every day.
Managed Power BI for Healthcare →
Fully-managed Power BI on top of the warehouse — we build, host, and maintain the reporting layer.
AI Agents & Automation →
Add intelligence on top of your pipelines — agents that chase denials, route work, and answer billing questions.
Stop Reconciling Four Systems by Hand
Let's get your EHR, clearinghouse, billing, and payroll data into one warehouse with one set of definitions — so month-end close is a review, not an argument.
Book a Discovery Call