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HL7 Data Extraction Analyst
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The HL7 Data Extraction Analyst is a senior-level data engineering specialist responsible for extracting, transforming, and validating clinical and administrative data from ambulatory EHR/EMR systems to support CMS MIPS and Value-Based Care programs. This role requires deep expertise in HL7 (ADT, ORU, SIU, VXU), CCDA, FHIR bundles, EDI formats (837, 835), SQL optimization, and EMR database schema structures across systems such as NextGen, eClinicalWorks, Greenway, Athena, Allscripts, and other ambulatory platforms.
The analyst builds and maintains scalable data ingestion pipelines, performs complex SQL transformations, ensures data quality and lineage, and collaborates directly with MIPS Advisors and clients to ensure accuracy of measure calculations and regulatory submissions. This role is mission-critical to ensure that clinicians meet CMS reporting requirements and that Value-Based Care performance metrics are precise, audit-ready, and delivered on schedule.
RESPONSIBILITIES
HL7, CCDA, and FHIR Data Extraction & Parsing
- Extract, transform, and validate patient clinical data from EMR/EHR systems using HL7 v2.x, CCDA, and FHIR bundles.
- Interpret HL7 segments (PID, PV1, ORC, OBR, OBX, DG1, RXA, etc.) for clinical measure mapping.
- Troubleshoot inconsistent or malformed HL7 messages and resolve data quality gaps with vendors.
- Build robust parsing logic to normalize data across heterogeneous EMR systems.
EMR/EHR Database Querying & Measure Data Retrieval
- Query EMR databases (NextGen, eCW, Greenway, Athena, etc.) to extract structured and unstructured clinical data required for MIPS measures.
- Understand vendor-specific table schemas, metadata dictionaries, and proprietary data models.
- Translate measure specifications into SQL logic based on CMS MIPS calculation rules.
- Validate measure completeness, timeliness, and accuracy prior to client submission.
Technical Standards, Architecture Alignment & Governance
- Maintain and enforce engineering implementation standards, documentation requirements, and build methodologies.
- Ensure all engineering work aligns with defined solution architecture, technology standards, and security baselines.
- Lead efforts to improve standard configurations, automation, templates, and reusable frameworks.
- Partner with the Manager, Methodology, to ensure engineering processes map to ITIL practices and operational workflows.
- Ensure engineering quality and consistency through audits, peer reviews, and structured validation.
Data Pipeline Engineering & Transformation
- Build scalable ingestion pipelines using SQL, Spark (batch & streaming), Python, Databricks, EMR, or OCI Data Flow.
- Develop metadata-driven pipelines supporting multiple clients and EMR platforms.
- Implement data quality frameworks (DQ checks, thresholds, reconciliation reports).
- Maintain robust lineage, audit trails, and governance compliance for CMS readiness.
Regulatory Data Support for MIPS & Value-Based Care
- Support MIPS Advisors with extraction of numerator/denominator data for clinical quality measures.
- Produce audit-ready documentation and reproducible calculations for CMS submission.
- Map EHR data elements to CMS measure logic, identifying gaps or vendor remediation needs.
- Validate that clients meet annual CMS submission timelines and data completeness requirements.
Cross-Functional Collaboration
- Work closely with:
- Value-Based Care Advisors & Sr. Advisors
- MIPS measure analysts
- Client IT/EMR administrators
- Security & Compliance teams (for PHI handling controls)
- vCIO/vCISO for healthcare data risk and governance alignment
- Translate technical data issues into actionable insights for non-technical MIPS Advisors.
- Coordinate with EMR vendors to resolve data extraction failures or schema changes.
EDUCATION AND EXPERTISE
Required
- 10+ years in data engineering, healthcare data extraction, or clinical informatics.
- Deep expertise with SQL, Python, Spark (batch + streaming) on Databricks, EMR, or DataFlow.
- Strong experience with HL7 v2.x, CCDA, FHIR, EDI X12 (837/835).
- Proven ability to query and interpret ambulatory EMR/EHR schemas (NextGen, eCW, Greenway, etc.).
- Hands-on optimization experience with Autonomous Data Warehouse, Snowflake, or Redshift.
- Experience with cloud platforms (AWS, Azure, OCI).
- Skilled in building metadata-driven pipelines, implementing data lineage, auditability, and governance.
- Experience with Airflow or similar orchestration tools.
- Experience with Git, CI/CD, Terraform, DataOps workflows.
- Ability to work under pressure, manage multiple deadlines, and support regulatory timeframes.
Preferred
- Bachelor’s degree in Computer Science, Information Systems, Health Informatics, or related field.
- Experience supporting CMS eCQMs, MIPS/MACRA, ACO performance measures, or quality reporting initiatives.
- Familiarity with clinical terminology (SNOMED, LOINC, RxNorm, CPT/HCPCS, ICD-10).
- Experience with Delta Lake / Lakehouse architectures.
- Previous experience in a healthcare IT vendor, MSP, EMR company, or consulting environment.
Core Competencies
- Healthcare Data Domain Expertise
- HL7 Parsing & Clinical Data Interpretation
- SQL / ETL Engineering Excellence
- Analytical & Critical Thinking Skills
- Communication & Cross-Functional Collaboration
- Quality Assurance & Data Governance
- Cloud Engineering & Modern Data Stack Proficiency
- Diligence & Regulatory Mindset
WHY ANATOMY IT?
Anatomy IT embraces those that demonstrate a deep passion for solving the problems of healthcare with enthusiasm for building positive working relationships and winning as a team. We believe in putting our customers first, empowering our people to drive growth, being technologically innovative, simplifying the complex, delivering results to our commitments with a sense of urgency while embracing diversity, equity, and inclusion.
THE COMPANY
Anatomy IT helps healthcare providers deliver exceptional patient care through technology and cybersecurity solutions. With 30+ years of experience, we understand healthcare organizations' unique risks, opportunities, and challenges. Anatomy IT is one of the largest and fastest-growing healthcare IT companies, partnering with over 19,000 providers and healthcare staff nationwide, including ASCs, physician groups and hospitals.
BENEFITS
We love collaborating and working together as a team. Our benefits include healthcare (medical, dental & vision), 401K fund contribution, paid-time-off, short & long-term disability, and a family atmosphere of caring and concern for each team member.
EQUAL OPPORTUNITY EMPLOYER
We are proud to be an equal opportunity employer – and celebrate our employees' differences regardless of race, color, religion, gender, sexual orientation, gender identity, national origin, age, disability, or Veteran status. Different makes us better.
**The above statements are intended to describe the general nature and level of work being performed by individuals assigned to this position. They are not intended to be a comprehensive list of all responsibilities, and skills required of employees.
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