Senior Data Engineer
Zifo RnD Solutions21 days ago
Remote, United StatesSenior
Base Salary
$130k - $160k/yr
Responsibilities
- Build ingestion pipelines for clinical trial protocols, ICF documents, SmPCs, CSRs, and published articles, including PDF parsing, text extraction, and normalization.
- Design data models in Amazon Aurora and GraphDB for clinical trial entities and relationships.
- Develop embedding, vectorization, chunking, metadata enrichment, and vector-store population pipelines for RAG retrieval.
- Build and maintain ETL/ELT workflows that transform unstructured clinical content into linked, queryable data across relational and graph stores.
- Implement clinical data quality validation covering document classification, entity extraction, and cross-reference integrity.
- Build Python/FastAPI data-serving APIs for Angular frontends and LangGraph agent workflows.
- Set up data lineage tracking and audit trails to support regulatory traceability.
- Design multi-stage workflow pipelines with dependency management, retries, monitoring, and error handling.
- Use Terraform or AWS CDK, Docker, and Git to test and deploy pipelines on AWS.
Requirements
- Strong Python development experience and experience with PDF and document parsing libraries such as PyMuPDF, pdfplumber, or unstructured.io.
- Advanced PostgreSQL-compatible SQL experience, including schema design, migrations, query optimization, and indexing for large clinical datasets.
- Hands-on experience with graph databases such as Neptune or Neo4j, plus SPARQL or Cypher and biomedical ontology or knowledge-graph modeling.
- Experience with AWS services including Aurora PostgreSQL, S3, Lambda, Step Functions, SQS/SNS, and IAM.
- Experience with PDF text extraction, document section classification, clinical or biomedical named entity recognition, embedding models, and vector stores such as OpenSearch, pgvector, or Pinecone.
- Experience building asynchronous data-serving APIs with FastAPI and integrating backend services.
- Experience preparing data for LangChain/LangGraph applications and designing RAG pipelines involving chunking, retrieval, reranking, and prompt-data integration.
- Experience with Airflow, Prefect, AWS Step Functions, Temporal, or comparable workflow orchestration tools.
- Understanding of clinical trial structure and familiarity with MeSH, MedDRA, SNOMED, ATC codes, CDISC, 21 CFR Part 11, EU Annex 11, and ALCOA+ principles is preferred or advantageous.
- Nice-to-have experience includes biomedical knowledge graphs, PubMed/MEDLINE, ClinicalTrials.gov API, EMA/CTIS data, Apache Spark, Databricks, and dbt.
Benefits
- Remote work in the United States.
- Accrued vacation, medical, dental, vision, 401(k) with company matching, life insurance, and flexible spending accounts.
- Work with a global R&D solutions provider serving pharmaceutical, biotech, medical device, manufacturing QC, specialty chemical, and other research-based organizations.
- Equal opportunity workplace with an employee-built, science-focused culture.
Tech Stack
Categories
Data Engineering
About Zifo RnD Solutions
Zifo RnD Solutions provides scientific informatics and data services to pharma, biotech, medical devices, and other R&D-driven organizations. It implements and supports ELN/LIMS/EDC and clinical data management, builds custom integrations and analytics, and offers validation, managed services, and cloud/HPC support. Founded in 2008 and headquartered in Deerfield, Illinois, it is privately held and backed by TA Associates, and serves global biopharma companies, including several top-10 firms.