Data Engineer - Lilly Medicine Foundry

Eli Lilly and Company; Indianapolis (IN); On-site; USD 129,000 - 231,000; Full time

Benefits offered by this job

Company bonus

401(k)

Pension

Vacation benefits

Medical, dental, vision benefits

Flexible benefits

Life insurance

Well-being program

Job summary

Eli Lilly and Company is seeking a Data Engineer for the Lilly Medicine Foundry in Indiana. You will design data pipelines spanning lab systems, process engineering, and manufacturing execution to enable analytics and compliant data products.

You will work with AWS/Azure data lakehouse architectures, ensure data integrity, and partner with IT and business teams to drive scalable data solutions across GMP workflows.

Qualifications

• Bachelor’s degree in Computer Science, Data Science, Engineering or related technical field.
• 5+ years of experience in data modeling, ETL/ELT, ontology development, semantic graphs, and linked data.
• 2+ years of data engineering in a pharma GMP setting.

Responsibilities

• Design and build data pipelines across lab systems, process engineering, MES, LIMS and QA.
• Integrate IT and OT sources with cloud data lakehouse architecture (AWS/Azure).
• Ensure data integrity, compliance, and scalable analytics products for GMP environments.
• Collaborate with Data Architects, Data Scientists and business partners to deliver data as a product.

Skills

Data modeling

ETL/ELT

Ontology development

Semantic graph construction

Linked data

Relational schema design

SQL

Education

Bachelor’s degree in Computer Science, Data Science, Engineering or related technical field

Tools

ER/Studio

Erwin

TOAD

PostgreSQL

Redshift

Aurora

MongoDB

Kafka

MQTT

Job description

At Lilly, the work is demanding because patients are waiting. We unite caring with discovery to help make life better for people around the world, knowing that every decision, every detail, and every day matters. Headquartered in Indianapolis, Indiana, our over 50,000 employees around the globe take on complex challenges to discover and deliver life-changing medicines, strengthen how health is understood and managed, and support the communities we serve. This is hard, urgent, selfless work—but it’s work worth doing. If you’re driven by purpose and ready to bring your best to work that truly matters for patients, we invite you to join us.

Lilly is entering an exciting period of growth, and we are committed to delivering innovative medicines to patients around the world. LRL has increasing needs for in-house manufacture of material for clinical supplies and will therefore construct a new campus to manufacture Clinical Trial (CT) Active Pharmaceutical Ingredient (API) to meet needs for an expanding portfolio (more and new areas), to accelerate development timelines, and to enhance supply chain robustness.

The brand-new facility also known as Lilly Medicine Foundry will utilize the latest technology to augment the current clinical supply chain for small molecules (SM), oligonucleotides, peptides, and Antibody Drug Conjugates (ADCs), monoclonal antibodies and bioconjugates, and add new capabilities including mRNA.

The new site will be built using the latest high-tech equipment, advanced highly integrated and automated manufacturing systems, and have a focus on minimizing the impact to our environment.

What You'll Be Doing

As a Data Engineer based at the Lilly Medicine Foundry, you will design and build data pipelines for the site's many systems. Working closely with the Data Architect and Data Scientists, you'll engage directly with business and operational collaborators to understand how data flows across the Foundry — from lab systems, process engineering, and manufacturing execution to quality and process analytics — and translate that understanding into reliable, scalable data products.

Your core focus will be integrating IT and OT source systems with cloud data Lakehouse architecture spanning AWS and Azure, enabling the advanced analytics and AI/ML capabilities that will define how the Foundry operates. This includes the full data value chain: capture, ingestion, integration, contextualization, harmonization, and delivery as reusable data domains and data-as-a-product. You will work across enterprise and edge systems, navigate a diverse technology landscape, and ensure that everything you build meets the data integrity and compliance standards required in a GMP-regulated manufacturing environment.

How You'll Succeed

• Build and deliver high-quality data solutions.: You design and develop robust data pipelines for ingestion, transformation, and integration across cloud platforms (AWS and Azure), applying modern patterns such as medallion architecture, streaming ingestion, and API-based extraction. You write clean, maintainable code, optimize for performance, and think carefully about how data flows from source systems into trustworthy, analytics-ready products.
• Ensure compliance: You understand the data integrity requirements of a GxP manufacturing environment and apply Quality guidelines and Good Manufacturing Practices from the start. You participate in design reviews, maintain traceability, and contribute to governance frameworks that keep the Foundry consistently compliant.
• Translate business needs into technical outcomes. You engage proactively with stakeholders across multiple modalities and business teams including Operations, Quality, Lab, and Engineering to understand their data needs. You're comfortable eliciting requirements, identifying gaps, and translating operational realities into sound technical designs — and explaining your architectural decisions back to a non-technical audience.
• Navigate a diverse enterprise landscape: The Foundry operates within a broader Lilly ecosystem of enterprise systems including ERP, ELN, MES, LIMS, Historians, PLM, and QMS platforms. You invest time in understanding upstream and downstream dependencies, seek opportunities to reuse existing services and integrations, and build with the broader data architecture in mind.
• Continuous learning: You track emerging tools and technologies across the AWS and Azure data ecosystems, bring informed perspectives on what's worth adopting, and actively contribute to the team's collective capability.
• Bring a foundational set of knowledge in: communication, leadership, teamwork, problem solving skills, solution definition, business acumen, architectural processes (e.g. blueprinting, reference architecture, governance, etc.), technical standards, project delivery, and industry knowledge.
• Staying abreast of tools and technologies to influence Technology at Lilly strategy so that it provides best usage opportunities for business
• Analyze large, complex data domains and craft practical solutions for subsequent data exploitation via analytics.
• Design, develop and maintain data solutions for data capture, storage, integration and analytics in partnership with Technology at Lilly teams.
• Review and provide practical recommendations on design patterns, performance considerations & optimization, database versions, and database deployment strategies
• Knowledgeable in data functions such as Data Governance, Master Data Management, Business Intelligence

Your Basic Qualifications:

• Bachelor’s degree in Computer Science, Data Science, Engineering or related technical field
• 5+ years of experience in several of the following disciplines: data modeling, ETL/ELT, ontology development, semantic graph construction and linked data, relational schema design.
• 2+ years of that data engineering experience should be in a relevant pharmaceutical GxP (CM&C, Discovery R&D, or Manufacturing)

Additional Skills / Preferences

• Experience with cloud platforms (e.g., AWS, Azure).
• Experience with AI/ML/LLM Concepts and tools and building agentic AI solution sets
• 1-3 years of experience designing large scale data models for functional, operational, and analytical environments (Conceptual, Logical, Physical & Dimensional).
• Demonstrated SQL and data modeling proficiency.
• Experience with data modeling tools such as, ER*Studio and Erwin or TOAD.
• Experience with data integration such as data streaming, Industrial IOT, using MQTT, AQMP, Kafka and related protocols.
• Understanding of modern data architecture, data lakehouse, data warehousing and/or big data concepts.
• Experience with security models and development on large data sets.
• Experience with multiple database solutions (e.g. Postgres, Redshift, Aurora, Athena, Graph DB like Neptune, No SQL like DynamoDB, MongoDB) and formal database designs (3NF, Dimensional Models).
• Experience with Agile Development, CI/CD, Github, Automation platforms.
• Demonstrated ability to analyze large, complex data domains and craft practical solutions for subsequent data exploitation via analytics.
• Ability to review and provide practical recommendations on design patterns, performance considerations & optimization, database versions, and database deployment strategies.
• Knowledgeable in data functions such as Data Governance, Master Data Management, Business Intelligence.
• Prior work experience working in pharma or other GMP setting.
• Solid knowledge of Computer System Validation process.
• Demonstrated ability to analyze, anticipate, and resolve complex issues through sound problem-solving skills.
• Demonstrated learning agilityand curiosity.
• Desire and ability to communicate using a variety of methods in diverse forums.

Other Information

• This position is onsite in Lebanon, IN beginning late 2027-2028. Until then the work location is Indianapolis, IN.

About the Organization:

Lilly IT builds and maintains capabilities using groundbreaking technologies like most prominent tech companies. What differentiates Lilly IT is that we create new possibilities through tech to advance our purpose – creating medicines that make life better for people around the world, like data driven drug discovery and connected clinical trials.

We hire the best technology professionals from a variety of backgrounds, so they can bring an assortment of knowledge, skills, and diverse thinking to deliver innovative solutions in every area of our business.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia (AMECA), Black Employees at Lilly (BE@Lilly), Chinese Culture Network (CCN), EnAble, Evolve, Lilly Indian Network (LIN), Organization of Latinx at Lilly (OLA), Pride (LGBTQ+ Allies), Veterans Leadership Network (VLN) and Women’s Initiative for Leading at Lilly (WILL).

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location. The anticipated wage for this position is

$129,000 - $231,000

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance).

• company-sponsored 401(k)
• pension
• vacation benefits
• eligibility for medical, dental, vision and prescription drug benefits
• flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts)
• life insurance and death benefits
• certain time off and leave of absence benefits
• well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)
• company bonus (depending, in part, on company and individual performance)