Advisor, Knowledge Engineering and Data Management

100 Eli Lilly and Company; Indianapolis (IN); On-site; USD 126,000 - 205,000; Full time

Job summary

Lilly, headquartered in Indianapolis, seeks an Advisor, Knowledge Engineering and Data Management to lead semantic and data governance for the DDCS organization. This role focuses on creating, maintaining, and governing ontologies, taxonomies, metadata, and knowledge graphs that transform fragmented information into connected, trusted knowledge for search, analytics, and AI-enabled applications.

The position involves hands-on development of agentic AI grounded in DDCS knowledge assets, with

Qualifications

• Master’s degree with at least 5 years of relevant experience.
• Experience developing ontologies, taxonomies, or knowledge graphs.
• Experience with semantic technologies such as RDF, OWL, SPARQL, SHACL.
• Python programming for data integration and analytics.

Responsibilities

• Design and maintain ontologies, taxonomies, controlled vocabularies, and semantic models.
• Collaborate with engineers, scientists, quality and regulatory teams to translate knowledge into models.
• Establish ownership, stewardship, metadata, lineage, change control, and lifecycle practices.
• Work with source-system owners to improve data definitions and semantic consistency.
• Design, build, and operate knowledge graph capabilities across systems.
• Develop entity resolution, metadata harmonization, and semantic enrichment.
• Enable semantic search and AI-ready knowledge structures grounded in governed data assets.
• Design, build, and evaluate AI agents and LLM apps grounded in knowledge assets.
• Apply version control, testing, validation, monitoring, and documentation for regulated environments.
• Communicate modeling decisions and governance expectations clearly to stakeholders.
• Mentor scientists, engineers, analysts, and data professionals on semantic technologies.

Skills

Semantic technologies

Knowledge graphs

Python programming

Stakeholder collaboration

Data governance

Education

Master’s degree in Information Science, Data Science, Computer Science, Engineering, Biomedical Informatics, or related

PhD with relevant experience

Tools

RDF/OWL/SPARQL

LangGraph/LangChain

Graph databases

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.

Company Overview

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader committed to developing innovative medicines and healthcare solutions that improve outcomes for patients worldwide. We are looking for people who are determined to make life better for people around the world.

Organization Overview

Delivery, Devices, and Connected Solutions (DDCS) sits within Lilly’s Product Research & Development organization. DDCS discovers, designs, develops, and commercializes patient-centric drug delivery systems, combination products, connected health solutions, and enabling technologies across the product lifecycle. The DDCS Data Science and Digital Transformation team builds trusted data, analytics, AI, and digital capabilities that connect scientific, engineering, quality, regulatory, manufacturing, and commercial knowledge. The team helps DDCS improve traceability, accelerate decision-making, and scale reusable data and knowledge assets.

Position Overview

The Advisor, Knowledge Engineering and Data Management will lead the development and governance of semantic and data management capabilities for DDCS. This role will create, maintain, and govern ontologies, taxonomies, controlled vocabularies, metadata, and knowledge graph assets that transform fragmented technical information into connected, reusable, and trusted knowledge. This position is focused on the semantic and governance foundation required for search, traceability, analytics, knowledge discovery, and AI-enabled applications. Part of the role will involve hands‑on agentic AI development, building agents and large language model applications that are grounded in DDCS knowledge assets. This work is anchored in a strong semantic and data management foundation, so that the AI systems the role helps build remain trustworthy, well‑governed, and traceable to authoritative sources.

Key Responsibilities

• Design and maintain ontologies, taxonomies, controlled vocabularies, and semantic models for DDCS concepts such as device components, materials, formulations, test methods, requirements, design outputs, quality events, manufacturing processes, and connected-device data.
• Partner with device engineers, formulation scientists, quality professionals, regulatory experts, manufacturing stakeholders, and digital teams to translate domain knowledge into practical semantic models and reusable data assets.
• Establish ownership, stewardship, metadata, lineage, change control, versioning, release management, and lifecycle practices for shared semantic and knowledge graph assets.
• Work with source-system owners to improve data definitions, source authority, semantic consistency, traceability, and quality across structured and unstructured information.
• Design, build, and operate knowledge graph capabilities that integrate information from engineering systems, quality systems, PLM platforms, laboratory systems, manufacturing systems, document repositories, and other enterprise sources.
• Develop approaches for entity resolution, metadata harmonization, semantic enrichment, and relationship modeling across DDCS information assets.
• Enable semantic search, graph-backed retrieval, entity extraction, and AI-ready knowledge structures grounded in governed DDCS data assets.
• Design, build, and evaluate AI agents and large language model applications, including retrieval augmented generation and graph based retrieval, that are grounded in governed DDCS knowledge assets and validated for regulated use.
• Apply version control, automated testing, validation, monitoring, and documentation practices appropriate for regulated environments and intended use.
• Communicate modeling decisions, governance expectations, assumptions, and limitations clearly to technical and non‑technical stakeholders.
• Mentor and guide scientists, engineers, analysts, and data professionals on practical use of semantic technologies and data management practices.

Basic Requirements

• Master’s degree in Information Science, Data Science, Computer Science, Engineering, Biomedical Informatics, Bioinformatics, or a related quantitative discipline, with a minimum of 5 years of relevant experience.
• Experience developing ontologies, taxonomies, controlled vocabularies, semantic models, or knowledge graphs.
• Experience with semantic technologies such as RDF, OWL, SPARQL, SHACL, or equivalent frameworks.
• Python programming experience for data integration, automation, or analytics.
• Experience translating scientific, engineering, business, or data requirements into technical solutions.
• Demonstrated ability to collaborate with scientific, engineering, quality, regulatory, digital, and business stakeholders.

Additional Preferences

• PhD with a minimum of 2 years of relevant experience
• Experience implementing knowledge graphs, semantic platforms, metadata products, or governed data assets in production environments.
• Experience with data management practices such as stewardship, metadata management, lineage, data quality, data classification, or enterprise data governance.
• Experience with graph databases or semantic platforms such as Neo4j, Neptune, Stardog, GraphDB, or similar technologies.
• Experience in regulated industries such as pharmaceuticals, medical devices, healthcare, biotechnology, or manufacturing.
• Knowledge of pharmaceutical, medical device, or combination-product development processes, including design controls, DHF, DMR, requirements traceability, complaint handling, or UDI frameworks.
• Familiarity with GxP data integrity principles, ALCOA+, and life‑science standards or vocabularies such as CDISC, IDMP, UNII, UCUM, or UDI/GUDID.
• Experience with enterprise metadata management, data catalog, governance, LIMS, ELN, PLM, quality management, or technical document management platforms.
• Experience supporting semantic search, retrieval, knowledge discovery, analytics, or AI‑enabled applications using governed knowledge assets.
• Experience building AI agents or agentic workflows using frameworks such as LangGraph, LangChain, LlamaIndex, AutoGen, CrewAI, or Semantic Kernel.
• Experience with retrieval augmented generation (RAG) and graph based retrieval (GraphRAG) that grounds large language models in knowledge graphs and governed data, including the use of embeddings, vector search, and semantic indexing.
• Familiarity with large language model orchestration, tool and function calling, and protocols for connecting agents to enterprise tools and data, such as the Model Context Protocol (MCP).
• Experience with prompt and context engineering, and with evaluating agent behavior through testing, tracing, observability, and guardrails using tools such as LangSmith or comparable evaluation frameworks.
• Understanding of responsible and trustworthy AI practices, including grounding, traceability, human oversight, and validation of AI and agentic systems for regulated (GxP) environments.
• Publications, patents, open‑source contributions, or recognized technical leadership in semantic technologies, knowledge engineering, or data management.

Employment and Compensation

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response. 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 $126,000 - $204,600. Full‑time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a 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; and well‑being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities). Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

We Are Lilly

At Lilly we strive to ensure our employees are part of a team that cares about them and our shared purpose of making life better for those around the world. How do we do this? We continue to look for ways to include, innovate, accelerate and deliver while maintaining integrity, excellence and respect for people. We hope that you seek to join us on our journey as we create medicine and deliver improved outcomes for patients across the globe!