Knowledge Engineer II
Apolis
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Job Details
Skills
Summary
Job Title: Knowledge Engineer II
Location: Remote (USA)
Job Summary
We are seeking a highly skilled Knowledge Engineer II to join our team and contribute to the development of enterprise-scale Knowledge Graph solutions within the life sciences domain. The ideal candidate will possess expertise in ontology engineering, semantic web technologies, linked data, and biomedical ontologies. This role involves designing semantic data models, implementing knowledge graph architectures, supporting AI/LLM initiatives, and enabling advanced data integration for research and analytics.
Key Responsibilities
- Design, develop, and maintain enterprise Knowledge Graphs for life sciences and biomedical applications.
- Define semantic data models, ontology structures, entity relationships, and schema governance standards.
- Develop and maintain RDF-based knowledge models using semantic web technologies.
- Build ontology mappings and vocabulary alignment using industry-standard biomedical ontologies.
- Create and maintain SPARQL queries, OWL ontologies, SKOS vocabularies, SHACL constraints, and RML/R2RML mappings.
- Implement linked data principles and semantic interoperability across enterprise data platforms.
- Develop data serialization models using JSON Schema, LinkML, and related standards.
- Write Python scripts for ontology mapping, metadata enrichment, data validation, and automation.
- Support AI and LLM initiatives through entity linking, metadata enrichment, embedding pipelines, and Retrieval-Augmented Generation (RAG) solutions.
- Collaborate with data engineers, architects, and business stakeholders to build scalable semantic data solutions.
- Ensure data quality, governance, and consistency across knowledge graph implementations.
- Document technical designs, ontology standards, and best practices.
Required Qualifications
- Master''s degree in BioSciences, Biomedical Science, Biomedical Engineering, Biotechnology, or a related Life Sciences discipline.
- 6+ years of experience in Knowledge Graph development and semantic technologies.
- Hands-on experience with:
- Knowledge Graph development
- Entity modeling
- Relationship design
- R2RML
- Schema governance
- Strong expertise in:
- Protégé
- SPARQL
- OWL
- SKOS
- SHACL
- RML
- RDF-Star
- Working knowledge of biomedical and life sciences ontologies, including:
- Gene Ontology (GO)
- OBO Foundry Ontologies (CL, UBERON, HPO, MONDO, CHEBI, EFO, CLO)
- MeSH
- SNOMED CT
- UMLS
- Strong understanding of linked data principles and Semantic Web technologies.
- Experience with JSON Schema, LinkML, or equivalent data serialization frameworks.
- Proficiency in Python for scripting, data modeling, automation, and quality validation.
- Experience supporting AI/LLM workflows and semantic data integration.
Preferred Qualifications
- Experience with data governance and data quality tools such as Ataccama, Informatica, Talend, OpenRefine, Great Expectations, or dbt.
- Experience building AI-ready knowledge ecosystems, including:
- Metadata enrichment
- Entity linking
- Embedding pipelines
- Retrieval-Augmented Generation (RAG)
- Understanding of vector databases such as Weaviate and Chroma.
- Experience with graph databases including Neo4j, Amazon Neptune, Stardog, GraphDB, or TigerGraph.
- Familiarity with cloud platforms such as AWS, Microsoft Azure, or Google Cloud Platform.
- Experience designing scalable semantic data pipelines for enterprise life sciences applications.
- Dice Id: 10106862
- Position Id: 26-04970
- Posted 1 hour ago
Company Info
About Apolis
Founded 1996, RJT Compuquest, Inc. is an ERP and IT consulting services provider focused on providing innovative and successful business solutions. We are capable of working across all technology platforms, operating systems and infrastructures. RJT has experience in performing implementations, technical and functional upgrades, optimization projects, and full service staffing.
RJT consultants have real world experience across a broad spectrum of industries and can apply that knowledge to best face your business needs. Our recruiting process selects only the most highly qualified individuals for your project. If we cannot find the best consultant for your project, then we have a large pool of third-party consultants that we recruit from to ensure your business needs are met.
Our consultants have up to twenty years of business experience and an average of more than six years of IT and ERP experience. This means that the project team not only understands how systems work, they also understand how the technology impacts the business processes of organizations. We believe that the success of an engagement is determined by strong project management, as well as clear communication and mutual commitment working collaboratively. Our methodology begins with listening to the customer about their needs, then working with their team to gain a clear understanding of the requirements, while providing a knowledge transfer of best practices for the organization. The RJT team is committed to this goal.
When you leverage our exceptional recruiting and management capabilities and unparalleled client service skills, you take the most important step toward accomplishing your business goals. As a trusted advisor to companies of all sizes, we make it our business to become a specialized, physical extension of your team. We listen to your goals, assess your needs, and then take the steps necessary to achieve your objectives. Built on long-term, trusted client and employee relationships, RJT strives to consistently and efficiently plan, execute and deliver high quality services and results.
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