Scientific Knowledge Engineer, Ontology & Data Modeling

<p><strong>About&nbsp;Xebia</strong></p> <p>For&nbsp;more&nbsp;than&nbsp;25&nbsp;years,&nbsp;our&nbsp;global&nbsp;network&nbsp;of&nbsp;passionate&nbsp;technologists&nbsp;and&nbsp;pioneering&nbsp;craftspeople&nbsp;has&nbsp;delivered&nbsp;cutting-edge&nbsp;technology&nbsp;and&nbsp;game-changing&nbsp;consulting&nbsp;to&nbsp;companies&nbsp;on&nbsp;the&nbsp;brink&nbsp;of&nbsp;AI&nbsp;driven&nbsp;digital&nbsp;transformation.&nbsp;Since&nbsp;2001,&nbsp;we&nbsp;have&nbsp;grown&nbsp;into&nbsp;a&nbsp;full&nbsp;service&nbsp;digital&nbsp;consulting&nbsp;company&nbsp;with&nbsp;6000+&nbsp;professionals&nbsp;working&nbsp;on&nbsp;a&nbsp;worldwide&nbsp;ambition.&nbsp;Driven&nbsp;by&nbsp;the&nbsp;desire&nbsp;to&nbsp;make&nbsp;a&nbsp;difference,&nbsp;we&nbsp;keep&nbsp;innovating.&nbsp;Fuelling&nbsp;the&nbsp;growth&nbsp;of&nbsp;our&nbsp;company&nbsp;with&nbsp;our&nbsp;knowledge&nbsp;worker&nbsp;culture.&nbsp;When&nbsp;teaming&nbsp;up&nbsp;with&nbsp;Xebia,&nbsp;expect&nbsp;in-depth&nbsp;expertise&nbsp;based&nbsp;on&nbsp;an&nbsp;authentic,&nbsp;value-led,&nbsp;and&nbsp;high&nbsp;quality&nbsp;way&nbsp;of&nbsp;working&nbsp;that&nbsp;inspires&nbsp;all&nbsp;we&nbsp;do.</p> <p>At Xebia, we put ‘People First’—committed to attracting diverse talent and fostering an inclusive, respectful workplace where everyone is valued for their contributions. We welcome all individuals and evaluate solely on the quality of their work and teamwork.</p> <p><strong>About&nbsp;the&nbsp;Role</strong></p> <p><strong>Scientific&nbsp;Knowledge&nbsp;Engineer,&nbsp;Ontology&nbsp;&amp;&nbsp;Data&nbsp;Modeling</strong></p> <p>This role is responsible for maximizing the value of our data assets over a lifetime to bring purpose to data by acting as translators of highly technical information from domain experts into an appropriate data model – complete with significant ontology and vocabulary - that can be utilized to effectively structure and index the data. Specifically working with Product managers and R&amp;D subject matter expertise to define the language (data models, ontology, standards, etc.) of science into data products by acting as the voice of “Knowledge base” and interoperability/value of asset.</p> <p><strong>&nbsp;&nbsp;Key&nbsp;responsibilities&nbsp;include:</strong></p> <ul> <li>Definition&nbsp;of&nbsp;schemas/ontology&nbsp;and&nbsp;data&nbsp;models&nbsp;of&nbsp;scientific&nbsp;information&nbsp;required&nbsp;for&nbsp;the&nbsp;creation&nbsp;of&nbsp;value&nbsp;adding&nbsp;data&nbsp;products.&nbsp;This&nbsp;includes&nbsp;accountability&nbsp;for&nbsp;the&nbsp;quality&nbsp;control&nbsp;and&nbsp;mapping&nbsp;specifications&nbsp;to&nbsp;be&nbsp;industrialized&nbsp;by&nbsp;data&nbsp;engineering&nbsp;and&nbsp;maintained&nbsp;in&nbsp;platform&nbsp;provisioned&nbsp;tooling.</li> <li>Accountable&nbsp;for&nbsp;the&nbsp;quality&nbsp;control&nbsp;(through&nbsp;validation&nbsp;and&nbsp;verification)&nbsp;of&nbsp;mapping&nbsp;specifications&nbsp;to&nbsp;be&nbsp;industrialized&nbsp;by&nbsp;data&nbsp;engineering&nbsp;and&nbsp;maintained&nbsp;in&nbsp;platform&nbsp;provisioned&nbsp;tooling&nbsp;–&nbsp;e.g.,&nbsp;models,&nbsp;schemas,&nbsp;controlled&nbsp;vocab.</li> <li>Working&nbsp;with&nbsp;Product&nbsp;managers/engineers&nbsp;confidently&nbsp;convert&nbsp;business&nbsp;need&nbsp;into&nbsp;defined&nbsp;deliverable&nbsp;business&nbsp;requirements&nbsp;to&nbsp;enable&nbsp;the&nbsp;integration&nbsp;of&nbsp;large-scale&nbsp;biology&nbsp;data&nbsp;to&nbsp;predict,&nbsp;model,&nbsp;and&nbsp;stabilize&nbsp;therapeutically&nbsp;relevant&nbsp;protein&nbsp;complex&nbsp;and&nbsp;antigen&nbsp;conformations&nbsp;for&nbsp;drug&nbsp;and&nbsp;vaccine&nbsp;discovery.</li> <li>Collaborate&nbsp;with&nbsp;external&nbsp;groups&nbsp;to&nbsp;align&nbsp;data&nbsp;standards&nbsp;with&nbsp;industry/&nbsp;academic&nbsp;ontologies&nbsp;ensuring&nbsp;that&nbsp;data&nbsp;standards&nbsp;are&nbsp;defined&nbsp;with&nbsp;usage/analytics&nbsp;in&nbsp;mind.&nbsp;</li> <li>Provides&nbsp;bespoke&nbsp;subject&nbsp;matter&nbsp;expertise&nbsp;for&nbsp;R&amp;D&nbsp;data&nbsp;to&nbsp;translate&nbsp;deep&nbsp;science&nbsp;into&nbsp;data&nbsp;for&nbsp;actionable&nbsp;insights</li> <li>Contribute&nbsp;to&nbsp;and&nbsp;maintain&nbsp;documentation&nbsp;of&nbsp;data&nbsp;standards,&nbsp;ontology&nbsp;decisions,&nbsp;and&nbsp;mapping&nbsp;rationale&nbsp;to&nbsp;support&nbsp;organizational&nbsp;knowledge&nbsp;transfer&nbsp;and&nbsp;auditability</li> </ul> <p><strong>Basic&nbsp;Qualifications:</strong></p> <p>We&nbsp;are&nbsp;looking&nbsp;for&nbsp;professionals&nbsp;with&nbsp;these&nbsp;required&nbsp;skills&nbsp;to&nbsp;achieve&nbsp;our&nbsp;goals:</p> <ul> <li>Masters&nbsp;degree&nbsp;in&nbsp;Bioinformatics,&nbsp;Biomedical&nbsp;Science,&nbsp;Biomedical&nbsp;Engineering,&nbsp;Molecular&nbsp;Biology,&nbsp;or&nbsp;Computer&nbsp;Science&nbsp;(with&nbsp;a&nbsp;life&nbsp;science&nbsp;application&nbsp;focus)</li> <li>6+&nbsp;years&nbsp;of&nbsp;relevant&nbsp;work&nbsp;experience</li> <li>Specific&nbsp;experience&nbsp;contributing&nbsp;to&nbsp;Knowledge&nbsp;Graph&nbsp;development&nbsp;efforts,&nbsp;including&nbsp;entity&nbsp;modeling,&nbsp;relationship&nbsp;design,&nbsp;and&nbsp;schema&nbsp;governance</li> <li>Hands-on&nbsp;experience&nbsp;with&nbsp;open-source&nbsp;ontology&nbsp;tools&nbsp;and&nbsp;languages:&nbsp;Protégé,&nbsp;SPARQL,&nbsp;OWL,&nbsp;SKOS,&nbsp;SHACL,&nbsp;RML,&nbsp;RDF/Turtle</li> <li>Working&nbsp;knowledge&nbsp;of&nbsp;major&nbsp;life&nbsp;sciences&nbsp;ontologies:&nbsp;Gene&nbsp;Ontology&nbsp;(GO),&nbsp;OBO&nbsp;Foundry&nbsp;ontologies&nbsp;(CL,&nbsp;UBERON,&nbsp;HPO,&nbsp;MONDO,&nbsp;CHEBI,&nbsp;EFO,&nbsp;CLO),&nbsp;MeSH,&nbsp;SNOMED&nbsp;CT,&nbsp;UMLS</li> <li>Familiarity&nbsp;with&nbsp;linked&nbsp;data&nbsp;principles&nbsp;and&nbsp;semantic&nbsp;web&nbsp;technologies</li> <li>Experience&nbsp;with&nbsp;industry-standard&nbsp;tools&nbsp;for&nbsp;building&nbsp;data&nbsp;serialization&nbsp;protocols&nbsp;(e.g.,&nbsp;JSON&nbsp;Schema,&nbsp;LinkML)</li> <li>Proficiency in at least one programming language — preferably Python — for scripting vocabulary mappings, building data models, automating QC, and prototyping pipelines</li> </ul> <p><strong>Preferred&nbsp;Qualifications:</strong></p> <p>If&nbsp;you&nbsp;have&nbsp;the&nbsp;following&nbsp;characteristics,&nbsp;it&nbsp;would&nbsp;be&nbsp;a&nbsp;plus:</p> <ul> <li>Experience&nbsp;with&nbsp;data&nbsp;governance&nbsp;and&nbsp;data&nbsp;quality&nbsp;tooling&nbsp;(e.g.,&nbsp;Ataccama,&nbsp;Informatica,&nbsp;Talend,&nbsp;OpenRefine,&nbsp;Great&nbsp;Expectations,&nbsp;dbt)</li> <li>Experience&nbsp;with&nbsp;at&nbsp;least&nbsp;one&nbsp;programming&nbsp;language&nbsp;–&nbsp;e.g.&nbsp;Python&nbsp;–&nbsp;for&nbsp;scripting&nbsp;vocabulary&nbsp;mappings,&nbsp;building&nbsp;data&nbsp;models,&nbsp;etc</li> <li>Experience&nbsp;supporting&nbsp;LLM&nbsp;integration&nbsp;or&nbsp;AI-readiness&nbsp;workflows&nbsp;—&nbsp;including&nbsp;metadata&nbsp;enrichment,&nbsp;entity&nbsp;linking,&nbsp;embedding&nbsp;pipelines,&nbsp;or&nbsp;retrieval-augmented&nbsp;generation&nbsp;(RAG)&nbsp;architectures</li> <li>Understanding&nbsp;of&nbsp;vector&nbsp;databases&nbsp;and&nbsp;their&nbsp;role&nbsp;in&nbsp;semantic&nbsp;search&nbsp;and&nbsp;knowledge&nbsp;retrieval&nbsp;(e.g.,&nbsp;Weaviate,&nbsp;Chroma)</li> <li>Familiarity&nbsp;with&nbsp;cloud&nbsp;data&nbsp;platforms&nbsp;and&nbsp;infrastructure&nbsp;relevant&nbsp;to&nbsp;large-scale&nbsp;biological&nbsp;data&nbsp;(e.g.,&nbsp;AWS,&nbsp;GCP,&nbsp;Azure)</li> <li>Familiarity&nbsp;with&nbsp;graph&nbsp;database&nbsp;technologies&nbsp;(e.g.,&nbsp;Neo4j,&nbsp;Amazon&nbsp;Neptune,&nbsp;Stardog,&nbsp;GraphDB,&nbsp;TigerGraph)</li> </ul> <p><strong>What We Offer</strong></p> <ul> <li>Full time permanent contract.</li> <li>Salary Range: €58,000 – €68,000 gross per year, depending on experience, skills, and the outcome of the technical assessment process.</li> <li>27 days of annual leave plus national public holidays.</li> <li>100% remote work with flexible working hours.</li> <li>Flexible Compensation Plan covering meals, transport, private healthcare, childcare, and training, with tax-saving benefits.</li> <li>Private Health Insurance fully funded by Xebia, including mental health support and dental coverage.</li> <li>Wellhub membership with access to wellbeing apps and optional gym plans.</li> <li>Benefits Hub with exclusive employee discounts on a wide range of products and services.</li> <li>Paid Wellbeing Leave through our internal time-bank system for medical appointments or short-term health needs.</li> <li>Remote Work Allowance (€25/month).</li> <li>€900 annual learning budget for certifications, training, conferences, and professional development.</li> </ul>