Biological Ontologist (Staff Scientist) – BenchSci

Title of the Job: Biological Ontologist (Staff Scientist)

Location: Toronto, ON

Job Description: We are looking for an experienced Staff Scientist (Biological Ontologist) to join our growing Product & Science Team. You will be responsible for developing and managing ontologies to enhance data integration and support AI-driven drug discovery processes. This role will work with our innovative product, built on a knowledge graph of experimental evidence extracted from the corpus and a biological ontological knowledge base that acts as the semantic foundation for our proprietary data. We are seeking a candidate with subject matter expertise in biomedical data to continue evolving our proprietary biological ontological knowledge base.You Will:

• Devise and implement the strategy for developing and maintaining BenchSci’s proprietary biological ontology.
• Define the diverse biomedical data sources that will be integrated into our ontology, ensuring high-quality and comprehensive coverage.
• Work with Engineering to develop and deliver a data integration plan that guarantees interoperability and seamless integration of diverse biomedical data.
• Collaborate closely with engineering and product teams to maximise the impact of our ontology on product development.
• Collaborate with Engineering in defining the data strategy that ensures BenchSci’s ontology retains a high degree of connectivity enabling traversal and reasoning over our data by leveraging mid to high level ontologies and interoperability-enabling xref metadata.
• Advise Engineering colleagues on the evolution of our internal data model to ensure we minimise semantic lossiness when mapping entity types and predicates from third party ontologies to BenchSci’s proprietary ontology.
• Demonstrate strong leadership, making sound decisions in a fast-paced and evolving environment.
• Implement and oversee “quality by design” principles to maintain the accuracy, consistency, and completeness of BenchSci’s ontological data.
• Create and maintain thorough documentation of our ontology, including definitions, relationships, and user guidelines.
• Provide training and support to internal teams on ontological principles, design, development and best practices.

You Have:

• A minimum of a Master’s degree in Bioinformatics, Biology, Computer Science, Information Science, or a related field. A Ph.D. is preferred.
• 7+ years of industry experience in ontology development and management, particularly in biotechnology or life sciences.
• Experience leveraging high and mid-level biological ontologies such as BioLink.
• Proficiency in ontology languages (e.g., OWL, RDF), ontology development tools (e.g., Protégé), ontology query language (SPARQL, cypher, SQL, GQL), and some familiarity with relevant programming languages (e.g., Python).
• Familiar with ontology reasoning tools, particularly in the biology domain (e.g. ELK, HermiT, and Pellet).
• Experience with applying these tools for tasks like classification and consistency checking in biomedical ontologies.
• A solid understanding of graph validation concepts, including SHACL (Shapes Constraint Language), to ensure data integrity and compliance within ontological frameworks.
• Strong understanding of biological concepts and terminologies and a deep understanding of biomedical ontologies (e.g., MONDO, MeSH, SNOMED CT).Deep understanding of the crucial role that ontologies play in providing a foundational semantic layer to knowledge graphs.
• Ability to analyse complex data and develop logical, ontological structures.
• High accuracy and attention to detail in managing and curating biological ontological data.
• Strong problem-solving abilities to address data integration and interoperability challenges.
• Excellent written and verbal communication skills to effectively document and convey complex ontological information.
• Strong interpersonal skills and the ability to work collaboratively within multidisciplinary teams.
• Deep industry knowledge and awareness of current trends and advancements in biotechnology and life sciences.
• Ability to adapt to evolving technologies and methodologies in ontology and biotechnology.

Benefits and Perks:An engaging remote-first cultureA great compensation package that includes BenchSci equity optionsA robust vacation policy plus an additional vacation day every yearCompany closures for 14 more days throughout the yearFlex time for sick days, personal days, and religious holidaysComprehensive health and dental benefits.Annual learning & development budgetA one-time home office set-up budget to use upon joining BenchSciAn annual lifestyle spending account allowanceGenerous parental leave benefits with a top-up plan or paid time off optionsThe ability to save for your retirement coupled with a company match!About BenchSci:BenchSci’s mission is to exponentially increase the speed and quality of life-saving research and development. We empower scientists to run more successful experiments with the world’s most advanced, biomedical artificial intelligence software platform.Backed by Generation Investment Management, TCV, Inovia, F-Prime, Golden Ventures, and Google’s AI fund, Gradient Ventures, we provide an indispensable tool for scientists that accelerates research at 16 top 20 pharmaceutical companies and over 4,300 leading academic centers. We’re a certified Great Place to Work®, and top-ranked company on Glassdoor.Our Culture:BenchSci relentlessly builds on its strong foundation of culture. We put team members first, knowing that they’re the organization’s beating heart. We invest as much in our people as our products. Our culture fosters transparency, collaboration, and continuous learning.We value each other’s differences and always look for opportunities to embed equity into the fabric of our work. We foster diversity, autonomy, and personal growth, and provide resources to support motivated self-leaders in continuous improvement.You will work with high-impact, highly skilled, and intelligent experts motivated to drive impact and fulfill a meaningful mission. We empower you to unleash your full potential, do your best work, and thrive. Here you will be challenged to stretch yourself to achieve the seemingly impossible. Learn more about our .Diversity, Equity and Inclusion: We’re committed to creating an inclusive environment where people from all backgrounds can thrive. We believe that improving diversity, equity and inclusion is our collective responsibility, and this belief guides our DEI journey. Learn more about our .Accessibility Accommodations: Should you require any accommodation, we will work with you to meet your needs. Please reach out to .#LI-Remote

Company Name: BenchSci

Salary:

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