The Data Science Institute, in collaboration with the Department of Physiology, at the Medical College of Wisconsin seeks a highly motivated Research Scientist to join a collaborative research team focused on ontology and data curation for diverse research communities. This role supports the Hogan Laboratory in the Data Science Institute and the Rat Genome Database in the Department of Physiology by developing, maintaining, enhancing, and implementing biomedical ontologies in various software, annotation, and data management applications. The incumbent will gain experience in the theory and practice of biomedical, health, and behavioral ontologies, including advanced ontology development workflows. The incumbent will also extract relevant information from published journal articles, research laboratories, and databases and integrate this information with existing data.
A key project is the Advancing Prevention Research in Cancer through Ontology Tools (APRICOT) Project funded by the US National Institutes of Health (NIH), working with behavioral scientists and ontologists across three other European sites. This project is developing ontologies and associated tools and resources to be used in reporting behavior research. This position will work on the development of the Ontology for Modeling and Representation of Social Entities (OMRSE) and its interoperability with the Behaviour Change Intervention Ontology (BCIO).
The position also is an integral team member of the Rat Genome Database (RGD). RGD is the dedicated NIH-funded knowledgebase for the laboratory rat, along with human and several mammalian disease models; RGD curates multiple genomic data types, comprehensive disease and phenotype annotations, and develops novel tools to effectively mine, analyze and visualize the available data. The incumbent will independently conduct data curation including data acquisition, ontology development, and analysis for research projects whose focus is to provide comprehensive disease, clinical and physiological data to diverse research communities. They will work with technical team members on the development of data analytic tools and pipelines, as well as provide input into database and user interface design.
Data curation
Perform data acquisition and analysis, including identifying relevant sources of information, extracting clinical, disease, physiological and genetic information from text sources such as published literature and clinical records as well as web-based and other sources.
Develop content for web-based research resources.
Work with programmers and other curators to develop new and update existing data analysis tools, database design, and web interfaces.
Ontology development and implementation
Contribute to the development of the Ontology for Modeling and Representation of Social Entities (OMRSE); manage the issue tracker; create periodic releases; lead development meetings.
APRICOT project deliverables, including but not limited to developing interoperability between OMRSE and the BCIO and the annotation of Social Determinants of Health instruments and data.
Participate in APRICOT meetings, events.
Contribute to the development of the Rehabilitation Ontology (REHABO); manage the issue tracker; create periodic releases; lead development meetings.
Contribute to ontology and vocabulary development for the Rat Genome Database, including but not limited to the Rat Disease Ontology (RDO)
Contribute to the development of the Drug Ontology (DrOn); manage the issue tracker; create periodic releases; lead development meetings.
General Responsibilities
Mentor graduate students and contribute to training and scientific development within the lab
Assist with the development of grant proposals and collaborative research initiatives
Coordinate research study activities; lead and manage projects including presenting project updates at meetings
Assist in creating workshops, presentations, and educational materials
May oversee the work of laboratory personnel, including training and development as well as daily work direction/delegation/prioritizing
Other duties as assigned
Required knowledge: ontology, terminology, controlled vocabularies, data models
Technical knowledge: Familiarity with Web Ontology Language, Protégé, GitHub, relational database management systems / SQL, public sequence databases, and model organism databases is highly desired
Enthusiastic, highly motivated, and proven ability to work independently, manage time effectively, and troubleshoot experiments
Strong interest and aptitude for multi-disciplinary collaboration
Skills and abilities: writing skills, presentation skills, organization, time management, multi-tasking.
Minimum Required Education: PhD in Biomedical Informatics, Ontology, Molecular Biology, Physiology, Computer Science, Artificial Intelligence, Biomedical Engineering, Bioinformatics, Biological or Health Sciences or comparable field
Preferred Experience: 5 years of research experience
- Experience reviewing and interpreting scientific literature and research data.
- Experience using tools for ontology development, annotation, term matching, referent tracking, semantic web.
- Expertise using public genomic or disease data resources and software tools, data acquisition, integration or standardization; clinical, laboratory or informatics experience.
- Work experience with collaborating with domain experts to solicit priorities for ontology development and formulating term definitions and axioms.
- Strong publication record in peer-reviewed journals.
Appropriate experience may be substituted for education on an equivalent basis. Master’s degree plus an additional minimum of 3 years of relevant research experience may be considered in lieu of a PhD.
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Work requires occasionally lifting moderate weight materials, standing, or walking continuously.
Occasional exposure to dust, noise, temperature changes, or contact with water or other liquids. Work is performed in an environmentally controlled environment.
Ability to detect and translate speech or other communication required. May occasionally require the ability to distinguish colors and perceive relative distances between objects.
Why MCW?
- Outstanding Healthcare Coverage, including but not limited to Health, Vision, and Dental. Along with Flexible Spending options
- 403B Retirement Package
- Competitive Vacation and Paid Holidays offered
- Tuition Reimbursement
- Paid Parental Leave
- Employee & Family Assistance Program (EFAP)
- Pet Insurance
- On campus Fitness Facility, offering onsite classes
- Additional discounted rates on items such as: Select cell phone plans, local fitness facilities, Milwaukee recreation and entertainment etc.
For a brief overview of our benefits see: Benefits Overview
For a full list of positions see: MCW Careers
At MCW all of our endeavors, from our internal operations to our interactions with our partners, are driven by our shared organizational values: Caring – Collaborative – Curiosity – Inclusive – Integrity – Respect. We are committed to fostering an inclusive environment that values diversity in backgrounds, experiences, and perspectives through merit-based processes and in alignment with all applicable laws. We believe that embracing human differences is critical to realize our vision of a healthier world, and we recognize that a healthy and thriving community starts from within. Our values define who we are, what we stand for and how we conduct ourselves at MCW. If you believe in embracing individuality and working together according to these principles to improve health for all, then MCW is the place for you. For more information, please visit our institutional website.
MCW as an Equal Opportunity Employer and Commitment to Non-Discrimination:
The Medical College of Wisconsin (MCW) is an Equal Opportunity Employer. We are committed to fostering an inclusive community of outstanding faculty, staff, and students, as well as ensuring equal educational opportunity, employment, and access to services, programs, and activities, without regard to an individual's race, color, national origin, religion, age, disability, sex, gender identity/expression, sexual orientation, marital status, pregnancy, predisposing genetic characteristic, or military status. Employees, students, applicants or other members of the MCW community (including but not limited to vendors, visitors, and guests) may not be subjected to harassment that is prohibited by law or treated adversely or retaliated against based upon a protected characteristic.
Skills Required
- PhD in Biomedical Informatics, Ontology, Molecular Biology, Physiology, Computer Science, AI, Biomedical Engineering, Bioinformatics, Biological or Health Sciences or comparable field (or Master's plus additional experience)
- Knowledge of ontology, terminology, controlled vocabularies, and data models
- Experience conducting data curation, data acquisition, and extracting information from scientific literature and databases
- Writing, presentation, organization, time management, and multitasking skills
- Familiarity with Web Ontology Language (OWL), Protege, GitHub, relational databases / SQL, public sequence databases, and model organism databases
- Minimum ~5 years research experience (preferred)
- Experience using ontology development and annotation tools, term matching, referent tracking, and semantic web technologies
- Expertise with public genomic or disease data resources and data integration/standardization
- Experience collaborating with domain experts on ontology development and formulating term definitions/axioms
- Strong publication record in peer-reviewed journals (preferred)
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