Biomedical Software Jobs in Wisconsin (NOW HIRING)

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, Protege, 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.