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#96180 Biomedical Semantic Applications Programmer

Filing Deadline: Thu 10/25/2018

UCSD Layoff from Career Appointment: Apply by 10/15/18 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor.

Special Selection Applicants: Apply by 10/25/18. Eligible Special Selection clients should contact their Disability Counselor for assistance.


SciCrunch is a data sharing and display platform, which was designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. One such project, The Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources, it is an initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment. Established in 2004, the NIH Blueprint for Neuroscience Research brings the 16 NIH Institutes, Centers and Offices that support neuroscience research into a collaborative framework to coordinate their ongoing efforts and to plan new cross-cutting initiatives. Working together, representatives from the partner Institutes, Centers, and Offices identify pervasive challenges in neuroscience and any technological barriers to solving them. The NIF project is designed to serve the biomedical research community and now supports a number of initiatives. Another project, the NIDDK Information Network (dkNET) is another large pools of data relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK), it offers a search portal to find community-vetted materials, data and tools relevant to NIDDK, personalized search and display of results, and community news and social networking.

Works on assignments of moderate scope focused on the analysis and development of ontologies and terminologies. The Biomedical Semantic Applications Programmer will work as a member of our bioinformatics team and will be responsible for the maintenance, enhancement, and documentation of SciCrunch's terminologies, ontologies and semantic infrastructure. Specifically, the Programmer will be responsible for knowledge engineering and supporting systems involved in the querying, viewing, federating, analyzing and managing of large, bio-medical ontologies and utilizing these ontologies to annotate primary research data. The Programmer will also interact with domain scientists to research and build requirements specifications and test deployed systems. Infrastructure to be maintained include SciGraph, a Neo4J backed ontology service; InterLex, a community terminology portal; the NIF Ontologies, that brings together an extensive set of terms and concepts from community ontologies while also adding new terms and concepts important for the domains of neuroscience and biology.

Uses professional bioinformatics concepts. Applies computational procedures to resolve a variety of analysis and research issues. Works on assignments of moderate scope where analysis of data requires a review of a variety of factors. Assists in additional analyses as needed to achieve research objectives.


  • Bachelor's degree in biological science, computational / programming, or related area and / or equivalent experience / training.

  • Two (2) or more years of relevant experience.

  • Working knowledge of bioinformatics methods and data structures. Demonstrated ability to organize large volumes of data using creative tools, logs and databases created to use with multiple research projects.

  • Working knowledge of applications programming and web development.

  • Working knowledge of databases.

  • Working project management skills. Strong decision making skills and ability to use independent judgment and discretion to quickly set priorities and establish new procedures when needed. Demonstrated ability to research, analyze, recommend, communicate, and implement solutions. Must be able to function successfully with minimal direction

  • Working knowledge of modern biology and applicable field of research.

  • Interpersonal skills in order to work with both technical and non-technical personnel at various levels in the organization.

  • Ability to communicate technical information in a clear and concise manner. Strong interpersonal and communication skills, including tact, diplomacy, and flexibility. Ability to work successfully with a diverse group of people with varying perspectives and needs. Demonstrated ability to communicate clearly and concisely, both verbally and in writing.

  • Self motivated, able to learn quickly, meet deadlines and demonstrate problem solving skills.

  • Working knowledge of application and data security concepts.

  • Theoretical knowledge of neuroscience

  • Experience with ontologies and ontology maintenance tools and application software, especially Protege

  • Experience with standard ontology formalisms (e.g. OWL) and related semantic web standards (e.g. RDF).

  • Demonstrated ability in the development of software that utilizes biomedical ontologies.

  • Experience with biomedical ontologies such as the open biomedical ontologies (obo) and repositories such as the National Center for Biomedical Ontologies.

  • Demonstrated ability to interpret/coordinate research protocols and the corresponding data requirements.

  • Experience with the design, development, and maintenance of data collections used for data storage and analysis in a biomedical research environment.

  • Outstanding writing and editing skills using knowledge of conventions of academic style, English grammar, punctuation, and spelling. Demonstrated ability to re-write text that is ambiguous, unorganized or grammatically incorrect.

  • Demonstrated experience with scripting language such as Python.

  • Demonstrated ability to troubleshoot and problem solve in computational work.

  • Demonstrated ability to work with multiple computer programs such as Excel, Word, Outlook, Power Point, Access, as well as the ability to create and maintain databases/MySQL databases.

  • Ability to install, configure and work in a Unix environment.


  • Prior experience working in an environment where research relates to human diseases and developmental processes.

  • Demonstrated experience designing and creating web applications, web services and virtual machines.

  • Experience with compiled languages such as Java, C++ or C.

  • Experience with mark up languages such as HTML or XML.

  • Demonstrated ability in publishing and/or presenting scientific work in journal articles and/or academic conferences.


  • Employment is subject to a criminal background check.

UC San Diego Health is the only academic health system in the San Diego region, providing leading-edge care in patient care, biomedical research, education, and community service. Our facilities include two university hospitals, a National Cancer Institute-designated Comprehensive Cancer Center, Shiley Eye Institute, Sulpizio Cardiovascular Center, and several outpatient clinics. UC San Diego Medical Center in Hillcrest is a designated Level I Trauma Center and has the only Burn Center in the county. We invite you to join our dynamic team!


Applications/Resumes are accepted for current job openings only. For full consideration on any job, applications must be received prior to the initial closing date. If a job has an extended deadline, applications/resumes will be considered during the extension period; however, a job may be filled before the extended date is reached.


UC San Diego Health is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age, protected veteran status, gender identity or sexual orientation. For the complete University of California nondiscrimination and affirmative action policy see: http://www-hr.ucsd.edu/saa/nondiscr.html

UC San Diego is a smoke and tobacco free environment. Please visit smokefree.ucsd.edu for more information.

UC San Diego School of Medicine
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As a federally-funded institution, UC San Diego Health maintains a marijuana and drug free campus. New employees are subject to drug screening.