Job Summary:

The Semantic Engineer will contribute to the TISLab’s diverse portfolio of research including grant-funded programs, potential commercialization opportunities, and partnerships. The Semantic Engineer will develop and contribute to data models, ontologies, and semantic data harmonization and integration strategies for a variety of translational research contexts, including the following data types: clinical research variables, basic research experiments, imaging metadata, genotype-phenotype data, expression, and other ‘omics data. Other responsibilities include contributing to publications, submission of grants and funding applications, and collaborations with community-wide efforts aimed at promoting open, integrated, and rigorous practices in research, data engineering, and scholarly communication; this may involve traveling to conferences up to 3 times annually.

Key Responsibilities:

• Contribute to open-source software and informatics development projects in collaboration with lab members and external collaborators.
• Collaborate with laboratory members and external colleagues on open-source software and informatics development projects.
• Conduct projects applying semantic engineering skills and contribute to publications about the project.
• Assist in the preparation of progress reports, grant proposals, and other communique, and assist in documentation efforts for TISLab projects, internal knowledge base, and training resources.
• Participate in service activities within the laboratory, department, the university, and the broader scientific community that contribute to their missions and that promote the success and welfare of the broader scientific community. 

Why Join Us:

The Department of Biomedical Informatics at the University of Colorado School of Medicine invites applications for a Semantic Engineer. The new Semantic Engineer will join a highly interactive, supportive, and interdisciplinary group of faculty, staff scientists, postdoctoral fellows, and students and enjoy access to state-of-the-art equipment and facilities on the Anschutz Medical Campus. The Semantic Engineer will play an important role in advancing the mission of the Translational and Integrative Sciences Laboratory (TISLab), which is led by Dr. Melissa Haendel.

Researchers in the Department of Biomedical Informatics focus on computational approaches that advance research and medical practice. The TISLab focuses on areas such as automated and manual biocuration, knowledge representation, semantic engineering, automated reasoning, and the development and evaluation of algorithms and software systems that advance these practices in support of artificial intelligence. The Department of Biomedical Informatics is located on the Anschutz Medical Campus with the UC Health University of Colorado Hospital, Colorado Children's, and Rocky Mountain Regional VA Medical Center. The Anschutz Campus is home to Colorado’s only Comprehensive Cancer Center and the Colorado Clinical and Translational Sciences Institute. There are many opportunities on campus to translate data-intensive research advances into improved care.

The University of Colorado offers a comprehensive benefits package that includes health insurance, life insurance, retirement plans, tuition benefits, ECO pass, paid time off – vacation, sick, and holidays and more. To see what benefits are available, please visit: https://www.cu.edu/employee-services/benefits-wellness .

Diversity and Equity:

The University of Colorado Anschutz Medical Campus is committed to recruiting and supporting a diverse student body, faculty, and administrative staff. The university strives to promote a culture of inclusiveness, respect, communication and understanding. We encourage applications from women, ethnic minorities, persons with disabilities, persons within the LGBTQ+ community and all veterans. The University of Colorado is committed to diversity and equality in education and employment.

Qualifications:

Minimum Qualifications:

• Bachelor’s degree in computer science, clinical informatics, biomedical informatics, biosciences, or related field.
• Six (6) plus years of software or system engineering, bioinformatics, or directly related IT professional experience, including the following:
• Experience working with one or more of the following: graph databases, triplestores, ontologies, semantic data models, or other semantic technologies.
• Experience in the collection, storage, transformation, standardization, harmonization, and analysis of legacy data stored in a variety of formats (e.g., CSV, JSON, relational databases such as MySQL, PostgreSQL, and SQLServer Oracle, unstructured text, etc.).
• Experience with software project management tools and version control systems (e.g., Git/GitHub, Jira, Confluence).

Applicants must meet minimum qualifications at the time of hire.

Preferred Qualifications:

• MS or Ph.D. in computer science, clinical informatics, biomedical informatics, biosciences, or a related field.
• Experience with the development of HL7 (Health Level Seven) / FHIR (Fast Healthcare Interoperability Resources) standards and FHIR-based artifacts.
• Experience with the Observational Medical Outcomes Partnership (OMOP) data model and terminologies.
• Experience with web application and user interface development using semantic technologies and/or deploying semantic artifacts in the context of software system architecture, design, and implementation.
• Experience modeling and managing semantically annotated data.
• Experience developing and evaluating data curation workflows, data quality, and validation according to semantic standards.
• Experience managing informatics/information science projects.

Knowledge, Skills, and Abilities:

• Be communicative and can convey complex, technical topics clearly to multiple audiences, and to communicate effectively with geographically distributed collaborators. This includes email and instant messaging (e.g., Slack), but also, importantly, code and dependencies documentation.
• Be dedicated to diversity, with a disposition to contribute to building a diverse and inclusive research team comprising geographically distributed members with complementary skills and levels of experience.
• Can successfully complete semantic engineering projects and author publications on this and related subjects.
• Demonstrate the ability to work independently and effectively with others as part of a multidisciplinary scientific team.
• Be motivated and excited to learn. A successful candidate should be able to adapt to new environments, approaches, and tools and, when necessary, be able to extend approaches for a new purpose or, if necessary, develop an entirely new approach to solve a problem.
• Be self-directed. A successful candidate needs to be able to set their own schedule and goals but, at the same time, is willing and able to ask for guidance and assistance when uncertainty and blockers arise.
• Be collaborative. Contributions to open-source software development and informatics projects within DBMI and the TISLab and with members from diverse organizations from around the world.
• Be committed to quality. This position will require a focus on documentation and quality assurance.
• Evidence of contribution to open-source software projects.
• Track record of productivity in the practice of research as evidenced through the development and dissemination of software, data, and knowledgebases, preprints, and/or publications.
• Demonstrated ability to make independent decisions about approaches and tools to reach specific goals and demonstrated experience in self-training and exploring new technologies.
• Able to balance multiple priorities and initiatives in parallel.
• Strong verbal, written, and interpersonal skills (especially via teleconferencing venues).
• Working knowledge and hands-on experience using OWL, RDF, JSON-LD, SPARQL, and/or graph query languages such as Cypher, or other semantic technologies.
• Broad knowledge of medical/scientific terminologies, and/or experience with Open Biological and Biomedical Ontologies (OBO) and related OBO Library tools.
• A conceptual knack for interpreting data schemas and relating them to biomedical research applications.

How to Apply:

For full consideration, please submit the following document(s):

Questions should be directed to: Michelle Fiandra at michelle.fiandra@cuanschutz.edu

Screening of Applications Begins:

Screening of applications begins immediately and continues until position is filled.

Anticipated Pay Range:

The starting salary range (or hiring range ) for this position has been established as $97,081 to $123,487.

The above hiring range represents the University’s good faith and reasonable estimate of the range of possible compensation at the time of posting. This position may be eligible for overtime compensation depending on the level.

Your total compensation goes beyond the number on your paycheck. The University of Colorado provides generous leave, health plans and retirement contributions that add to your bottom line.

Total Compensation Calculator: http://www.cu.edu/node/153125

ADA Statement:

The University will provide reasonable accommodations to applicants with disabilities throughout the employment application process. To request an accommodation pursuant to the Americans with Disabilities Act, please contact the Human Resources ADA Coordinator at hr.adacoordinator@cuanschutz.edu .

Background Check Statement:

The University of Colorado Anschutz Medical Campus is dedicated to ensuring a safe and secure environment for our faculty, staff, students, and visitors. To assist in achieving that goal, we conduct background investigations for all prospective employees.

Vaccination Statement:

The University of Colorado has a requirement for COVID-19 vaccinations and full completion thereof by 9/1/21 or upon start date.  Information regarding this requirement, and exemptions can be found at:

Anschutz: https://www.ucdenver.edu/docs/librariesprovider284/default-document-library/3000-general-admission/3012---covid-19-vaccination-requirement-and-compliance.pdf?sfvrsn=4e9df3ba_2

Unit-Specific Exemptions:

• Anschutz Campus – Accommodations may be granted for medical or religious reasons.

The University of Colorado seeks individuals with demonstrated commitment to creating an inclusive learning and working environment. We value the ability to engage effectively with students, faculty, and staff of diverse backgrounds.