Assistant Research Professor in Ontologies and Curation

University of Colorado

Job Description

Assistant Research Professor in Ontologies and Curation  - 29362 
Research Faculty 



University of Colorado Anschutz Medical Campus

Department: Biomedical Informatics

Job Title: Assistant Research Professor in Ontologies and Curation

Position #:00807855  – Requisition #:29362

Job Summary:

The Department of Biomedical Informatics at the University of Colorado School of Medicine invites applications for an Assistant Research Professor Position, Ontologies and Curation . This new Assistant Research Professor 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 Assistant Research Professor in Ontologies and Curation will play an important role in advancing the mission of the Translational and Integrative Sciences Laboratory (TISLab), which is led by Dr. Melissa Haendel. The 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, curation and ontology development, 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 (DBMI) 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 cross-campus collaboration opportunities to translate data-intensive research advances into improved care.

The Assistant Research Professor in Ontologies and Curation will develop and contribute to data models, ontologies, and semantic data harmonization and integration strategies. The candidate will contribute to a diverse portfolio of TISLab research programs such as the cross-species genotype-phenotype program the Monarch Initiative, the Downs Syndrome program INCLUDE, the NCATS Data Translator, and the Bridge2AI program. Other duties include contributing to publications, 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:

  • Make contributions 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 scientific curation, author publications, assist in the preparation of progress reports and other communique and assist in documentation efforts for TISLab projects, internal knowledge base, and training resources
  • Liaise with all stakeholders of the data, from the producers/submitters to the consumers.
  • 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 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.


Minimum Qualifications:

Applicants must meet minimum qualifications at the time of hire.

  • Ph.D. in biological sciences (e.g., genetics, cell biology, neuroscience, etc.), biomedical informatics, or related field
  • 5+ years of experience in one of the relevant fields of expertise listed above
  • 5+ years of  hands-on experience with generating/processing/curating biological data 
  • 3+ years of experience using medical/scientific terminologies, ontologies, data models, or other semantic technologies for annotation
  • 3+ years of experience developing and evaluating data curation workflows, data quality, and validation according to semantic standards
  • Evidence of professional service to their place(s) of employment (institutional or organizational) or other national/international organizations (e.g., professional societies, etc.) over at least the past 2 years.

Preferred Qualifications:

  • Experience with software project management tools and version control systems (e.g., Git/GitHub, Jira, Confluence)
  • 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
  • Record of creation of semantic products such as terminologies or contributions to open-source software projects
  • Experience with Open Biological and Biomedical Ontologies (OBO) and related OBO Library tools
  • Demonstrated skills in the use of common data wrangling or Extract-Transform-Load software; or demonstrated skills in programming or in scripting languages (e.g., Python, pandas, R)
  • Demonstrated experience in the collection, storage, transformation, standardization, harmonization, and analysis of legacy data stored in a variety of formats (CSV, JSON, Relational databases like MySQL, PostgreSQL, SQLServer Oracle, unstructured text, etc.).
  • Experience using SPARQL and/or graph query languages such as Cypher
  • Experience modeling and managing semantically annotated data
  • Experience managing informatics/information science projects

Knowledge, Skills and Abilities:

  • A disposition to contribute to building a diverse and inclusive research team.
  • Ability to conduct scientific curation and author publications on this and related subjects, and to work effectively with others as part of a multidisciplinary scientific team.
  • An understanding of the life cycle of data and in particular the sharing of data for later reuse, as well as experience in the creation of metadata for curated datasets
  • An understanding of various data license types and how they impact the use and reuse of curated data available to the public and/or researchers.
  • Be self-directed. Ability to make independent decisions about approaches and tools to reach specific goals and demonstrated experience in self-training and exploring new technologies. The ability to set their own schedule and goals, and at the same time, have the willingness and ability to ask for guidance and assistance when needed.
  • Be motivated and excited to learn. A successful candidate is 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 committed to quality. This position requires a focus on documentation and quality assurance.
  • Be communicative. Able to communicate effectively with geographically-distributed collaborators, and able to convey complex, technical topics clearly to multiple audiences. This includes email, instant messaging (e.g., Slack), and code and dependencies documentation.
  • Be collaborative, contributing to open source software development and informatics projects within DBMI and the TISLab and with members from diverse organizations from around the world.
  • Be dedicated to diversity, participating in activities within the laboratory, department, the university, and the broader scientific community that promote the success and welfare of all people. 
  • Ability to balance multiple priorities and initiatives in parallel.

How to Apply:

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

  • A letter of interest describing relevant job experiences as they relate to listed job qualifications and interest in the position
  • Curriculum vitae / Resume
  • Three to five professional references including name, address, phone number (mobile number if appropriate), and email address
  • Note: This position is open to applicants seeking remote work opportunities.

    Applications are accepted electronically ONLY at www.cu.edu/cu-careers .

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

    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 $90,000 to $110,000.

    The above salary range (or hiring range ) represents the University’s good faith and reasonable estimate of the range of possible compensation at the time of posting. This position is not eligible for overtime compensation unless it is non-exempt.

    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@ucdenver.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 as well as sex offender screenings.

    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.

          Application Materials Required: Cover Letter, Resume/CV, List of References, Additional Attachments - Refer to Application Materials Instructions Below 
    Job Category
    : Faculty 
    Primary Location
    : Aurora 
    Department: U0001 -- DENVER & ANSCHUTZ MED CAMPUS - 21925 - SOM-BIOMED Informatics Gen Ops 
    : Full-time 
    Posting Date
    : Mar 20, 2023 
    Unposting Date
    : Ongoing 
    Posting Contact Name: Michelle Fiandra 
    Posting Contact Email: michelle.fiandra@cuanschutz.edu 
    Position Number: 00807855

    *Please mention you saw this ad on AcademicJobs.*

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