Full time Remote / Telecommute


Philadelphia, PA
0 other recent jobs
Created: April 12, 2021


Hello, Code4Lib Friends :D

Do you know SPARQL? Have experience modeling data? Want to have a real world impact?

University of Pennsylvania is looking for an ontologist. Our project is working on how to better understand medical data using semantic web technologies. Medical knowledge preferred but not required. Seeking applicants who have experience with SPARQL, RDF, and scripting.

Job listing is below. Apply at:

Penn is a nice place to work. We have great benefits. You can take classes for free. For retirement, Penn puts in 1.5 – 4%, based on age. Plus they 1:1 match up to 5%. So you put in 5%, and get 11.5 – 14% total towards retirement!

Here's a recent paper outling our work: https://doi.org/10.1016/j.yjbinx.2020.100086

If anyone has suggestions about where else to post this listing, please let me know. Feel free to forward this post to your friends. Hit me if you have any questions. If you are considering applying but aren't sure, please reach out.

Warm regards,




University Overview

The University of Pennsylvania, the largest private employer in Philadelphia, is a world-renowned leader in education, research, and innovation. This historic, Ivy League school consistently ranks among the top 10 universities in the annual U.S. News & World Report survey. Penn has 12 highly-regarded schools that provide opportunities for undergraduate, graduate and continuing education, all influenced by Penn’s distinctive interdisciplinary approach to scholarship and learning.

Penn offers a unique working environment within the city of Philadelphia. The University is situated on a beautiful urban campus, with easy access to a range of educational, cultural, and recreational activities. With its historical significance and landmarks, lively cultural offerings, and wide variety of atmospheres, Philadelphia is the perfect place to call home for work and play.

The University offers a competitive benefits package that includes excellent healthcare and tuition benefits for employees and their families, generous retirement benefits, a wide variety of professional development opportunities, supportive work and family benefits, a wealth of health and wellness programs and resources, and much more.

Posted Job Title
Application Developer / Ontologist

Job Profile Title
Application Developer B

Job Description Summary
The Perelman School of Medicine at the University of Pennsylvania is the oldest and one of the finest medical schools in the United States. Penn is rich in tradition and heritage and at the same time consistently at the forefront of new developments and innovations in medical education and research. Since its founding in 1765 the School has been a strong presence in the community and prides itself on educating the leaders of tomorrow in patient care, biomedical research, and medical education.  http://www.med.upenn.edu/

Job Description

The successful candidate will use biomedical ontologies to generate RDF triples from Penn Health System resources to integrate data and populate a graph database of patient cohorts. This activity will draw upon Open Biological and Biomedical Ontologies (obofoundry.org). Ontologies and graph databases are part of an exciting new movement in information technology that elevates data to the level of knowledge.  The technologies in this space are just beginning to gather steam.  As a result, there is significant opportunity to make an impact in what will likely become a popular field in informatics. Related duties will include using these to provide semantic structure for electronic health records working with a Natural Language Processing group and for an analytics group. Opportunities include participating in OBO Foundry ontology development. This position offers the opportunity to interact with leading medical investigators, ontology experts, and skilled programmers in a university setting.

Bachelor's degree and a minimum of one year of programming or systems analysis experience or an equivalent combination of education and experience. Master's or PhD degree with research experience related to biological sciences preferred.

    The ideal candidate will have experience with OWL2 and SPARQL.

    Programming experience with at least scripting languages also required.

    Strong preference for experience with ontologies, ideally biomedical ontologies.

    The successful candidate will have the ability to work well as part of a small highly motivated team.

This position is contingent upon grant funding.

Working Conditions
Office, library, computer room

Physical Effort
Typically sitting at a desk or table

Job Location - City, State
Philadelphia, Pennsylvania

Department / School
Perelman School of Medicine

Pay Range
$42,953.00 - $113,435.00

Affirmative Action Statement
Penn adheres to a policy that prohibits discrimination on the basis of race, color, sex, sexual orientation, gender identity, religion, creed, national or ethnic origin, citizenship status, age, disability, veteran status, or any other legally protected class.

Special Requirements
Background check required after a conditional job offer is made. Consideration of the background check will be tailored to the requirements of the job.

University Benefits

    Health, Life, and Flexible Spending Accounts: Penn offers comprehensive medical, prescription, behavioral health, dental, vision, and life insurance benefits to protect you and your family’s health and welfare. You can also use flexible spending accounts to pay for eligible health care and dependent care expenses with pre-tax dollars.

    Tuition: Take advantage of Penn's exceptional tuition benefits. You, your spouse, and your dependent children can get tuition assistance here at Penn. Your dependent children are also eligible for tuition assistance at other institutions.

    Retirement: Penn offers generous retirement plans to help you save for your future. Penn’s Basic, Matching, and Supplemental retirement plans allow you to save for retirement on a pre-tax or Roth basis. Choose from a wide variety of investment options through TIAA and Vanguard.

    Time Away from Work: Penn provides you with a substantial amount of time away from work during the course of the year. This allows you to relax, take vacations, attend to personal affairs, recover from illness or injury, spend time with family—whatever your personal needs may be.

    Long-Term Care Insurance: In partnership with Genworth Financial, Penn offers faculty and staff (and your eligible family members) long-term care insurance to help you cover some of the costs of long-term care services received at home, in the community or in a nursing facility. If you apply when you’re newly hired, you won’t have to provide proof of good health or be subject to underwriting requirements. Eligible family members must always provide proof of good health and are subject to underwriting.

    Wellness and Work-life Resources: Penn is committed to supporting our faculty and staff as they balance the competing demands of work and personal life. That’s why we offer a wide variety of programs and resources to help you care for your health, your family, and your work-life balance.

    Professional and Personal Development: Penn provides an array of resources to help you advance yourself personally and professionally.

    University Resources: As a member of the Penn community, you have access to a wide range of University resources as well as cultural and recreational activities. Take advantage of the University’s libraries and athletic facilities, or visit our arboretum and art galleries. There’s always something going on at Penn, whether it’s a new exhibit at the Penn Museum, the latest music or theater presentation at the Annenberg Center, or the Penn Relays at Franklin Field to name just a few examples. As a member of the Penn community, you’re right in the middle of the excitement—and you and your family can enjoy many of these activities for free.

    Discounts and Special Services: From arts and entertainment to transportation and mortgages, you'll find great deals for University faculty and staff. Not only do Penn arts and cultural centers and museums offer free and discounted admission and memberships to faculty and staff. You can also enjoy substantial savings on other goods and services such as new cars from Ford and General Motors, cellular phone service plans, movie tickets, and admission to theme parks.

    Flexible Work Hours: Flexible work options offer creative approaches for completing work while promoting balance between work and personal commitments. These approaches involve use of non-traditional work hours, locations, and/or job structures.

    Penn Home Ownership Services: Penn offers a forgivable loan for eligible employees interested in buying a home or currently residing in West Philadelphia, which can be used for closing costs or home improvements.

    Adoption Assistance: Penn will reimburse eligible employees on qualified expenses in connection with the legal adoption of an eligible child, such as travel or court fees, for up to two adoptions in your household.


Submitted by: tom.hutchinson@pennmedicine.upenn.edu

Published: Monday, April 12, 2021 23:00 UTC

Last updated: Monday, April 12, 2021 23:00 UTC