OREGON HEALTH & SCIENCE UNIVERSITY
UNCLASSIFIED ACADEMIC PERSONNEL
EXECUTIVE UNIT OF THIS APPOINTMENT: Academic Affairs
Primary Dept Rank: Research Associate
Working Title: Data Wrangler
Joint Appointment(s): n/a
Term: 12 month
Dates of Appointment: August 1, 2013 – June 30, 2014
Annual Salary (1.0 FTE): FTE: 1.0
For more information please contact: Melissa Haendel Mail Code: LIB Phone: 503-407-5970
The appointee shall provide services as assigned by the supervisor in furtherance of the university’s missions and goals of teaching, research, patient care, outreach and public service.
This position reports to (supervisor): Melissa Haendel, Assistant Professor
The duties of this position include:
The Data Wrangler serves as a member of the OHSU Library Ontology Development Group. This position works in the context of the Monarch project to develop a research platform in support of investigations of phenotype-genotype correlations across species. The Data Wrangler will work with ontologists and bioinformaticians at OHSU and consortium sites to design and implement tools and strategies for semantically mapping and manipulating data.
The primary duty of the Data Wrangler will be to research and develop automation for the ingestion and quality control of data coming from several biomedical and informatics databases. This will involve the development of custom scripts and ad-hoc SQL queries, semantic mapping, and data normalization strategies. After ingestion, s/he will contribute to the development of optimization strategies in order to transform these data sets to RDF triples through D2RQ mapping, to be published via a Virtuoso Server instance. S/he will also develop QA pipelines to ensure consistency and accuracy of the ingested data before and after transformation. Moreover, s/he will provide feedback and change requests to the ontologists in the project in order to ensure a consistent and accurate representation of the data. This position will require the ability of explore possible solutions and make decisions that will lead to the identification and implementation of effective end-user displays of the data, novel approaches for data analysis, and efficient testing to support data transformation.
- Master’s degree with major courses in relevant field or; Bachelor's degree with major courses in field of research plus 4 additional years related experience.
- 3 years of relevant work experience
- Ability to perform research and make independent decisions about approaches and tools to reach specific goals
- Experience with semantically annotated data
- Experience with Software Project Management tools (Jira, Confluence, SVN, Git)
- Hands-on experience with one or more scripting languages (e.g. Perl, Python, Ruby, Bash)
- Hands-on experience with SQL (Postgres preferred)
- Strong programming skills with a solid understanding of object oriented languages and principles
- Experience in Java programming
- Strong verbal, written, and interpersonal communication skills (especially via teleconferencing venues)
- Experience developing and evaluating data curation workflows
- Experience developing ontologies and data models
- Experience in developing Extract Transform Load (ETL) scripts
- Knowledge of SPARQL, RDF, OWL
- Experience in bioinformatics
- Experience in end-user usability for bioinformatics platforms
Duration of this appointment and indicated salary may be changed or eliminated if gift, grant, or contract funds supporting this position become unavailable.
Please contact Melissa Haendel at email@example.com for more information. Apply at: Oregon Health & Science University: http://www.ohsu.edu/xd/about/services/human-resources/ Position number: IRC40016