Junior Ontologist - Data Integration and Standardization

9420 Athena Cir, La Jolla, CA 92037, USA Req #126
Thursday, July 2, 2020

The Peters Lab at the La Jolla Institute for Immunology is currently looking for someone with a strong background in biology and an eye for detail to join their team. This new position will be remote, with the aim of bringing the role on-site when normal working conditions resume.

 

In this entry-level role, you will ensure that data is annotated in a consistent manner to allow for cross-dataset integration across multiple projects. These projects include several within infectious disease research, namely:

 

 

For each of these projects, we want to utilize a consistent vocabulary to represent the data within the project and beyond. To ensure these vocabularies meet our needs, we have contributed to the development of community-based ontologies developed under the Open Biological and Biomedical Ontology (OBO) umbrella, such as Ontology for Biomedical Investigations (OBI), the Cell Ontology and Disease Ontology. Each of these provides a hierarchical, logically defined set of terms that can be used to annotate data in a semantic-web format that allows for graph-based queries, consistency checking, and inference.

 

The tasks for this position are to:

  • Join project team meetings and identify needs for term requests and modifications
  • Submit and shepherd term requests to OBO ontologies using Github issue trackers that require reading and condensing biomedical literature
  • Familiarize and master existing tools for ontology engineering, such as ROBOT, to perform advanced ontology manipulation, quality control, and inconsistency detection
  • Use the annotated datasets to perform cross-dataset queries and advanced analysis to derive new biological hypothesis

 

Requirements:

  • Joy in paying attention to detail and scientific accuracy
  • An interest in the development of biological ontologies to standardize language and terminology across projects
  • Background in biomedical research, and the ability to read and grasp literature from a new knowledge domain quickly
  • Comfortable with creating, running and modifying python and R scripts to perform data analysis, as well as running scripts in a Linux, command line environment

 

How to apply:

Interested candidates, please upload your cover letter and resume in a single document here. Applications without a cover letter will not be considered.

 

Related Principle Investigator Publications: Dr. Bjoern Peters & IEDB on Google Scholar


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Other details

  • Job Function RA
  • Pay Type Salary
  • 9420 Athena Cir, La Jolla, CA 92037, USA