Open Position

Data Integration and Standardization Specialist

Data Integration and Standardization Specialist

The Peters Lab at the La Jolla Institute for Immunology is a multidisciplinary team of scientists working towards understanding, preventing and curing immune-related diseases by accurately translating immunological questions into a computable form. The group is currently looking for a data specialist with an eye for detail to join their team. This new position will be remote for now, with the aim of bringing the role on-site when normal working conditions resume.

The Peters Lab is generating and analyzing data that needs to be annotated in a consistent manner to allow for cross-dataset integration across multiple projects. These projects include several that are dealing with infectious disease research, namely:

Human Immunology Project Consortium (HIPC)
Immune Epitope Database (IEDB)
CoVIC-DB
IMPACC
● Computational Modeling of Immunity – Pertussis Boost (CMI-PB) (NEW, website in development)

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 OBO umbrella, such as OBI, the Cell Ontology, Disease Ontology, and so on. 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 the 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 exactness
● 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
● Comfortable with 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