Ontology Engineer
Ingenuity Systems - Redwood City, CA

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ING Ontology Engineer req# 120145

Company Introduction : Ingenuity Systems (Ingenuity) is a leader in life science & bio-medical information products and services enabling researchers and biologists to analyze and biologically interpret their experimental data and understand their data within the context of genes, pathways and networks. Ingenuity is passionate about its products, and dedicated to providing researchers and biologists with the knowledge required to make Better Decisions Faster™, accelerating the pace of drug discovery and development. Ingenuity has existing customer relationships with all of the top 40 pharmaceutical companies and large percentage of government, hospital/medical, academic, nonprofit and biotech customers.

Position Summary

As a member of the Content group, you will join a dynamic cross-functional team composed of biologists, ontologists, and software engineers working on truly cutting-edge technology. This is an excellent opportunity for individuals with training in biological or organic chemistry to contribute to the advancement of science.

The Ontology group is responsible for Ingenuity’s large, high-quality Knowledge Base of biological concepts and its use to integrate content curated from the literature and public databases into our customer applications. The focus of this position is on the portions of the Ontology relating to chemicals such as drugs and endogenous human metabolites.

Duties and Responsibilities

Participate in a variety projects to extend the Ingenuity Knowledge Base to meet customer needs to understand their –omics data.

Develop models to store chemical and biological information in a consistent and computable manner

Review and integrate of chemical and biological data from a variety of sources

Developing processes to acquire and integrate new types of content, maintaining and expanding the ontology, including integration with external databases

Key Responsibilities:
Responsible for maintaining the portion of the Ingenuity Knowledge Base relating to chemicals and drugs including:

Structural classification of chemicals especially drugs and endogenous metabolites

Approved drugs and their indications and molecular targets

Clinical trials data

Skills and Abilities

Strong organic chemistry knowledge

Sufficient knowledge of biology to contribute to scientific projects not directly related to chemistry

An energetic, open-minded person with excellent communication skills, both verbal and written

Strong ability in analytical thinking

Willingness and enthusiasm to learn and practice new technologies as needed to get the job done

Knowledge of biological ontologies, ontology query languages and knowledge base tools

Strong scripting skills


Academic or work experience in the classification of organic chemicals by their functional groups

Experience with public sources of information about biochemicals, such as PubChem

Experience with public sources of information about drugs, such as Drugs@FDA and ClinicalTrials.gov

Experience programming in a language such as Perl, Python, or Java

Experience developing or using chemical or biological databases or ontologies


PhD in biochemistry or organic chemistry

Go to www.Ingenuity.com and click our career page to apply.

“Ingenuity Systems is a EEO/AA employer”

About this company
Ingenuity can be found at the crossroads of information technology and biology. The company provides software tools that researchers use in...