About CSEO

Objective

CSEO is a specialized ontology of environmental exposure with particular focus on the description of the experimental elements and the impact that environmental exposure, e.g. cigarette smoke, poses to biological systems.

Conceptualizing and organizing this knowledge domain in the form of ontology allows for: 1. Efficient augmentation of biological knowledge retrieval and extraction with improving the sensitivity to which biological mechanisms are modulated in response to different risk factors. 2. Integration of this ontology in internal processes to ensure clear annotation of experimental datasets coming from in-vitro, in-vivo, and ex-vivo experiments using such controlled vocabularies. This will enable a systematic approach and create compliance with good practices and regulatory guidelines. 3. Provides a standard platform for interoperability of the environmental exposure knowledge and may become a global standard within the academic and industrial community.

We realize this need and want to catalyze the development of an environmental ontology within a broad scientific and industrial community.

Scope

The scope of CSEO is centered on the following elements:

• Exposure experiment
• Exposure condition
• Test system
• Sampling
• Disease outcome

Architecture

CSEO has been designed in such a way to be compliant with the upper-level standards adopted from Basic Formal Ontology (BFO). Environmental exposure Ontology (ExO) – a high level ontology for describing fundamental elements of environmental exposure – has been slightly modified to link the high-granularity ontology of cigarette smoke exposure (CSEO) to the upper-level standard ontology, BFO. The advantage of such a structure is that it preserves the consistency and coherence of the semantic integration at all levels.

Structure & resources used

Currently, CSEO version 0.10 contains 2224 concept classes and includes many existing standard resources such as MGED ontology, CDISC, NCI Thesaurus, ArrayExpress Ontology, Units Measurement Ontology, Experimental Factor Ontology, OpenToxipedia, and NCBITaxon.
Concepts are annotated by their corresponding definition, synonyms, and reference.