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The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

Alexander D Diehl¹, Terrence F Meehan², Yvonne M Bradford³

¹Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, Buffalo, NY, 14203, USA. addiehl@buffalo.edu.

Journal of Biomedical Semantics

|July 6, 2016

Summary

The Cell Ontology (CL) standardizes biological cell types for research. Ongoing improvements enhance its utility in genomics, transcriptomics, and biomedical research, increasing its value to the scientific community.

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Area of Science:

Bioinformatics
Ontology Development
Genomics

Background:

The Cell Ontology (CL) is a foundational OBO Foundry candidate ontology for biological cell types, established in 2005.
The CL has evolved significantly, particularly in representing hematopoietic cells and vertebrate in vivo cells, with adaptable classes for other metazoans.

Purpose of the Study:

To detail recent advancements and expansions in the Cell Ontology (CL).
To highlight the CL's role in standardizing cell type data and its integration with other biomedical ontologies.

Main Methods:

Expansion of cell type representations, including in vitro cells and coordination with related ontologies (e.g., Kidney and Urinary Pathway Ontology).
Transition to OWL encoding and increased use of logical definitions for improved ontology reasoning and modularity.
Development of new modules within the CL and related ontologies.

Main Results:

The CL now includes extended representations for various cell types and improved modularity for in vitro cells.
The ontology has transitioned to OWL, incorporating logical definitions for enhanced reasoning capabilities.
The CL serves as a metadata standard for major functional genomics and transcriptomics projects (e.g., FANTOM5, ENCODE).

Conclusions:

The Cell Ontology is a crucial resource for the OBO Foundry and the broader scientific community.
Continuous improvements and increasing interest underscore the CL's value in data annotation, querying, and analysis.
The CL facilitates consistent cell type representation across diverse biomedical ontologies and research projects.