Biomedical ontologies and their development, management, and applications in and beyond China

Abstract

Since the boom of biomedical big data studies, various big data processing technologies have been developed rapidly. As an important form of knowledge representation, ontology has become an important means for the utilization and integration of biomedical big data. The emergence of new technologies for ontology development has resulted in the generation of many biomedical ontologies by many ontology development communities. The Open Biological and Biomedical Ontology Foundry, an academic organization for bio-ontology developers, has provided a set of principles to guide community-based open ontology construction. The Open Biological and Biomedical Ontology Foundry have also built many widely used ontologies, such as Gene Ontology, Human Phenotype Ontology, and Chemical Entities of Biological Interest. Other various ontology repositories have also been created and used to support ontology reuse. Many efficient tools for ontology applications, such as data annotation and terms mapping, have also been developed. High quality ontologies are also being used to develop new methods and tools for biomedical data analysis. The applications of Gene Ontology and Human Phenotype Ontology for data analysis and integration in recent years are reviewed here. To promote the development and applications of biomedical ontologies in China, a research community, OntoChina, was founded recently. OntoChina aims to support the development of reference ontologies, especially bilingual and Chinese translated ontologies. OntoChina also encourages ontology developers to follow the Open Biological and Biomedical Ontology Foundry principles.