Ode to Ontologies: Helping Chinese collaborators share big data

A Global REACH-funded grant is helping to bring UMMS-developed big data technology to researchers China.

Associate Professor of Bioinformatics Oliver He and his research partners at the Biologic Medical Medicine Informational Center of China, in Beijing.

Associate Professor of Bioinformatics Oliver He completed a three-month sabbatical last summer and fall at the Biologic Medicine Information Center of China (BMICC), in Beijing, where he worked to install a suite of big data-organizing systems developed in his lab. Bioinformatics Ontologies define domains, terms and relationships necessary for computers to process, sort and analyze data at scale. Large-scale, cross-institutional studies wouldn’t be possible without the agreed upon framework ontologies provide.

“When you have huge datasets from different hospitals in different cities, or even different countries, you need a standard way to share and analyze that information, so we use the ontologies to sanitize and standardize big data,” said He, PhD. “BMICC plays a significant role in supporting China’s scientific data-sharing and promoting scientific progress. It was an honor that they invited me.”

A leading expert in informatics ontologies, He was first invited to BMICC to give a presentation of his work in 2016. That experience led to an extended invitation and collaboration. He spent nearly 14 weeks in China this summer, supported by the Chinese Academy of Medical Sciences, the BMICC, and a $10,000 Global REACH Partnership Development grant aimed at helping faculty foster new international partnerships.

While in Beijing, He completed the initial set-up of his two ontology systems and also trained some 40 BMICC colleagues to use it. These two software programs, called Ontobee and Ontofox, were developed in He’s lab and are now in use in more than 100 countries. At BMICC, He and colleagues have already begun using the systems to with different datasets, from integrating the information from disparate cell line banks, to organizing a national physique and health database containing detailed information on more than 160,000 Chinese citizens.

During the sabbatical, He and many of his collaborators, including BMICC professor Dr. Xiaolin Yang and professor Wei Zhou from the National Scientific Data Sharing Platform for Population and Health in China, also initiated a new China Biomedical Ontology Consortium of national ontologies experts to promote best practices when it comes to sharing big data. They call the group OntoChina.

Their collaborative paper,“Ontology:Foundation of Biomedical Big Data and Precision Medicine Research”, has also recently been accepted for publication in Chinese Journal of Bioinformatics. The article aims to introduce the cutting-edge ontology technology to the Chinese researchers and demonstrate its applications in big data and precision medicine research.   

“I believe it will greatly promote collaborative ontology research, development, and applications in China, and it will also likely promote close international collaborations between China and other countries, including the United States,” He said. “Having more Chinese medical data available to the whole world is a very good thing and would result in more international collaboration.”