The Bio-Ontologies SIG (#bioontologiesprovides a a vibrant forum for discussion of the latest and most innovative research in the application of ontologies and more generally the organization, presentation and dissemination of knowledge in biomedicine and the life sciences. Bio-Ontologies has existed as a SIG at ISMB for 18 years, making it one of the longest running. 

The 2016 meeting will be a two day SIG (July 8 and 9), with July 9th being the “Phenotype Day”, an event bring together researchers across many disciplines to discuss defining, representing, processing and using phenotype data. This year's 
Programme includes 2 keynote speakers, 7 full papers and 5 flash updates.

Download this year's programme booklet (4MB PDF) containing accepted research papers and flash updates.


Getting Bio-Ontologies into the Business - Challenges, Strategies and Success Stories
Martin Romacker, Data and Information Architect, Roche

The bio-medical domain is by far the scientific and industrial domain providing the richest set of well-designed and comprehensive ontologies. These ontologies cover all aspects of research and development. At the same time, the bio-medical domain has pioneered the creation and integration of ontologies both in the sciences and the industry during the last 30 years. Despite the wealth of resources and experience the adoption of ontology-driven data standards is still not very common in the Pharma Industry and in Pharma Research in particular. This is quite surprising given the importance of data quality and the need for a strategic management of corporate/ research data assets. In my presentation, I would like to highlight some of the causes for the limited range of Bio-Ontologies in Pharma and define some strategies to strengthen the role of Bio-Ontologies in Data Management. I would like to conclude with some success stories helping us to boost the acceptance and usage of Semantic Technologies in our industry."

Bio: Dr. Martin Romacker is a Principal Scientist in Data and Information Architecture and Terminologies at Roche Innovation Center Basel. His primary focus is the definition and application of Data Standards to facilitate data federation and answering of complex scientific queries. Current activities include Terminology Management, Semantic Engineeri
ng, Scientific Data Integration/Curation, Text Mining and Information Retrieval/ Search Technologies. Previously Martin was working as a Senior Knowledge Engineering Consultant at Novartis Institutes of Biomedical Research. He has more than 20 years of practical experience in knowledge management and holds a PhD in Computational Linguistics from University of Freiburg, Germany.

Boiling the ocean with tools of informatics: The Semantic Data Lake for Healthcare and Life Sciences
Dr. Parsa Mirhaji, Ph.D, MD
Albert Einstein College of Medicine

Promising prospects of precision medicine and radical change in delivery of care system from a service based economy to patient centered, outcomes driven, and learning healthcare system requires and advocates for relentless understanding of patients, populations, and interventions using all data, metadata, and knowledge that is available to us. In this presentation we will introduce and rationalize a design architecture for a semantic data lake that is developed from ground up with the notions of evidence generation for personalized medicine, and evidence based, accountable, and outcomes driven care. The Semantic Data Lake is a big-data analytics architecture based on principles of distributed computing (SPARK/GraphX/Hadoop) and the Semantic Web customized to support analytics in high dimensional, longitudinal, and multi-source big-data ecosystems such as
healthcare. We will review the technical architecture, and use-cases that are driving the design and implementation of the system, and provide an interim report on some of our findings.

Bio: Dr. Parsa Mirhaji MD. PhD. is an Associate Professor of Systems and Computational Biology and the Director of Clinical Research Informatics at the Albert Einstein College of Medicine and Montefiore Medical Center-Institute for Clinical Translational Research. He is also a co-investigator and the Chief Technology Officer for the New York City Clinical Data Research Network. Formerly, he was the director of the Center for Biosecurity and Public Health Informatics Research at the University of Texas at Houston where he developed clinical text understanding, semantic information integration technologies, and EMR interoperability solutions, for public health and disaster preparedness. Dr. Mirhaji and his fellow researchers were awarded “The Best Practice in Public Health Award-2002” by the U.S. Department of Health and Human Services for establishing the Defense of Houston web-portal for community awareness and public readiness in the aftermath of September 11 attacks.

Key Dates

April 8th, 2016 Submissions Due: Extended to April 15th, 2016!
May 9th, 2016   Notifications
May 20th, 2016 Final Version Due
July 8-9, 2016   Meeting


 The JBMS supplement from the 2015 meeting will published around July 2016

 Awards from F1000 for best paper/presentation were given to 
* Alison Callahan for Elucidating effects of nerve injury on gene expression using RegenBase, a knowledge base of spinal cord injury biology.
* Jisoo Park for Towards a More Molecular Taxonomy of Disease.
* Chris Mungall for k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction.