Public-Private Partnership to Facilitate Ontology Use and Application

February 14, 2018

Burlingame CA, Miami FL, and Stanford CA. A collaborative U01 grant titled “Unifying Templates, Ontologies and Tools to Achieve Effective Annotation of Bioassay Protocols” has been awarded to University of Miami together with Stanford University and Collaborative Drug Discovery. The principal investigators of this $2,088,678 U01 grant are Professor Stephan Schürer (University of Miami), Mark Musen (Stanford University), and Barry Bunin (Collaborative Drug Discovery). U01 grants are cooperative agreements that support specific and discrete goals and substantial programmatic involvement between the awardee and NIH. This particular award is part of a larger effort under the NIH Big Data to Knowledge (BD2K) program to support the development, improvement and implementation of tools and approaches that increase the efficiency and effectiveness of curation of digital biomedical research data. Data curation is a critical component to make digital research objects findable, accessible, interoperable and reusable (FAIR).

This four-year project is creating a glue technology, aptly named “OntoloBridge”, to bridge the gap between regular users of controlled scientific vocabularies and the creators of the underlying ontologies. Ontologies are sets of concepts and categories in a subject area or domain that shows their properties and the relations between them. The OntoloBridge will be built upon, and simultaneously validated by, three existing technologies: BioAssay Express (BAE) from CDD, the Center for Expanded Data Annotation and Retrieval (CEDAR) workbench from Stanford University, and the BioAssay Ontology (BAO) from University of Miami. The OntoloBridge system will provide a semi-automated, convenient, rigorous process for researchers around the world to update and extend the BioAssay Ontology (BAO). The approach will be general and extensible to other ontologies. APIs and tools—including extensions to the CEDAR workbench—will be created that allow users to request new ontology terms or to make changes to existing terms easily during the annotation process using the BioAssay Express.

This effort emerged from recognition of the need to update and request ontology terms more easily while annotating BioAssay protocols. Experimental bioassay domain experts identified this need while working directly with CDD’s new annotation tool, BioAssay Express ( BioAssay Express (BAE) allows users to annotate their bioassays in a semi-automated and standardized fashion using reference ontologies such as the BioAssay Ontology (BAO), Gene Ontology (GO), Cell Line Ontology (CLO), and Disease Ontology (DOID) and many others. Bioassay Express is a machine learning annotation tool that provides automated annotation term suggestions while giving domain experts control over how their bioassay protocol is annotated. BioAssay Express helps researchers map vocabularies to the widely accepted standardized vocabularies provided by the ontologies. OntoloBridge in the future could help users of annotation technologies such as CEDAR (researchers performing curation, dedicated curators, IT specialists, ontology owners, and librarians and maintainers of data repositories) to easily request and update ontologies.

This grant is managed by multiple principal investigators—each with a well-defined and complementary area of expertise. The Schürer group (University of Miami, PI Dr. Stephan Schürer) will develop, maintain and expand the underlying ontologies and build infrastructure to support submission and processing of new terms. The Musen group (Stanford University, PI Dr. Mark Musen) as part of the CEDAR initiative will use their metadata framework for defining templates, enabling structured and consistent annotations. And Collaborative Drug Discovery (CDD, PI Dr. Barry Bunin) will create and maintain tools for annotating assays, and coordinate economical annotation of increasing amounts of public and private data.

About this grant

The U01 grant supports collaborative substantial programmatic development between NIH and awarded institutes. Award Number 1U01LM012630-01 from National Center for Advancing Translational Sciences as described on NIH Reporter supports this project. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Center for Advancing Translational Sciences or the National Institutes of Health.

About CDD CDD’s ( flagship product, CDD Vault® is a modern web application for your chemical registration, assay data management and SAR analysis. CDD Vault® is a hosted database solution for secure management and sharing of biological and chemical data. It lets you intuitively organize chemical structures and biological study data, and collaborate with internal or external partners through an easy to use web interface. CDD Vault® is continuously growing its technology most recently to include ELN, Model and API functionality.

A complete list of the 58 CDD publications/patents can be found online on our resources page: 

For more information contact: Collaborative Drug Discovery, (650) 204-3084,

About Schürer Lab at University of Miami

The Schürer lab operates at the Department of Pharmacology in the Miller School of Medicine ( and the Center for Computational Science ( at the University of Miami. The core research theme at the Schürer group is systems drug discovery. We integrate and model small molecule-protein interaction, systems biology ‘omics’, and chemistry data to improve translation of disease models into novel functional small molecules. Using distributed and parallelized big data analytics, bio- and chemoinformatics tools we build sophisticated modeling pipelines to understand and predict drug mechanism of action, promiscuity and polypharmacology with a particular focus on kinases and epigenetic bromodomain reader proteins with application to cancer and other diseases. In several focused as well as larger-scale projects, we develop formal ontologies (e.g. BioAssay Ontology, Drug Target Ontology), data standards, and end-user multi-tier software applications. We have several drug discovery collaborations ranging from cancer to neurological disorders.

To physically make and test the most promising small molecules, we are developing computationally-optimized synthetic routes and we use parallel synthesis technologies to make small compound libraries. The combination of computational and chemistry methodologies accelerated lead optimization and the development towards clinical compounds.

The group participates in three national Consortia, the Library of Integrated Network-based Cellular Signatures (LINCS) project (, the Big Data to Knowledge (BD2K) program (, and the Illuminating the Druggable Genome (IDG) project ( Most recently we are also part of the recently established NIH Data Commons.

Schürer publications:

Contact: Stephan Schürer, PhD, University of Miami, 305-243-6552, 

About Stanford University's Center for Biomedical Informatics Research

The Stanford Center for Biomedical Informatics Research (BMIR; studies the development and evaluation of advanced computational methods to enhance biomedicine. BMIR is home to the Center for Expanded Data Annotation and Retrieval (CEDAR), which offers modular, REST-accessible software to accelerate the specification, collection, and publication of scientific metadata, while increasing the quality, quantity, and interoperability of the resulting metadata descriptions. From ontology creation (Protégé), to ontology and vocabulary dissemination (BioPortal), to semantic metadata management (CEDAR Workbench), BMIR provides transformative open source products and services used by millions of researchers.

References to all our projects' publications are provided at

Media Contact: Mark Musen, MD, PhD, Stanford University, (650) 725-3384

Last Updated: 
Feb 14 2018 - 1:29pm