Ontologies

CVRG ontology development and application focuses in three major areas.  We have developed a preliminary ontology for describing all aspects of ECG data collection, ECG waveform features, and ECG data analysis. We coupled ontology development with the development of an ECG data model.  The CVRG award supports the ECG ontology and data model development. 

Support for the development of a web-based tool (ECGrid Toolkit) for analyzing, visualizing and annotating ECG signals comes from a Driving Biomedical Project with the National Center for Biomedical Ontologies (NCBO). 

While focusing on ECGs, we are continuing the development of an ontology for describing cardiovascular experimental data, including information about experimental preparations (e.g., cell isolation, tissue isolation, whole organ preparation, species, solutions, etc), recording technologies (e.g., patch-clamp electrode, sharp electrode, single and multi-channel fluorescent imaging, measurement instrumentation, etc), and data collection protocols (e.g., voltage-clamp, current-clamp, waveform-clamp, etc).

Further details can be found in the CVRG wiki, under Ontology Development.

Approach

The CVRG approach to ontology development is to link to existing ontologies, as needed, for relevant terms. Examples of these ontologies include the Foundational Model of Anatomy, the Gene Ontology, etc. We then focus on “bottom-up” development of domain-specific ontologies such as those for ECG and EP experiment and data description. Ontologies are deposited at the NCBO, and are managed using NCBO tools (Protégé, BioPortal).

Bioportal has a mechanism for community input on ontology development, making it possible for users of NCBO-managed ontologies to create marginal notes critiquing terms in the ontology, suggesting new terms, and assessing the overall quality of the ontology. Bioportal also enables ontology peer-review, making it possible for users of CVRG ontologies to describe how they use the ontologies, and describe how useful the ontology was in their project. In addition, we have formed an expert review panels that will be the “first line of support” in advising on terms needed in ontologies. As we receive input on the ontology, suggested revisions to ontology terms, and suggestions for new terms, this panel will perform final adjudication. Finally, we are creating community-wide working groups in different ontology areas to assure that we have broad input on ontology development.

CVRG Ontology Advisory Board

The CVRG has extablished a CVRG Ontology Advisory Board. The purpose of this board is to provide regular review and critique of ontologies being developed as part of the CVRG Project. Current board members are Mark Musen, Daniel Rubin, Mary Shimoyama and Barry Smith.