Removing roadblocks: leveraging ontologies for data aggregation and computation


The scientific literature is the cornerstone of biomedical research: it is where we put our collective knowledge about science. Recent years have seen a vast increase in diverse biomedical databases that complement and extract information from this literature, and they contain unparalleled content about genetics, genomics, anatomy, environmental interactions, developmental processes, and research resources. Researchers face a daunting challenge in using these vast stores of biomedical data to inform their understanding of biological mechanisms and drive their research activities toward novel discovery. Key contributors to this problem include a lack of unique reference to biomedical entities (e.g. genes, disease) and the research artifacts used to investigate them (e.g. antibodies, model organisms), as well as a lack of conceptual and technical interoperability between databases. These barriers make it difficult to fully exploit this enormous body of knowledge to facilitate sound and reproducible science as a foundation for continued discovery. 


Ontologies represent a key technology that can address many of these core challenges, by supporting unambiguous identification of research entities and helping bridge gaps between different data sources. Moreover, use of ontological logic in combination with aggregated data sources can enable inferred connections to be made, and improve navigation and analysis of biological data. In this presentation, we will discuss various projects in which multiple ontologies have been leveraged together to enhance data integration and exploration.



Dr. Haendel is an Assistant Professor at Oregon Health & Science University Library. She has a Ph.D. in Neuroscience, where she studied early cell and molecular development in mouse, chick, and zebrafish model organisms. Her team works on projects that leverage ontologies for translational research, including linking human diseases to model organism data and identification and linking of research resources to publications and people. Her interest is in using ontologies as a nexus for linking and querying across many types of data - genomic, biomedical, evolutionary, and research profiling.



Meeting information 
March 6, 2013 
Time: 10:00 am, Pacific Standard Time (San Francisco, GMT-08:00) 
Meeting Number: 925 343 903 
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