This planning application will create a Center for Excellence in Biomedical Computing that will help to bring about an information framework that would link together diverse types of biomedical data and knowledge in a large scale distributed information system. Such a framework has been envisioned many times, in such initiatives as the Matrix of Biological Knowledge, the Semantic Web, the Digital Human, and the Human Brain Project, yet its realization remains elusive. In planning for the Center we will bring together diverse groups of researchers to address what we see as the fundamental problems inherent in building such a framework: representing and relating diverse forms of data, and sharing data stored in widely distributed systems. In addressing these problems we will make the following assumptions: 1) no single massive database will be feasible for all biological data 2) the most reasonable means for relating diverse forms of data is through the anatomical organization of the body and 3) a promising strategy for achieving information sharing is through the incremental interconnection of information sources in various combinations, rather than creating a monolithic combined information resource.
The specific aims reflect these assumptions: 1) Plan for the organization of the Center; 2) Understand the information management needs of biological researchers in targeted areas of cancer biology, developmental biology and neuroscience, as a basis for building shared information systems of direct use in their research; 3) Develop anatomical structure-based methods for organizing and managing information generated by researchers in the target domains; 4) Develop methods for aligning ontologies developed in the targeted domains, as the primary mechanism for linking information together in a structural information framework; 5) Develop peer data management techniques for sharing data stored in widely dispersed Internet-accessible information systems;
Aim 1 and 2 are primarily planning activities.
Aims 3, 4 and 5 constitute the Developmental Projects. The name of the proposed Center will be the Interdisciplinary Center for Structural lnformatics, reflecting both the interdisciplinary nature of our work, and the hypothesis that, because the study of anatomical structures ranging in size from molecules to organisms is the foundation for understanding in biology, the study of information about anatomical structures will provide a foundation for organizing and understanding most if not all forms of biological information. ? ?
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| Louie, Brenton; Mork, Peter; Martin-Sanchez, Fernando et al. (2007) Data integration and genomic medicine. J Biomed Inform 40:5-16 |
| Au, Alan P; Li, Xiang; Gennari, John H (2006) Differences among cell-structure ontologies: FMA, GO, & CCO. AMIA Annu Symp Proc :16-20 |
| Fong, Christine; Brinkley, James F (2006) Customizable Electronic Laboratory Online (CELO): a web-based data management system builder for biomedical research laboratories. AMIA Annu Symp Proc :922 |
| Anderson, Nicholas R; Tarczy-Hornoch, Peter; Bumgarner, Roger E (2006) On the persistence of supplementary resources in biomedical publications. BMC Bioinformatics 7:260 |
| Brinkley, James F; Suciu, Dan; Detwiler, Landon T et al. (2006) A framework for using reference ontologies as a foundation for the semantic web. AMIA Annu Symp Proc :96-100 |
| Jeng, S; Wang, K; Barbero, J et al. (2005) A pilot bridging data integration and analytics: BioMediator and R? AMIA Annu Symp Proc :995 |
| Warren, Wayne; Brinkley, James F (2005) Knowledge-based, interactive, custom anatomical scene creation for medical education: the Biolucida system. AMIA Annu Symp Proc :789-93 |
| Shapiro, Linda G; Chung, Emily; Detwiler, Landon T et al. (2005) Processes and problems in the formative evaluation of an interface to the Foundational Model of Anatomy knowledge base. J Am Med Inform Assoc 12:35-46 |
| Wang, K; Tarczy-Hornoch, P; Shaker, R et al. (2005) BioMediator data integration: beyond genomics to neuroscience data. AMIA Annu Symp Proc :779-83 |
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