A 3D Data Base for Electron Microscopy and Related Fields ofUltrastructure

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Several techniques of three-dimensional imaging are about to revolutionize the study of macromolecular assemblies, subcellular structures, and their interactions. 3D electron microscopy and confocal light microscopy are obvious examples. These techniques produce large amounts of data stored in various formats and accessible only through special arrangements with the authors. Only few aspects of a structure represented by a low-resolution density distribution can be captured in scientific publications. There is a large potential for "data mining" by other researchers within the same field or overlapping fields that is currently unused because the data are virtually inaccessible. With this application to the Databases Activities Program of NSF, the PI wishes to continue and expand a joint US-Europe initiative for the establishment of a distributed database that would accommodate ANY low-resolution (non-atomic) 3D data produced by using various experimental methods (EM, LM, x-ray, etc.). The proposal builds on an existing prototype that was developed jointly by the PI and Dr. Jose Maria Carazo in Madrid and that is already publicly accessible through Mosaic/WWW. According to the proposal, Dr. Carazo will visit the Wadsworth Center twice, for a period of five months each, to continue the design and testing of the distributed database and associated software tools, in close interaction with the PI and his group. A graduate student in Computer Science, who will be supervised by the PI and Dr. Daniel Rosenkrantz at SUNY, will design new tools allowing segmentation data to be entered and used in complex 3D data queries, as for instance required in docking of two low-resolution structures, or in the comparison of two structures that have a part-whole relationship. We plan to organize a workshop in mid-term (to be jointly funded by the European Government) that will bring together scientists from centers of 3D ultrastructural imaging and specialists in the areas of scienti fic databases and networking. With the workshop we seek to solicit critical input and start a discussion on how responsibilities might best be shared in the screening of data and how to ensure continuity of the endeavor.