Improved biological annotation of EMDB data

Abstract

In this Final degree Project are explained all processes required to create the segmentation and biological annotation parts of Segmentation File Format (SFF) project. The segmentation file format is an Electron Microscope Data Base (EMDB) project, which is a combination of two projects, the “OMERO volume slicer” and the “Segmentation annotation tool”. This project was developed in order to build the segmentation and annotation sets for the “Segmentation annotation tool” step. The project was divided into two steps, Segmentation using Chimera, that permitted the downloading of the EMDB and PDB structure and proceed to do the segmentation, then this segmentation was saved as an Segger or HDF5 file. The segmentation of a structure is the decomposition by the different components that forms it. The second part consisted to create a biological annotation of the components previously segmented and building a link with other databases in order to identify them. The objective of this project was to create a SFF, this application would permit to the user to visualize segmentations on a EM tomogram, in order to identify and distinguish all the components that composed it. The annotation and segmentation that is explained in this project was made as a data set to build this new EMDB application. On the end of the project a collection of 100 segmentation and annotation sets were obtained, three types of structures can be distinguished; Helicases, Chaperones and Ribosomes.