Showing papers on "Munich Information Center for Protein Sequences published in 2006"
TL;DR: The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis, and maintains automatically generated and manually annotated genome-specific databases and provides tools for the comprehensive analysis of protein sequences.
Abstract: The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein-protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.gsf.de).
523 citations
TL;DR: The implementation of a web-based PPI-analysis tool allows analysis and visualization of protein interaction networks and facilitates integration of curated data with high-throughput datasets.
Abstract: In recent years, the Munich Information Center for Protein Sequences (MIPS) yeast protein-protein interaction (PPI) dataset has been used in numerous analyses of protein networks and has been called a gold standard because of its quality and comprehensiveness [H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J. D. Han, N. Bertin, S. Chung, M. Vidal and M. Gerstein (2004) Genome Res., 14, 1107-1118]. MPact and the yeast protein localization catalog provide information related to the proximity of proteins in yeast. Beside the integration of high-throughput data, information about experimental evidence for PPIs in the literature was compiled by experts adding up to 4300 distinct PPIs connecting 1500 proteins in yeast. As the interaction data is a complementary part of CYGD, interactive mapping of data on other integrated data types such as the functional classification catalog [A. Ruepp, A. Zollner, D. Maier, K. Albermann, J. Hani, M. Mokrejs, I. Tetko, U. Guldener, G. Mannhaupt, M. Munsterkotter and H. W. Mewes (2004) Nucleic Acids Res., 32, 5539-5545] is possible. A survey of signaling proteins and comparison with pathway data from KEGG demonstrates that based on these manually annotated data only an extensive overview of the complexity of this functional network can be obtained in yeast. The implementation of a web-based PPI-analysis tool allows analysis and visualization of protein interaction networks and facilitates integration of our curated data with high-throughput datasets. The complete dataset as well as user-defined sub-networks can be retrieved easily in the standardized PSI-MI format. The resource can be accessed through http://mips.gsf.de/genre/proj/mpact.
363 citations
TL;DR: The FGDB provides information on two gene sets independently derived by automated annotation of the F.graminearum genome sequence, which can be accessed to retrieve information from bioinformatics analyses and functional classifications of the proteins.
Abstract: The MIPS Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the F.graminearum genome sequence. A complete manually revised gene set will be completed withinthe near future.Theinitialresultsof systematic manual correction of gene calls are already part of the current gene set. The database can be accessed to retrieve information from bioinformatics analyses and functional classifications of the proteins. The data are also organized in the well established MIPS catalogs and novel query techniques are available to search the data. The comprehensive set of gene calls was also used for the design of an Affymetrix GeneChip. The resource is accessible on http://mips.gsf.de/genre/proj/fusarium/.
82 citations
22 Jun 2006
TL;DR: SYMBIOS is presented, a fully-fledged biomedical information integration solution based on semantic pervasive services that combine a Service Oriented Architecture (SOA) and semantically-empowered techniques to ascertain biomedical information intelligent integration.
Abstract: Applying semantic pervasive services to Biomedical research is providing a new breed of intelligent applications which can tackle with the heterogeneity and intrinsic complexity of biomedical information integration. Using semantics leverages the potential of enabling cross-interoperability among a variety of storage and data formats widely distributed both across the Internet and within individual organizations. In this paper, we present SYMBIOS, a fully-fledged biomedical information integration solution based on semantic pervasive services that combine a Service Oriented Architecture (SOA) and semantically-empowered techniques to ascertain biomedical information intelligent integration. We discuss our approach with a proof-of-concept implementation where the breakthroughs and efficiency of integrating the biomedical publications database MEDLine, the Database of Interacting Proteins (DIP) and the Munich Information Center for Protein Sequences (MIPS) has been tested.