Note: Intro -- Database Annotation in Molecular Biology -- Contents -- Preface -- List of Contributors -- 1 Annotation and Databases: Status and Prospects -- 1.1 Introduction -- 1.2 Annotation of Genomic Data -- 1.3 Databases: Concepts and Definitions -- 1.4 Access to Annotation Databases -- Glossary -- References -- I THE DATABANKS -- 2 Survey of Sequence Databases: Archival Projects -- 2.1 Introduction -- 2.2 Nucleotide Sequence Databases -- 2.3 Swiss-Prot -- 2.4 TrEMBL -- 2.5 PIR -- 2.6 UniProt -- References -- 3 Survey of Sequence Databases: Derived Databases -- 3.1 Introduction -- 3.2 Protein and Gene Family Databases -- 3.3 Discussion -- References -- 4 Databanks of Macromolecular Structure -- 4.1 Introduction -- 4.2 Background -- 4.3 Archival Structural Databases Now -- 4.4 Contextual Databases -- 4.5 Derived Structural Data Databases -- 4.6 Summary and View of the Future -- References -- 5 Gene Expression Databases -- 5.1 Introduction -- 5.2 What Do We Mean by Microarray Gene Expression Data? -- 5.3 Data Complexity -- 5.4 Minimum Information About a Microarray Experiment (MIAME) -- 5.5 Journals and MIAME -- 5.6 Storage and Exchange Formats: MAGE-OM and MAGE-ML -- 5.7 ArrayExpress -- 5.8 Annotation Tools -- 5.9 Curation -- 5.10 Standardization and Semantics -- 5.11 Public Microarray Databases -- 5.12 ArrayExpress, an Example of a Public Repository -- 5.13 Submissions to ArrayExpress -- 5.14 MIAMExpress and Other MIAME Compliant Annotation Systems -- 5.15 Databases of Protein Expression Patterns -- 5.16 The Gene Expression Database (GXD) -- 5.17 Conclusion -- References -- II THE BASIS OF ANNOTATION -- 6 Taxonomy: a Moving Target for Sequence Data -- 6.1 Introduction -- 6.2 Nomenclature -- 6.3 Operational Definitions -- 6.4 Searching for the Taxonomic Gold Standard -- 6.5 Conclusions -- References. , 7 Genomics and Proteomics: Design and Sources of Annotation -- 7.1 Beyond the Sequence: the Challenge of Complete Genome Analysis -- 7.2 Extracting the Genes -- 7.3 Organism Specific Peculiarities -- 7.4 Topology of Genomes -- 7.5 Gene Extraction Pipelines -- 7.6 Added Value and Knowledge -- 7.7 Beyond the Parts List -- References -- 8 Annotation of Protein Sequences -- 8.1 Introduction -- 8.2 What is Annotation? -- 8.3 UniProt: Universal Protein Resource -- 8.4 Protein Family Classification -- 8.5 InterPro: Integrated Resource of Protein Families, Domains and Sites -- 8.6 PIR Protein Families and Superfamilies -- 8.7 Ontologies -- 8.8 Protein Names, Source Information and Unique Identifiers -- 8.9 Common Identification Errors -- 8.10 Evidence Attribution -- 8.11 Position Specific Annotations -- 8.12 Rule-based Annotation -- 8.13 Conclusions -- Acknowledgements -- References -- 9 Issues in the Annotation of Protein Structures -- 9.1 Data Harvesting -- 9.2 Identification of the Biologically Relevant Assembly -- 9.3 Taxonomy -- 9.4 Sequence Recognition and Cross-reference -- 9.5 Recognition of Secondary Structure Elements -- 9.6 Validation of Structures -- 9.7 Residue Identification -- 9.8 Hetgroup Identification -- 9.9 Solvent Handling -- 9.10 Miscellaneous Annotation Issues -- 9.11 Conclusions -- References -- 10 Classification of Protein Function -- 10.1 Introduction -- 10.2 Mechanisms of Divergence of Protein Function -- 10.3 Classification of Protein Functions -- 10.4 Methods for Assigning Protein Function -- 10.5 Applications of Full-organism Information: Inferences from Genomic Context and Protein Interaction Patterns -- 10.6 Conclusions -- References -- III DATABASE DESIGN AND INTEGRATION -- 11 Information Flow and Data Integration of Databanks -- 11.1 Introduction -- 11.2 Information Flow Among Databanks -- 11.3 Database Distribution Format. , 11.4 Genome Annotation Errors and Error Propagation -- 11.5 Data Integration and Knowledge Discovery: iProClass Case Study -- 11.6 Conclusions -- Acknowledgements -- References -- 12 Models of Database Interconnectivity -- 12.1 Introduction -- 12.2 Heterogeneity in Bioinformatics Data Management -- 12.3 Data Models -- 12.4 Architectures for Data Integration -- 12.5 Implementing a Database Federation -- 12.6 Conclusions -- References -- 13 The European Bioinformatics Institute Macromolecular Structure Relational Database Technology -- 13.1 Database Design Process -- 13.2 Loading and Exporting Data in mmCIF -- 13.3 Exporting mmCIFs or XML Files from the Deposition Database -- 13.4 Subtypes and 'Leaf Views' -- 13.5 Maintenance Aspects -- 13.6 Data Clean-up -- 13.7 The Search Database -- 13.8 Transformation -- 13.9 Incremental Transformation -- 13.10 Replication -- 13.11 Oracle Cartridge Applications -- 13.12 Related Data Warehouse -- Acknowledgements -- References -- IV CONCLUSIONS AND PROSPECTS -- 14 Looking Around, Looking Ahead -- Index.