The Integrated Microbial Genomes (IMG) system integrates microbial community aggregate genomes (metagenomes) with genomes from all domains of life. IMG provides tools for analyzing and reviewing the structural and functional annotations of metagenomes and genomes in a comparative context. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets provided by scientific users, as well as public bacterial, archaeal, eukaryotic, and viral genomes from the US National Center for Biotechnology Information genomic archive and a rich set of engineered, environmental and host associated metagenomes. Genomes and metagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing pipelines and then are integrated into the data warehouse using IMG's data integration toolkit. Microbial genome and metagenome application specific user interfaces provide access to different subsets of IMG's data and analysis toolkits. Genome and metagenome analysis is a gene centric iterative process that involves a sequence (composition) of data exploration and comparative analysis operations, with individual operations expected to have rapid response time.

Summary form only given. The Object-Protocol Model (OPM) data management tools provide facilities for rapid development, documentation, and flexible exploration of scientific databases. The tools are based on OPM, an object-oriented data model which is similar to the ODMG standard, but also supports extensions for modeling scientific data. Databases designed using OPM can be implemented using a variety of commercial relational DBMSs, using schema translation tools that generate complete DBMS database definitions from OPM schemas. Further, OPM schemas can be retrofitted on top of existing databases defined using a variety of notations, such as the relational data model or the ASN.1 data exchange format, using OPM retrofitting tools. Several archival molecular biology databases have been designed and implemented using the OPM tools, including the Genome Database (GDB) and the Protein Data Bank (PDB), while other scientific databases, such as the Genome Sequence Database (GSDB), have been retrofitted with semantically enhanced views using the OPM tools.

The Object-Protocol Model (OPM) data management tools provide facilities for rapid development, documentation, and flexible exploration of scientific databases. The tools are based on OPM, an object oriented data model which is similar to the ODMG standard, but also supports extensions for modeling scientific data (L.A. Chen and V.M. Markowitz, 1995). Databases designed using OPM can be implemented using a variety of commercial relational DBMSs, using schema translation tools that generate complete DBMS database definitions from OPM schemas (L.A. Chen and V.M. Markowitz, 1996). Further OPM schemas can be retrofitted on top of existing databases defined using a variety of notations, such as the relational data model or the ASN.1 data exchange format, using OPM retrofitting tools (L.A. Chen et al., 1997).

Scientific databases (ScDBs) are used to archive and retrieve data describing objects of scientific inquiry. Since these ScDBs must provide continuous and efficient access to large communities of scientists, they are often developed with reliable commercial relational database management systems (DBMSs) or file systems. However, relational DBMSs and flat files do not provide constructs for representing directly ScDB-specific objects and experimental procedures, and therefore they are often hard to develop, maintain, and explore. In this paper, we present a retrofitting tool for constructing and maintaining ScDB views using an object-oriented data model, and describe our experience with retrofitting ScDBs that have been originally developed using relational DBMSs and file systems. The retrofitting tool is part of a data management toolkit based on the Object-Protocol Model (OPM). The OPM toolkit provides facilities for developing databases defined using OPM and for querying and browsing...