Federation views as a basis for querying and updating database federations

This paper addresses the problem of how to query and update so-called database federations. A database federation provides for tight coupling of a collection of heterogeneous component databases into a global integrated system. This problem of querying and updating a database federation is tackled by describing a logical architecture and a general semantic framework for precise specification of such database federations, with the aim to provide a basis for implementing a federation by means of relational database views. Our approach to database federations is based on the UML/OCL data model, and aims at the integration of the underlying database schemas of the component legacy systems to a separate, newly defined integrated database schema. One of the central notions in database modelling and in constraint specifications is the notion of a database view, which closely corresponds to the notion of derived class in UML. We will employ OCL (version 2.0) and the notion of derived class as a means to treat (inter-)database constraints and database views in a federated context. Our approach to coupling component databases into a global, integrated system is based on mediation. The first objective of our paper is to demonstrate that our particular mediating system integrates component schemas without loss of constraint information. The second objective is to show that the concept of relational database view provides a sound basis for actual implementation of database federations, both for querying and updating purposes.

P2CS:Updates of the prokaryotic two-component systems database

International audienceThe P2CS database (http://www.p2cs.org/) is a comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164 651 TCS proteins, from 2758 sequenced prokaryotic genomes. Several important new features have been added to P2CS since it was last described. Users can search P2CS via BLAST, adding hits to their cart, and ho-mologous proteins can be aligned using MUSCLE and viewed using Jalview within P2CS. P2CS also provides phylogenetic trees based on the conserved signaling domains of the RRs and HKs from entire genomes. HK and RR trees are annotated with gene organization and domain architecture, providing insights into the evolutionary origin of the contemporary gene set. The majority of TCSs are encoded by adjacent HK and RR genes, however, 'orphan' unpaired TCS genes are also abundant and identifying their partner proteins is challenging. P2CS now provides paired HK and RR trees with proteins from the same genetic locus indicated. This allows the appraisal of evolutionary relationships across entire TCSs and in some cases the identification of candidate partners for orphan TCS proteins

P2CS: a database of prokaryotic two-component systems

P2CS (http://www.p2cs.org) is a specialized database for prokaryotic two-component systems (TCSs), virtually ubiquitous signalling proteins which regulate a wide range of physiological processes. The primary aim of the database is to annotate and classify TCS proteins from completely sequenced prokaryotic genomes and metagenomes. Information within P2CS can be accessed through a variety of routes—TCS complements can be browsed by metagenome, replicon or sequence cluster (and these genesets are available for download by users). Alternatively a variety of database-wide or taxon-specific searches are supported. Each TCS protein is fully annotated with sequence-feature information including replicon context, while properties of the predicted proteins can be queried against several external prediction servers to suggest homologues, interaction networks, sub-cellular localization and domain complements. Another unique feature of P2CS is the analysis of ORFeomes to identify TCS genes missed during genome annotation. Recent innovations for P2CS include a CGView representation of the distribution of TCS genes around a replicon, categorization of TCS genes based on gene organization, an expanded domain-based classification scheme, a P2CS ‘gene cart’ and categorization on the basis of sequence clusters