SRS is a widely used system for integrating biological databases. Currently, SRS relies only on locally provided copies of these databases. In this paper we propose a mechanism that also allows the seamless integration of remote databases. To this end, our proposed mechanism splits the existing SRS functionality into two components and adds a third component that enables us to employ peer-to-peer computing techniques to create optimized overlay-networks within which database queries can efficiently be routed. As an additional benefit, this mechanism also reduces the administration effort that would be needed with a conventional approach using replicated databases.

Abstract Motivation: The current data explosion is intractable without advanced data management systems. The numerous data sets become really useful when they are interconnected under a uniform interface—representing the domain knowledge. The SRS has become an integration system for both data retrieval and applications for data analysis. It provides capabilities to search multiple databases by shared attributes and to query across databases fast and efficiently. Results: Here we present recent developments at the EBI SRS server (http://srs.ebi.ac.uk). The EBI SRS server contains today more than 130 biological databases and integrates more than 10 applications. It is a central resource for molecular biology data as well as a reference server for the latest developments in data integration. One of the latest additions to the EBI SRS server is the InterPro database—Integrated Resource of Protein Domains and Functional Sites. Distributed in XML format it became a turning point in low level XML–SRS integration. We present InterProScan as an example of data analysis applications, describe some advanced features of SRS6, and introduce the SRSQuickSearch JavaScript interfaces to SRS. Availability: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration. Contact: [email protected]; [email protected]

MOTIVATION: Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. AVAILABILITY: SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.

A new SRS (Sequence Retrieval System) user interface has been developed for SRS v.4. Key features are the support of simple character-oriented (ASCII, VT100) terminals by coding in Tcl augmented by some dedicated Curses calls, support of graphics terminals in an X-Windows version by using the Tk extension to Tcl, and support of a client/server environment by using the TDP extension to Tcl. The Sequence Retrieval System (SRS) is a powerful tool for the fast extraction of information from flat file libraries (Etzold and Argos, 1993) and has rapidly established itself as a major research instrument for the bio-informatics community. Internally the system employs a query language, which is user accessible through either a command-line user interface, 'getz', or a more user friendly, character-oriented window interface. For SRS versions up to release v. 3, this window interface supported VT100-compatible terminals. Because of major changes in the underlying SRS libraries, the v. 3 interface became fully incompatible with the most recent version of SRS (v. 4.x). Thus the many users with only a simple terminal/terminal emulator connection were either deprived of access to SRS, or were forced to use the ASCII WWW client LYNX. This prompted us to develop a character-oriented SRS v. 4 window interface with the look and feel of its SRS v. 3.1 predecessor and coded to be as library independent as possible to maintain compatibility with future SRS releases. In addition, some 'extensions' were coded to widen the applicability to graphics terminals and to a client/server environment. At the time of preparation of this paper, the SRS interface described had been implemented in one form or another on most EM Bnet nodes and on all the platforms given in Table II. The code has been stored at the EMBL in Heidelberg, where it will be available, with installation instructions and scripts, as part of the SRS distribution.

SRS (Sequence Retrieval System) is an information indexing and retrieval system designed for libraries with a flat file format such as the EMBL nucleotide sequence databank, the SwissProt protein sequence databank or the Prosite library of protein subsequence consensus patterns. SRS supports the data structure of these libraries by providing special indices for implementing lists of subentities (e.g. feature tables) or hierarchically structured data-fields (e.g. taxonomic classification). A language (ODD) has been designed for the convenient specification of library format and organization, representation of individual data-fields within the system (design of indices) and structuring other data needed during retrieval. This ensures flexibility required for coping with different library formats, which are subject to continuous change. Queries and inspection of retrieved entries can be performed from a user interface with pull-down menus and windows. SRS supports various input and output formats but is particularly well adapted to the GCG programs.

SRS (Sequence Retrieval System), an indexing system for flat file libraries, provides fast access to individual library entries via retrieval by keywords from various data fields. SRS is now also able to build indices using cross-references that most libraries provide. Fifteen libraries of DNA and protein sequences and structures have been selected. These libraries interact with at least one other by means of cross-references. Indexing these cross-references allows a complete network of libraries to be built. In the network an entry from one library can be linked in principle to every other library. If two libraries are not directly cross-referenced, the linkage can be made with a succession of single links between neighbouring, cross-referenced libraries. A new operator has been added to the query language of SRS for convenient specification of links amongst complete libraries or entry sets generated by previous queries on particular libraries. All the information in the network can now be used to retrieve an entry in a specific library, e.g. the full information given in amino acid sequence entries from SwissProt can now be used to retrieve related tertiary structure entries from PDB. Furthermore, a search in a single library can be extended to a search in the complete library network, e.g. all entries in all databases pertaining to elastase can be found.