The need to distribute objects on the Internet and to offer views from databases has found a solution with the advent of CORBA. Most database management systems now offer CORBA interfaces which are generally simple mapping of the database schema to the CORBA world. This approach does not address all the problems of database interoperation because (i) such a view is static (ii) its semantic is completely bound to the semantic of the schema and it is not possible to re-model it (iii) only one view per database can be offered (iv) access may be limited to reading and no mechanism is given to write in the database through the view. To solve these problems, we have designed a language, the Interface Mapping Definition Language (IMDL) and some tools, grouped in the Interface Mapping Service (IMS). IMDL is used to define CORBA views from OODBMS, while IMS generates an IDL construct and a full CORBA implementation from an IMDL construct and a database schema.

Abstract Motivation: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML for data interchange between databases and other sources of data. Finally the discussion is illustrated by a test case of a pedigree data model in XML. Contact: [email protected] * To whom correspondence should be addressed. 3 Present address: Cereon Genomics, 45 Sidney St, Cambridge, MA 02139, USA.

Zoomable User Interfaces (ZUIs) are difficult to use on large information spaces in part because they provide insufficient context. Even after a short period of navigation users no longer know where they are in the information space nor where to find the information they are looking for. We propose a temporary in-place context aid that helps users position themselves in ZUIs. This context layer is a transparent view of the context that is drawn over the users' focus of attention. A second temporary in-place aid is proposed that can be used to view already visited regions of the information space. This history layer is an overlapping transparent layer that adds a history mechanism to ZUIs. We complete these orientation aids with an additional window, a hierarchy tree, that shows users the structure of the information space and their current position within it. Context layers show users their position, history layers show them how they got there, and hierarchy trees show what information is available and where it is.

This paper introduces the EYEDB object oriented database management system (OODBMS). EYEDB implements all the standard features of OODBMS, is language oriented, provides a generic object model and a support for data distribution using CORBA. It can deal with very large databases, and is both efficient and scalable. It is used in the genome project where a huge amount of data have to be managed and intricate data structures needs to be modeled. Online information and a trial version of EYEDB can be obtained from http://www.sysra.com/eyedb.

MOTIVATION: The scientific community urgently needs to standardize the exchange of biological data. This is helped by the use of a common protocol and the definition of shared data structures. We have based our standardization work on CORBA, a technology that has become a standard in the past years and allows interoperability between distributed objects. RESULTS: We have defined an IDL specification for genome maps and present it to the scientific community. We have implemented CORBA servers based on this IDL to distribute RHdb and HuGeMap maps. The IDL will co-evolve with the needs of the mapping community. AVAILABILITY: The standard IDL for genome maps is available at http:// corba.ebi.ac.uk/RHdb/EUCORBA/MapIDL.htm l. The IORs to browse maps from Infobiogen and EBI are at http://www.infobiogen.fr/services/Hugemap/IOR and http://corba.ebi.ac.uk/RHdb/EUCORBA/IOR CONTACT: [email protected], [email protected]

SUMMARY: We developed a collaborative pedigree environment called CoPE. This environment includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. AVAILABILITY: At http://www.infobiogen.fr/services/CoPE

MOTIVATION: The problems caused by the difficulty in visualizing and browsing biological databases have become crucial. Scientists can no longer interact directly with the huge amount of available data. However, future breakthroughs in biology depend on this interaction. We propose a new metaphor for biological data visualization and browsing that allows navigation in very large databases in an intuitive way. The concepts underlying our approach are based on navigation and visualization with zooming, semantic zooming and portals; and on data transformation via magic lenses. We think that these new visualization and navigation techniques should be applied globally to a federation of biological databases. RESULTS: We have implemented a generic tool, called Zomit, that provides an application programming interface for developing servers for such navigation and visualization, and a generic architecture-independent client (Javatrade mark applet) that queries such servers. As an illustration of the capabilities of our approach, we have developed ZoomMap, a prototype browser for the HuGeMap human genome map database. AVAILABILITY: Zomit and ZoomMap are available at the URL http://www.infobiogen.fr/services/zomit.