XML, bioinformatics and data integration.

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: Emmanuel.Barillot@infobiogen.fr

MappetShow: non-linear visualization for genome data.

The genome mapping projects now produce very dense maps with up to several thousands of markers per chromosome. Besides synteny plays a increasing role in mapping: enrichment of poor maps from the maps of close genomes (in terms of evolution) is a high-reward task. We propose a map viewer adapted to this situation: MappetShow gives a clear view of very dense maps and compares efficiently several maps. MappetShow is based on non-linear viewing and is written in Java. A map description language isolates the software from the data sources. This software was easily used on data coming from as different sources as an Object Request Broker, an Object-Oriented Database, or a flat data stream. MappetShow can be browsed at the URL http:¿www.infobiogen.fr/services/Mappet. More generally we discuss how to use the non-linear viewing concept in molecular biology data visualization.

DBcat: a catalog of 500 biological databases.

The DBcat (http://www.infobiogen.fr/services/dbcat ) is a comprehensive catalog of biological databases, maintained and curated at Infobiogen. It contains 500 databases classified by application domains. The DBcat is a structured flat-file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for download from Infobiogen anonymous ftp server.

CoPE: a collaborative pedigree drawing environment.

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

A proposal for a standard CORBA interface for genome maps.

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: manu@infobiogen.fr, tome@ebi.ac.uk

DBcat: a catalog of biological databases.

The DBcat (http://www.infobiogen.fr/services/dbcat) is a comprehensive catalog of biological databases, maintained and curated on a daily basis at GIS Infobiogen. It contains more than 400 databases classified by application domains. The DBcat is a structured flat file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for downloading from Infobiogen anonymous ftp server.

Virgil database for rich links (1999 update).

With so many databases available for research in the Human Genome Project, it is crucial to efficiently relate information from different resources. For that purpose, we maintain Virgil, a database of rich links for data browsing, data analysis and database interconnection. Virgil current version contains more than 40 000 rich links from five major databases: SWISS-PROT, GenBank, PDB, GDB and OMIM. Materials described in this paper are available from http://www.infobiogen.fr/services/virgil/

The HuGeMap Database: interconnection and visualization of human genome maps.

The HuGeMap database stores the major genetic and physical maps of the human genome. HuGeMap is accessible on the Web at http://www. infobiogen.fr/services/Hugemap and through a CORBA server. A standard genome map data format for the interconnection of genome map databases was defined in collaboration with the EBI. The HuGeMap CORBA server provides this interconnection using the interface definition language IDL. Two graphical user interfaces were developed for the visualization of the HuGeMap data: ZoomMap (http://www.infobiogen.fr/services/zomit/Zoom Map.html) for navigation by zooming and data transformation via magic lenses, and MappetShow (http://www.infobiogen.fr/services/Mappet) for visualizing and comparing maps.

HuGeMap: a distributed and integrated Human Genome Map database.

The HuGeMap database stores the major genetic and physical maps of the human genome. It is also interconnected with the gene radiation hybrid mapping database RHdb. HuGeMap is accessible through a Web server for interactive browsing at URL http://www.infobiogen. fr/services/Hugemap , as well as through a CORBA server for effective programming. HuGeMap is intended as an attempt to build open, interconnected databases, that is databases that distribute their objects worldwide in compliance with a recognized standard of distribution. Maps can be displayed and compared with a java applet (http://babbage.infobiogen.fr:15000/Mappet/Show. html ) that queries the HuGeMap ORB server as well as the RHdb ORB server at the EBI.

Zomit: biological data visualization and browsing.

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.

A second-generation linkage map of the human genome.

A linkage map of the human genome has been constructed based on the segregation analysis of 814 newly characterized polymorphic loci containing short tracts of (C-A)n repeats in a panel of DNAs from eight large families. Statistical linkage analysis placed 813 of the markers into 23 linkage groups corresponding to the 22 autosomes and the X chromosome; 605 show a heterozygosity above 0.7 and 553 could be ordered with odds ratios above 1,000:1. The distance spanned corresponds to approximately 90% of the estimated length of the human genome.