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Nucleic Acids Research Pages 106-108  

HuGeMap: a distributed and integrated Human Genome Map database
Contents Of The Database
   The HuGeMap database
   Interconnection with RHdb
Data Distribution
   WWW server
   CORBA server
Graphical User Interface
Perspectives
Acknowledgement
References

HuGeMap: a distributed and integrated Human Genome Map database

HuGeMap: a distributed and integrated Human Genome Map database

Emmanuel Barillot*, Frédéric Guyon, Christophe Cussat-Blanc, Eric Viara1, Guy Vaysseix

GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif Cedex, France and 1Sysra Informatique, 7 rue de Bièvres, 92140 Clamart, France

Received September 2; Revised and Accepted October 3, 1997

ABSTRACT

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/MappetShow.html ) that queries the HuGeMap ORB server as well as the RHdb ORB server at the EBI.

CONTENTS OF THE DATABASE

The HuGeMap database

The HuGeMap database includes (i) the genetic maps from Généthon (1) and the Cooperative Human Linkage Consortium (2), (ii) the physical maps from CEPH-Généthon (3-5) and from the Whitehead Institute, MIT (6). It also contains mapping data for STS (full sequences, primer sequences, heterozygosity, allele sizes, positive clones, etc.) and clones (sizing, fingerprints, positive STS, clones associated by fingerprint analysis or Alu-PCR mediated cross-hybridizations, cytogenetic location, etc.).

Interconnection with RHdb

HuGeMap is interconnected with the RHdb database (http://www.ebi.ac.uk/RHdb ) (7). The interconnection is based on CORBA servers (see below). A common metaschema has been built on top of both databases schemas. The central object of the metaschema is the map object. The data within RHdb and HuGeMap are available worldwide through this common interface. For the client programs, RHdb and HuGeMap appear as a single database.

DATA DISTRIBUTION

WWW server

A WWW server has been built on top of the HuGeMap database. This service can be found at URL http://www.infobiogen.fr/services/Hugemap . Navigation is mapped to the database schema. HuGeMap uses an object-oriented DBMS, EYEDB (developed by Sysra Informatique, see http://www.infobiogen.fr/services/eyedb). Thus, browsing gives access to all the objects of the metaschema and to the meta-objects as well. When browsing a meta-object, the user can also consult its semantic description.

CORBA server

CORBA (see http://www.omg.org/omg00/wicorba.htm or ref. 8 for an introduction to CORBA) is a standard to distribute objects worldwide. Basically, objects are defined in an IDL (Interface Definition Language) and invoked by an ORB (Object Request Broker). Object invocation can be local or remote: when an ORB is asked to deliver an object, it first checks if the object is available locally. If not, it locates another ORB that can deliver this object. This mechanism is transparent for the user, it is entirely handled by the ORB.

CORBA achieves a real interconnection between databases: programs can easily access distributed objects in local or remote databases. We used this technology to interconnect HuGeMap and RHdb.

GRAPHICAL USER INTERFACE

We used the BioWidgets (http://agave.humgen.upenn.edu/bioWidgetsJava/) concepts and some of its software components to develop a graphical user interface. The applet fetches human genome maps from HuGeMap and/or RHdb: the ORB server is queried for this data and returns it to the program in the format specified in the interface. Then an integrated and compared view of the maps is displayed. Figure 1 shows an example with two maps from human chromosome 18. The applet can be found at URL http://babbage.infobiogen.fr:15000/Mappet/MappetShow.html


Figure 1 Graphical comparison of two chromosome 18 maps.

PERSPECTIVES

We are defining a more complete IDL schema for the ORB server. The new IDL schema will model in more detail maps and markers (for the time being, it only includes the necessary data for map display). The idea is not to enrich the database itself, but to encompass domains related to human genome mapping in the IDL (sequence analysis, comparative mapping, etc.). This will create the foundation to interconnect HuGeMap with other databases, provided they also implement an ORB server.

At the same time, We are improving the graphical applet. It will be optimized for faster display. New functionalities will be implemented, such as `find a named marker', `change the order of the maps', the position of the marker names on the map will be optimized for a better readability, etc.

ACKNOWLEDGEMENT

This work is partly granted by the EC contract BIO4-CT95-0037.

REFERENCES

1. Dib,C. et al). (1996) Nature, 380, 152-154. MEDLINE Abstract

2. Sheffield,V.C. et al). (1995) Hum. Mol. Genet., 4, 1837-1844. MEDLINE Abstract

3. Bellanné-Chantelot,C. et al. (1992) Cell, 70, 1059-1068. MEDLINE Abstract

4. Cohen,D., Chumakov,I. and Weissenbach,J. (1993) Nature, 336, 698-701.

5. Chumakov,I. et al). (1995) Nature, 377, 175-298. MEDLINE Abstract

6. Hudson,T.J. et al). (1995) Science, 270, 1945-1954. MEDLINE Abstract

7. Rodriguez-Tomé,P. and Lijnzaad.P. (1997) Nucleic Acids Res., 25, 81-84. [See also this issue, Nucleic Acids Res. (1998) 26, 102-105].

8. Achard,F. and Barillot,E. (1997) In Altman,R., Dunker,K., Hunter,L. and Klein,T. (eds) Pacific Symposium on Biocomputing `97. World Scientific, 1997. pp. 39-50.

*To whom correspondence should be addressed. Tel: +33 1 49 58 36 82; Fax: +33 1 49 58 36 89; Email: emmanuel.barillot@infobiogen.fr

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Last modification: 17 Dec 1997
Copyright© Oxford University Press, 1998.

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