Ulf Leser

Quality-driven Integration of Heterogenous Information Systems

Integrated access to information that is spread over multiple, distributed, and heterogeneous sources is an important problem in many scienti c and commercial domains. While much work has been done on query processing and choosing plans under cost criteria, very little is known about the important problem of incorporating the information quality aspect into query planning. In this paper we describe a framework for multidatabase query processing that fully includes the quality of information in many facets, such as completeness, timeliness, accuracy, etc. We seamlessly include information quality into a multidatabase query processor based on a view-rewriting mechanism. We model information quality at di erent levels to ultimately nd a set of high-quality queryanswering plans.

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

Query Planning with Information Quality Bounds

Query planning for information integration using a local-as-view approach is exponential in the size of the user query. Furthermore, it may generate an exponential number of plans, many of which will produce results of very poor quality. We propose to use information quality reasoning to speed up query planning. We construct tight upper quality bounds for a branch & bound algorithm. The algorithm uses these quality scores to filter out non-promising plans early on. Experiments show that this approach dramatically improves planning time without compromising the quality of the result.

Issues in developing integrated genomic databases and application to the human X chromosome.

MOTIVATION In the past decade, a vast amount of mapping data has been generated on the human X chromosome, without a mechanism which would provide a global view of exactly what has been achieved. Large datasets are available electronically, but in heterogeneous formats and with incompatible access modes. In addition, relationships between objects in different datasets are often not specified. RESULTS We discuss the problem of integrating these data into one database and define a number of requirements that are vital for any integration approach. We have developed IXDB, the Integrated X chromosome database, which fulfils those requirements and aims at providing a global view on genomic data at a chromosomal level. IXDB represents a conceptual framework based on identifying, storing and analysing relationships between biological objects, and includes a series of tools to automate the integration of such information. It currently focuses on physical mapping data, as a starting point towards a map of the human X chromosome that should provide a uniform and global research resource for ongoing and future sequencing and functional studies. AVAILABILITY IXDB is available at http://ixdb.mpimg-berlin-dahlem.mpg.de. The iace2ixdb software and a description of the Iace data format are available from the authors. CONTACT hrc@genoscope.cns.fr

IXDB, AN X CHROMOSOME INTEGRATED DATABASE (UPDATE)

Chromosome specific databases are an important research tool as they integrate data from different directions, such as genetic and physical mapping data, expression data, sequences etc. They supplement the genome-wide repositories in molecular biology, such as GenBank, Swiss-Prot or OMIM, which usually concentrate on one type of information. The Integrated X Chromosome Database (IXDB, http://ixdb.mpimg-berlin-dahlem.mpg.de/) is a repository for physical mapping data of the human X chromosome and aims at providing a global view of genomic data at a chromosomal level. We present here an update of IXDB which includes schema extensions for storing submaps and sequence information, additional links to external databases, and the integration of an increasing number of physical and transcript mapping data. The gene data was completely updated according to the approved gene symbols of the HUGO Nomenclature Committee. IXDB receives over 1000 queries per month, an indication that its content is valuable to researchers seeking mapping data of the human X chromosome.

IXDB, an X chromosome integrated database.

The integrated X chromosome database (IXDB) is a repository for physical mapping data of the human X chromosome. Its current content is the result of a strict integration of data stemming from many different sources. The main features of IXDB include a flexible and extendible schema, a comfortable and fully cross-referenced WWW interface (http://ixdb.mpimg-berlin-dahlem.mpg.de ) and a graphical map viewer implemented in JAVA. The database stores objects used in physical mapping as well as the maps resulting from this work, but a strong emphasis is placed on recording experiments that connect objects together. This should greatly contribute to fulfilling one of the major goals of the database: to support the construction of an integrated physical, genetic, transcript and sequence map of the human X chromosome.

Designing a Global Information Resource for Molecular Biology (Short Paper)

Research in molecular biology is continuously producing an immense amount of data, but this information is spread over numerous heterogeneous data repositories. Their integration into a federated information system would drastically reduce the time a biologist has to spend browsing different WWW sites or databases in search for a particular piece of information.

Globale Anfragebearbeitung mit verteilten und heterogenen Datenquellen

Im Rahmen des Berlin/Brandenburger Graduiertenkolleg „Verteilte Informationssysteme“ (GKVI2) arbeiten zur Zeit 15 Stipendiaten an verschiedenen Aspekten der Konzeption, Erstellung und des Betriebs von Informationssystemen in verteilten und heterogenen Umgebungen. Die prinzipiell interdisziplinare Ausrichtung des GKVI, die eine fruchtbare Verbindung zwischen Wirtschaftsinformatik, Datenbanktechnik und Aspekten der Softwaretechnik sucht, schafft ein breites Themenspektrum, das von Internet-Pricing [20] und Indexstrukturen [8] uber objektorientierte Middleware [6] bis zur Modellierung von Benutzerschnittstellen [15] reicht.