Information about CADRE

The initial CADRE Project

Aspergillus is a genus of moulds that are found world-wide. Over 300 species of it have been recognised, a small number of which cause illness in animals (including humans): A. fumigatus, A. flavus, A. terreus and A. niger. Most humans are naturally immune and do not develop any of the diseases caused by these moulds. However, when disease does occur, it takes several forms, ranging from an allergy-type illness to life-threatening systemic infection. The severity of the infection is determined by various factors, but one of the most important is the state of the immune system of the person. [more information]

The most frequently isolated of these moulds from immuno-compromised patients is A. fumigatus. In order to better understand the pathogenicity of this organism, an international genome sequencing project was initiated in 1998. The co-operating institutions were: the University of Manchester, the Wellcome Trust Sanger Institute, The Institute for Genomic Research, the University of Salamanca, Complutense University, the Centro de Investigaciones Biológicas, and the Pasteur Institute. This project was completed in August 2004.

In order to effectively utilise the information produced by this sequencing effort, the University of Manchester was funded by the Wellcome Trust to manage and curate A. fumigatus genomic data. In addition, since the species within the genus Aspergillus have recently evolved from each other, the University of Manchester was funded, as part of the same grant, to enable comparitive studies by gathering other Aspergilli genomic data into a central data repository. To this end, CADRE (the Central Aspergillus Data REpository) was initiated in October 2001.

Aspergillus Genomes: a medical twist on Aspergillus data

This resource has arisen from the merging of CADRE and The Aspergillus Website, which took place in June 2008. The principal role of CADRE is to aid the Aspergillus research community by managing Aspergillus genome data and by providing visualisation tools, ranging from relatively simple annotation displays to more complex data integration displays. In contrast, The Aspergillus Website provides a range of information to the medical community (i.e., clinicians, patients and scientists) regarding the genus Aspergillus and the diseases, such as Aspergillosis, that it can cause. We hope, that by bringing this information together, we can extensively cross-link medical information with genomic data to provide a unique resource - one that spans all Aspergillus communities.

Both CADRE and The Aspergillus Website are funded by the Fungal Research Trust.

Ensembl Genomes: a new partnership seeking to improve data availability for the Aspergilli

This collaboration has arisen to expand annotation available for the Aspergillus genomes through automated methods, whilst maintaining manual afforts. Ensembl Genomes is an expansion of the original Ensembl site that has a bias towards higher eukaryotes. To balance this, Ensembl Genomes includes five new sections: Protists, Metazoa, Bacteria, Plants and Fungi. We have, of course, been able to contribute to the Fungi section, which was released in October 2009. In doing so, we are able to provide results of comparative analyses via Ensembl Genomes. In addition, Ensembl pipelines are able to maintain automated annotation to improve information provide for each feature. The role of the CADRE team is to help direct the Aspergillus work and to maintain manual annotation.

Implementation

• a database schema, which has been devised for storing annotated eukaryotic genomes. The schema is implemented with the MySQL relational database management system.
• several specialised programming modules for building interfaces (i.e., BioPerl and Ensembl API modules).
• a series of programs (i.e., Perl CGI scripts using the API modules) for viewing genomic data within a web browser.

Further information