Database

The Autoimmune Disease Database: a dynamically compiled literature-derived database

Thomas Karopka¹ , Juliane Fluck² , Heinz-Theodor Mevissen² and Änne Glass¹

¹  Institute for Medical Informatics and Biometry, University of Rostock, Rembrandt-Str. 16/17, 18055 Rostock, Germany

²  Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Department of Bioinformatics, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany

author email corresponding author email

BMC Bioinformatics 2006, 7:325doi:10.1186/1471-2105-7-325

Published:	27 June 2006

Abstract

Background

Autoimmune diseases are disorders caused by an immune response directed against the body's own organs, tissues and cells. In practice more than 80 clinically distinct diseases, among them systemic lupus erythematosus and rheumatoid arthritis, are classified as autoimmune diseases. Although their etiology is unclear these diseases share certain similarities at the molecular level i.e. susceptibility regions on the chromosomes or the involvement of common genes. To gain an overview of these related diseases it is not feasible to do a literary review but it requires methods of automated analyses of the more than 500,000 Medline documents related to autoimmune disorders.

Results

In this paper we present the first version of the Autoimmune Disease Database which to our knowledge is the first comprehensive literature-based database covering all known or suspected autoimmune diseases. This dynamically compiled database allows researchers to link autoimmune diseases to the candidate genes or proteins through the use of named entity recognition which identifies genes/proteins in the corresponding Medline abstracts. The Autoimmune Disease Database covers 103 autoimmune disease concepts. This list was expanded to include synonyms and spelling variants yielding a list of over 1,200 disease names. The current version of the database provides links to 541,690 abstracts and over 5,000 unique genes/proteins.

Conclusion

The Autoimmune Disease Database provides the researcher with a tool to navigate potential gene-disease relationships in Medline abstracts in the context of autoimmune diseases.