AllerBase: a comprehensive allergen knowledgebase

Allergic diseases represent a major health concern worldwide due to steady rise in their prevalence leading to increased disease burden. The field of allergy research has witnessed significant progress and the focus of studies has shifted to molecular level. Vast amounts of data for allergens are archived in allergen databases, which cover diverse aspects of allergens and allergenicity with varying degrees of completeness. Users are required to refer to multiple databases including general purpose immunological databases to obtain relevant data of allergens. AllerBase, a relational database, has been developed with the objective of integrating protein allergens and related data from prevailing bioinformatics resources and published literature. AllerBase is a manually curated comprehensive knowledgebase of experimentally validated allergens where various attributes of allergenicity are made available on a single platform. Links to sequences, structures and immunological data are provided, where available, for all allergens. Data for specific features such as IgE-binding epitopes, IgE cross-reactivity and IgE antibodies are curated and archived. Bibliographic data reporting assays used for experimental characterization of allergens are compiled and processed using text mining approach. AllerBase, thus provides enhanced coverage of data with high granularity. The database can be browsed by category of allergens, epitopes or antibodies. It can also be queried using various attributes such as allergen name, isoallergens/variants, taxonomic level, source organism, sequences, structures, epitopes, antibodies and cross-reactive allergens. AllerBase also provides interface for sequence-based analyses and visualization of structure/epitope which can be used as a framework for translational research. A Completeness Index has been devised to indicate the availability of data on nine attributes for every allergen. This index will also serve as a pointer to identify allergen-specific areas of further research. AllerBase can be used to understand various aspects of allergy and allergenicity at molecular level and to design anti-allergy therapeutics. Database URL: http://bioinfo.net.in/AllerBase/Home.html