AbSoc - Databases

Abstract from the Antibody Society / IBC Antibody Engineering Conference, San Diego 2007

IMGT, the Informatics Framework to Support Effective Collaboration in Complex Environments Standardization for genome, proteome, genetics and 3D structure antibody data is required for molecular analysis comparison in complex environments. With its databases, tools and Web resources, based on the IMGT-ONTOLOGY concepts of identification (specificity), description (labels), classification (gene and allele nomenclature) and numeratation (IMGT Colliers de Perles), IMGT®, the international ImMunoGeneTics information system® provides the informatics framework for standardized molecular characterization of monoclonal therapeutic antibodies.

Website: http://imgt.cines.fr

Marie-Paule Lefranc, Ph.D., Professor,
Montpellier University,
The University Institute of France,
CNRS.

Institute of Human Genetics,
IMGT,
France

Overview

The international ImMunoGeneTics information system®, (IMGT®) is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species, created in 1989 by Marie-Paule Lefranc (Université Montpellier, France ; CNRS). IMGT, a European project since 1992, works in close collaboration with EBI.

IMGT consists of sequence databases (IMGT/LIGM-DB, a comprehensive database of IG and TR from human and other vertebrates, with translation for fully annotated sequences, IMGT/MHC-DB, IMGT/PRIMER-DB), genome database (IMGT/GENE-DB) and structure database (IMGT/3Dstructure-DB), Web resources (IMGT Marie-Paule page) and interactive tools.

The IMGT homepage (Montpellier, France) provides a common access to all Immunogenetics data.

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The Human Antibody Initiative (HUPO)

Overview

Website: www.proteinatlas.org

The Human Antibody Initiative aims to promote and facilitate the use of antibodies for proteomics research. The initiative consists of two separate activities: (1) the generation of a catalogue of validated antibodies from many different sources and (2) a protein atlas for the expression and localization of human proteins in normal and disease tissue. The two separate activities have as their primary deliverables to generate databases with free public accessibility.

The Antibody Resource database is aimed to produce a comprehensive catalogue of validated antibodies towards human proteins. This initiative depends on input from a large number of academic groups and commercial companies. The pilot phase will be initiated Q3 2005. By Q1 2007, we anticipate starting the "production phase" with the objective of having quarterly releases of all approved data (the data will be approved by a designated curator).

The Protein Atlas initiative aims to provide a comprehensive, annotated database of high-resolution images containing tissue profiles of normal and cancer tissues. The first release of the database will be at the fourth Annual HUPO Conference (August 2005 in Munich) with 300,000 images representing 600 human proteins. An updated release of the database will be done thereafter in conjunction with the annual HUPO conference with at least 500,000 additional images (1000 proteins) each time. Both databases will be open to the public without restriction (no passwords).

The overall, long-term goal of this Initiative is to, within 10 years, generate a uniform antibody collections against every human protein (non-redundant set) and to use these reagents to functionally explore the corresponding proteins, protein variants (isoforms) and protein interactions.

Collaborations with other Initiatives

Antibodies developed in the Plasma Proteome Project will be included in the database

Antibodies included in our database will be used to cross reference those for several of the subprojects in the Human Liver Proteome Project (HLPP). In addition, any antibodies created in the HLPP will be added to our database.

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The Immune Epitope Database and Analysis Resource (IEDB)

Abstract from the Antibody Society / IBC Antibody Engineering Conference, San Diego 2007

Evaluating B-cell Epitope Prediction Tools: Datasets and Metrics

The prediction of B-cell epitopes is highly desirable, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell epitope prediction methods depends on community-accepted datasets and metrics to develop and evaluate such tools. Using the Immune Epitope Database, we have assembled several datasets of epitopes corresponding to different prediction tasks, and report the performance of prediction tools to on these sets.

Website: http://www.immuneepitope.org/home.do

Bjoern Peters, Ph.D.,
Research Scientist,
ImmuneEpitope Database and Analysis Resource (IEDB),
La Jolla Institute for Allergy and Immunology

Overview

The Immune Epitope Database and Analysis Resource (IEDB) is a project hosted by scientists at the La Jolla Institute for Allergy and Immunology (LIAI), with support from the National Institute of Allergy and Infectious Diseases (NIAID), a part of the National Institutes of Health (NIH), and Department of Health and Human Services (HHS). While not strictly limited, the current focus is presenting information that facilitates the dissemination of immune epitope information, the generation of new research tools, diagnostic techniques, vaccines and therapeutics for emerging and re-emerging diseases. The IEDB contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species. Curation of data relating to NIAID Category A, B, and C priority pathogens (including Influenza) and NIAID Emerging and Re-emerging infectious diseases is complete through June 2007. Curation of Malaria, Hepatitis B, Clostridium tetani, Leishmania, and Candida albicans is current through June 2007. Present efforts include herpesviruses and allergen epitopes. Curation of autoimmune epitopes will start in second quarter 2008. The database also contains MHC binding data from a variety of different antigenic sources and immune epitope data from the FIMM (Brusic), HLA Ligand (Hildebrand), TopBank (Sette), and MHC binding (Buus) databases. These databases and their investigators are hereby acknowledged as major contributors to the IEDB. For more information about our curation procedures please refer to our Curation Manual.

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This page last modified 27 April, 2008 by Berend Tolner