IMGT/LIGM-DB: a systematized approach for ImMunoGeneTics database coherence and data distribution improvement.
ABSTRACT IMGT, the international ImMunoGeneTics database (http:(/)/imgt.cnusc.fr:8104), created by Marie-Paule Lefranc, Montpellier, France, is an integrated database specializing in antigen receptors and MHC of all vertebrate species. IMGT includes LIGM-DB, developed for Immunoglobulins and T-cell-receptors. LIGM-DB distributes high quality data with an important increment value added by the LIGM expert annotations. LIGM-DB accurate immunogenetics data is based on the standardization of biological knowledge related to keywords, annotation labels and gene identification. The management of such data resulting from biological research requires an high flexible implementation to quickly reflect up-to-date results, and to integrate new knowledge. We developed a systematized approach and defined LIGM-DB systems which manage and realize the major tasks for the database survey. In this paper, we will focus on the coherence system, which became absolutely crucial to maintain data quality as the database is growing up and as the biological knowledge continues to improve, and on the distribution system which makes LIGM-DB data easy to access, download and reuse. Efforts have been done to improve the data distribution procedures and adapt them to the current bioinformatics needs. Recently, we have developed an API which allows Java programmers to remotely access and integrate LIGM-DB data in other computer environments.
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ABSTRACT: IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.In silico biology 02/2005; 5(1):45-60.
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ABSTRACT: MOTIVATION: IMGT, the international ImMunoGeneTics database (http:@imgt.cines.fr:8104), created by M.-P. Lefranc, is an integrated database specializing in antigen receptors (immunoglobulins and T-cell receptors) and major histocompatibility complex (MHC) of all vertebrate species. IMGT accurate immunogenetics data are based on the standardization of the biological knowledge provided by the 'ImMunoGeneTics' IMGT-ONTOLOGY. The IMGT-ONTOLOGY describes the classification and specification of terms needed for immunogenetics and bioinformatics. IMGT-ONTOLOGY covers four main concepts: 'IDENTIFICATION', 'DESCRIPTION', 'CLASSIFICATION' and 'OBTENTION'. These concepts allow an extensive and standardized description and characterization of immunoglobulin and T-cell receptor data. The controlled vocabulary and the annotation rules are indispensable to ensure accuracy, consistency and coherence in IMGT. IMGT-ONTOLOGY allows scientists and clinicians to use, for the first time, identical terms with the same meaning in immunogenetics. It provides a semantic repository that will improve interoperability between specialist and generalist databases.Bioinformatics 01/2000; 15(12):1047-54. DOI:10.1093/bioinformatics/15.12.1047 · 4.62 Impact Factor