IMGT-ONTOLOGY, IMGT Databases, Tools, and Web Resources for Immunoinformatics - Immunoinformatics - page 13

The IMGT/LIGM-DB Web service is the first Web service currently developed
and implemented with Axis (Lefranc et al. 2004a). It includes the “queryKnowledge”
and “querySeqData” services. The queryKnowledge service provides the lists of
instances for the IMGT-ONTOLOGY concepts, for example the list of chain types,
functionalities, specificities defined in the IDENTIFICATION concept, the lists of
groups and subgroups defined in the CLASSIFICATION concept, or the list of labels
defined in the DESCRIPTION concept. The querySeqData service allows the
retrieval of any sequence-related data that are identified, classified, and described in
IMGT/LIGM-DB according to the IMGT concepts. The querySeqData input has the
form of an incomplete IMGT-ML data entry in which the given values are used as
criteria to query IMGT/LIGM-DB. The result is a list of data entries, in IMGT-ML
format, sharing these given values. Other Web services are developed to automati-
cally query IMGT ® databases and tools.
1.6.4 Perspectives
Composition and chaining of IMGT ® Web services through IMGT-Choreography
will enable processing of complex significant biological and clinical requests involv-
ing every part of the IMGT ® information system. IMGT-Choreography has for goal
to combine and join the IMGT ® database queries and analysis tools.
In order to keep only significant approaches, a rigorous analysis of the scientific
standards of the biologist research (Giudicelli and Lefranc 1999; Lefranc and
Lefranc 2001a; Lefranc and Lefranc 2001b; Osipova et al. 1999; Dard et al. 2001;
Chardes, Chapal, Bresson, Bes, Giudicelli, Lefranc, and Peraldi-Roux 2002;; Chas-
sagne, Laffly, Drouet, Herodin, Lefranc, and Thullier 2004; Bertrand, Duprat,
Lefranc, Marti, and Coste 2004) and of the clinician's needs (Ghia, Stamatopoulos,
Belessi, Moreno, Stella, Giuda, Michel, Crespo, Laoutaris, Montserrat, Anag-
nostopoulos, Dighiero, Fassas, Caligaris-Cappio, and Davi 2005; Stamatopoulos,
Belessi, Papadaki, Kalagiakou, Stavroyianni, Douka, Afendaki, Saloum, Parasi,
Anagnostou, Laoutaris, Fassas, and Anagnostopoulos 2004) has been undertaken in
parallel with the modelling of interactions between the IMGT ® components (data-
bases, tools, and Web resources). To increase interoperability with other biological
information systems and ontologies, IMGT-ONTOLOGY is currently being imple-
mented with Protégé (http://protege.stanford.edu/) (Noy, Fergerson, and Musen 2000).
1.7 Conclusions
Since July 1995, IMGT ® has been available on the Web at the IMGT ® Home page
http://imgt.cines.fr (Montpellier, France). IMGT ® has an exceptional response with
more than 140,000 requests a month. IMGT ® is the international reference in immu-
nogenetics and immunoinformatics and provides a common access to standardized
data which include nucleotide and protein sequences, oligonucleotide primers, gene
maps, genetic polymorphisms, specificities, 2D and 3D structures, based on IMGT-
ONTOLOGY. Although the IMGT ® genome, sequence, and 3D structure databases,
IMGT ® analysis tools, and IMGT Repertoire Web resources, were initially imple-