IMGT-ML is a set of XML schemas which describe, as XML elements, the IMGT-ONTOLOGY concepts and the data of IMGT®, the international ImMunoGeneTics information system®.
IMGT-ML has been developed by Kora Combres and Denys Chaume in the frame of the EU ORIEL project (IST-2001-32688).
| IMGTCommune | html (English) | html (French) | xml-schema |
Set of schemas used by other XML schemas. |
| Taxonomy | html (English) | html (French) | xml-schema |
XML schemas for taxonomy defined by the NCBI-Taxonomy . |
| Literature | html (English) | html (French) | xml-schema |
XML schemas for literature references as defined in EMBL Nucleotide Sequence Database. |
| IMGT-IDENTIFICATION | html (English) | html (French) | xml-schema |
The IMGT-ONTOLOGY 'IDENTIFICATION' concept is a set of concepts that allow scentists to identify IG or TR sequences according to fundamental biological and immunogenetic characteristics. |
| IMGT-DESCRIPTION | html (English) | html (French) | xml-schema |
The IMGT-ONTOLOGY 'DESCRIPTION' concept corresponds to the classification of terms and rules which are necessary to describe the organization and the components of the IG and TR sequences, and to characterize their specific and conserved motifs. |
| IMGT-CLASSIFICATION | html (English) | html (French) | xml-schema |
The IMGT-ONTOLOGY 'CLASSIFICATION' concept organizes the immunogenetics knowledge useful to name and classify IG and TR genes in IMGT. |
| IMGT-NUMEROTATION | html (English) | html (French) | xml-schema |
The IMGT-ONTOLOGY 'NUMEROTATION' concept is a set of rules which allow to position the knowledge in one or several dimensional space. |
| IMGT-OBTENTION | html (English) | html (French) | xml-schema |
The IMGT-ONTOLOGY 'OBTENTION' concept is a set of standardized terms that precise the origins of the sequence (the 'origin' concept) and the conditions in which the sequences have been obtained (the 'methodology' concept). |
| IMGTData | html (English) | html (French) | xml-schema |
The data managed by IMGT/LIGM-DB are described by these schemas. They include the metadata (cataloguing), and factual data as sequences. |
English and French documentation files are generated from XML-Schema annotations to HTML files by a transformation defined by XSLT. This transformation is made on fly by Apache/Cocoon.
References:
[1] Chaume, D., et al.
"IMGT-ML a XML language for IMGT-ONTOLOGY and IMGT/LIGM-DB data"
In: CORBA and XML: Towards a Bioinformatics Integrated Network Environment,
Proceedings of NETTAB 2001, Network Tools and Applications in Biology, pp 71-75 (2001).
[2] Chaume, D., Combres, K., Giudicelli, V. and Lefranc, M.-P.
"Retrieving factual data and documents using IMGT-ML in the IMGT information system®"
Technologies and technological platforms of interest to the field, with emphasis on: Ontologies, Databases and Applications of Semantics in Bioinformatics.
NETTAB 2005 Workflows management: new abilities for the biological information overflow. Naples, Italy.
NETTAB., 47-51 (2005).
[3] Lefranc, M.-P. et al.,
"IMGT-Choreography for Immunogenetics and Immunoinformatics"
In Silico Biology, 2005, 5, 45-60, Epub 2005, 5, 0006, 24 Dec 2004.
http://www.bioinfo.de/isb/2004/05/0006/,
PMID: 15972004