Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Open Reading Frame (ORF)

Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_672

Definition

ORF” (open reading frame) is a  leafconcept of the “ FunctionalityType” concept of identification (generated from the  IDENTIFICATION Axiom) of  IMGT-ONTOLOGY, the global reference in  immunogenetics and  immunoinformatics (Giudicelli and Lefranc 1999; Lefranc et al. 2004, 2005, 2008; Duroux et al. 2008), built by IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) ( IMGT® Information System).

ORF” identifies, whatever the molecule type (  MoleculeType), the functionality of  Molecule_EntityType leafconcepts in undefined or germline configuration (  Configuration Type), whose coding region has an open reading frame (ORF), but:
  • Alterations have been described in the splicing sites, recombination signals ( Recombination Signal (RS)) and/or regulatory elements

  • And/or changes of conserved amino acids have been suggested by the authors to lead to uncorrect folding

  • And/or the entity is an orphon ( Location Type)

“ORF” is one of the three leafconcepts...

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References

  1. Duroux P, Kaas Q, Brochet X, Lane J, Ginestoux C, Lefranc M-P, Giudicelli V (2008) IMGT-Kaleidoscope, the Formal IMGT-ONTOLOGY paradigm. Biochimie 90:570–583PubMedGoogle Scholar
  2. Giudicelli V, Lefranc M-P (1999) Ontology for immunogenetics: the IMGT-ONTOLOGY. Bioinformatics 12:1047–1054Google Scholar
  3. Lefranc M-P, Giudicelli V, Ginestoux C, Bosc N, Folch G, Guiraudou D, Jabado-Michaloud J, Magris S, Scaviner D, Thouvenin V, Combres K, Girod D, Jeanjean S, Protat C, Yousfi Monod M, Duprat E, Kaas Q, Pommié C, Chaume D, Lefranc G (2004) IMGT-ONTOLOGY for immunogenetics and immunoinformatics. In Silico Biol 4:17–29PubMedGoogle Scholar
  4. Lefranc M-P, Clément O, Kaas Q, Duprat E, Chastellan P, Coelho I, Combres K, Ginestoux C, Giudicelli V, Chaume D, Lefranc G (2005) IMGT-Choreography for immunogenetics and immunoinformatics. In Silico Biol 5:45–60PubMedGoogle Scholar
  5. Lefranc M-P, Giudicelli V, Regnier L, Duroux P (2008) IMGT, a system and an ontology that bridge biological and computational spheres in bioinformatics. Brief Bioinform 9:263–275PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Laboratoire d’ImmunoGénétique Moléculaire, Institut de Génétique Humaine UPR 1142, Université Montpellier 2MontpellierFrance