Difference between revisions of "Immunoinformatics"
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'''Immunoinformatics''' is a sub-branch of [[bioinformatics]] that focuses on the use of data management and computational tools to improve immunological research. The scope of immunoinformatics covers a wide variety of territory, from genomic and proteomic study of the immune system to molecular- and organism-level modeling, putting it in close ties with [[genome informatics]].<ref name="NovImmunoNew">{{cite book |url=https://books.google.com/books?id=iBJc1JO1WuwC&pg=PA3 |chapter=Immunoinformatics - The new kid in town |title=Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function |author=Brusic, Vladimir; Petrovsky, Nikolai; Novartis Foundation |publisher=John Wiley & Sons |year=2004 |pages=3–22 |isbn=9780470090756 |accessdate=20 January 2015}}</ref><ref name="FlowerImm">{{cite book |url=https://books.google.com/books?id=IJtZurJ5BvoC&pg=PA1 |chapter=Immunoinformatics and the In Silico Prediction of Immunogenicity: An Introduction |title=Immunoinformatics: Predicting Immunogenicity in Silico |author=Flower, Darren R. |publisher=Springer Science & Business Media |pages=1–15 |year=2007 |isbn=9781603271189}}</ref> | |||
==History== | |||
Immunology researchers like Hans-Georg Rammensee trace the history of immunoinformatics back to the study of theoretical immunology. In June 1987, the Theoretical Immunology Workshop was hosted in Santa Fe, New Mexico to discuss "the topics of immune surveillance, mathematical models of HIV infection, complexities of antigen-antibody systems, immune suppression and tolerance, and idiotypie networks."<ref name="WVPressTheo">{{cite web |url=http://westviewpress.com/books/theoretical-immunology-part-one/ |title=Theoretical Immunology, Part One |publisher=Westview Press |accessdate=20 January 2015}}</ref><ref name="NovImmunoChair">{{cite book |url=https://books.google.com/books?id=iBJc1JO1WuwC&pg=PA1 |chapter=Chair's introduction |title=Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function |author=Rammensee, Hans-Georg; Novartis Foundation |publisher=John Wiley & Sons |year=2004 |pages=1–2 |isbn=9780470090756 |accessdate=20 January 2015}}</ref><ref name="PerelsonTheo">{{cite book |url=http://books.google.com/books/about/Theoretical_immunology.html?id=DxxrAAAAMAAJ |title=Theoretical Immunology: The Proceedings of the Theoretical Immunology Workshop, held June 1987, in Santa Fe, New Mexico |author=Perelson, Alan S. (Ed.) |publisher=Addison-Wesley Pub. Co |year=1988 |volume=1 and 2 |pages=811 |isbn=9780201156829 |accessdate=20 January 2015}}</ref> | |||
One of the first immunoinformatics efforts to result in a long-term informatics solution was the construction of the IMGT information system in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM). Created to "standardize and manage the complexity of the immunogenetics data" coming out of the lab, the information system went on to become an international public reference for genetic and proteomic data related to immunology.<ref name="SchönbachImm">{{cite book |url=https://books.google.com/books?id=YgjWcFng-4YC&pg=PA1 |title=Immunoinformatics |author= Schönbach, Christian; Ranganathan, Shoba; Brusic, Vladimir (Eds.) |publisher=Springer Science & Business Media |year=2007 |pages=200 |isbn=9780387729671 |accessdate=20 January 2015}}</ref> In July 1995, IMGT moved to the web, and by 2007 it was handling more than 140,000 requests per month.<ref name="LefrancImm">{{cite book |url=https://books.google.com/books?id=IJtZurJ5BvoC&pg=PA19 |chapter=IMGT: The International ImmunoGeneTics Information System for Immunoinformatics |title=Immunoinformatics: Predicting Immunogenicity in Silico |author=Lefranc, Marie-Paule; Flower, Darren R. (Ed.) |publisher=Springer Science & Business Media |pages=19–42 |year=2007 |isbn=9781603271189 |accessdate=20 January 2015}}</ref> | |||
In 1999, the SYFPEITHI database for MHC ligands and T-cell epitopes – a component of an antigen or antibody generator – went public.<ref name="RammenseeSYF">{{cite journal |url=http://www.ncbi.nlm.nih.gov/pubmed/10602881 |title=SYFPEITHI: Database for MHC ligands and peptide motifs |journal=Immunogenetics |author=Rammensee, H.; Bachmann, J; Emmerich, N. P.; Bachor, O. A.; Stevanović, S. |volume=50 |issue=3–4 |pages=213–219 |year=November 1999 |doi=10.1007/s002510050595 |pmid=10602881 |accessdate=20 January 2015}}</ref> | |||
In 2003, the Anthony Nolan Research Institute and the European Bioinformatics Institute developed the Immuno Polymorphism Database (IPD) "to provide a centralised system for the study of polymorphism in genes of the immune system."<ref name="IPD">{{cite web |url=http://www.ebi.ac.uk/ipd/ |title=Immuno Polymorphism Database |publisher=EMBL-European Bioinformatics Institute |acessdate=20 January 2015}}</ref> | |||
==Application== | ==Application== | ||
Immunoinformatics can help tackle problems and tasks such as the following<ref name="SchönbachImm" />: | Immunoinformatics can help tackle problems and tasks such as the following<ref name="SchönbachImm" /><ref name="NovImmunoNew" />: | ||
* improving the development of biological therapeutics | * improving the development of biological therapeutics | ||
* developing and improving analysis and data management solutions for immunogenetics | * developing and improving analysis and data management solutions for immunogenetics | ||
* developing and improving allergen databases | * developing and improving allergen and other immunological databases | ||
* creating better computer models of the immune system | * creating better mathematical and computer models of the immune system | ||
==Informatics== | ==Informatics== | ||
| Line 18: | Line 22: | ||
==See also== | ==See also== | ||
* [[Genome informatics]] | * [[Genome informatics]] | ||
* [[Infectious disease informatics]] | * [[Infectious disease informatics]] | ||
==Further reading== | |||
* {{cite book |url=https://books.google.com/books?id=IJtZurJ5BvoC&pg=PA1 |chapter=Immunoinformatics and the In Silico Prediction of Immunogenicity: An Introduction |title=Immunoinformatics: Predicting Immunogenicity in Silico |author=Flower, Darren R. |publisher=Springer Science & Business Media |pages=1–15 |year=2007 |isbn=9781603271189}} | |||
==External links== | ==External links== | ||
* [http://www.imgt.org/ IMGT Information System] | * [http://www.imgt.org/ IMGT Information System] | ||
* [http://www.imcportal.org/ Immune Modeling Community] | |||
* [http://www.ebi.ac.uk/ipd/ Immuno Polymorphism Database] | |||
* [http://www.syfpeithi.de/0-Home.htm SYFPEITHI] | |||
==References== | ==References== | ||
Revision as of 18:41, 20 January 2015
Immunoinformatics is a sub-branch of bioinformatics that focuses on the use of data management and computational tools to improve immunological research. The scope of immunoinformatics covers a wide variety of territory, from genomic and proteomic study of the immune system to molecular- and organism-level modeling, putting it in close ties with genome informatics.[1][2]
History
Immunology researchers like Hans-Georg Rammensee trace the history of immunoinformatics back to the study of theoretical immunology. In June 1987, the Theoretical Immunology Workshop was hosted in Santa Fe, New Mexico to discuss "the topics of immune surveillance, mathematical models of HIV infection, complexities of antigen-antibody systems, immune suppression and tolerance, and idiotypie networks."[3][4][5]
One of the first immunoinformatics efforts to result in a long-term informatics solution was the construction of the IMGT information system in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM). Created to "standardize and manage the complexity of the immunogenetics data" coming out of the lab, the information system went on to become an international public reference for genetic and proteomic data related to immunology.[6] In July 1995, IMGT moved to the web, and by 2007 it was handling more than 140,000 requests per month.[7]
In 1999, the SYFPEITHI database for MHC ligands and T-cell epitopes – a component of an antigen or antibody generator – went public.[8]
In 2003, the Anthony Nolan Research Institute and the European Bioinformatics Institute developed the Immuno Polymorphism Database (IPD) "to provide a centralised system for the study of polymorphism in genes of the immune system."[9]
Application
Immunoinformatics can help tackle problems and tasks such as the following[6][1]:
- improving the development of biological therapeutics
- developing and improving analysis and data management solutions for immunogenetics
- developing and improving allergen and other immunological databases
- creating better mathematical and computer models of the immune system
Informatics
See also
Further reading
- Flower, Darren R. (2007). "Immunoinformatics and the In Silico Prediction of Immunogenicity: An Introduction". Immunoinformatics: Predicting Immunogenicity in Silico. Springer Science & Business Media. pp. 1–15. ISBN 9781603271189. https://books.google.com/books?id=IJtZurJ5BvoC&pg=PA1.
External links
References
- ↑ 1.0 1.1 Brusic, Vladimir; Petrovsky, Nikolai; Novartis Foundation (2004). "Immunoinformatics - The new kid in town". Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function. John Wiley & Sons. pp. 3–22. ISBN 9780470090756. https://books.google.com/books?id=iBJc1JO1WuwC&pg=PA3. Retrieved 20 January 2015.
- ↑ Flower, Darren R. (2007). "Immunoinformatics and the In Silico Prediction of Immunogenicity: An Introduction". Immunoinformatics: Predicting Immunogenicity in Silico. Springer Science & Business Media. pp. 1–15. ISBN 9781603271189. https://books.google.com/books?id=IJtZurJ5BvoC&pg=PA1.
- ↑ "Theoretical Immunology, Part One". Westview Press. http://westviewpress.com/books/theoretical-immunology-part-one/. Retrieved 20 January 2015.
- ↑ Rammensee, Hans-Georg; Novartis Foundation (2004). "Chair's introduction". Immunoinformatics: Bioinformatic Strategies for Better Understanding of Immune Function. John Wiley & Sons. pp. 1–2. ISBN 9780470090756. https://books.google.com/books?id=iBJc1JO1WuwC&pg=PA1. Retrieved 20 January 2015.
- ↑ Perelson, Alan S. (Ed.) (1988). Theoretical Immunology: The Proceedings of the Theoretical Immunology Workshop, held June 1987, in Santa Fe, New Mexico. 1 and 2. Addison-Wesley Pub. Co. pp. 811. ISBN 9780201156829. http://books.google.com/books/about/Theoretical_immunology.html?id=DxxrAAAAMAAJ. Retrieved 20 January 2015.
- ↑ 6.0 6.1 Schönbach, Christian; Ranganathan, Shoba; Brusic, Vladimir (Eds.) (2007). Immunoinformatics. Springer Science & Business Media. pp. 200. ISBN 9780387729671. https://books.google.com/books?id=YgjWcFng-4YC&pg=PA1. Retrieved 20 January 2015.
- ↑ Lefranc, Marie-Paule; Flower, Darren R. (Ed.) (2007). "IMGT: The International ImmunoGeneTics Information System for Immunoinformatics". Immunoinformatics: Predicting Immunogenicity in Silico. Springer Science & Business Media. pp. 19–42. ISBN 9781603271189. https://books.google.com/books?id=IJtZurJ5BvoC&pg=PA19. Retrieved 20 January 2015.
- ↑ Rammensee, H.; Bachmann, J; Emmerich, N. P.; Bachor, O. A.; Stevanović, S. (November 1999). "SYFPEITHI: Database for MHC ligands and peptide motifs". Immunogenetics 50 (3–4): 213–219. doi:10.1007/s002510050595. PMID 10602881. http://www.ncbi.nlm.nih.gov/pubmed/10602881. Retrieved 20 January 2015.
- ↑ "Immuno Polymorphism Database". EMBL-European Bioinformatics Institute. http://www.ebi.ac.uk/ipd/.
