Curation of Complex, Context-dependent Immunological Data

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2006 Jul 14

PMID 16836764

Citations 19

Authors

Randi Vita

Kerrie Vaughan

Laura Zarebski

Nima Salimi

Ward Fleri

Howard Grey

Muthu Sathiamurthy

John Mokili

Huynh-Hoa Bui

Philip E Bourne

Julia Ponomarenko

Romulo de Castro Jr

Russell K Chan

John Sidney

Stephen S Wilson

Scott Stewart

Scott Way

Bjoern Peters

Alessandro Sette

Affiliations

Soon will be listed here.

Abstract

Background: The Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org.

Description: To identify and extract relevant data from the scientific literature in an efficient and accurate manner, novel processes were developed for manual and semi-automated annotation.

Conclusion: Formalized curation strategies enable the processing of a large volume of context-dependent data, which are now available to the scientific community in an accessible and transparent format. The experiences described herein are applicable to other databases housing complex biological data and requiring a high level of curation expertise.

Citing Articles

The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community.

Kosaloglu-Yalcin Z, Blazeska N, Carter H, Nielsen M, Cohen E, Kufe D Front Immunol. 2021; 12:735609.

PMID: 34504503 PMC: 8421848. DOI: 10.3389/fimmu.2021.735609.

The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook.

Martini S, Nielsen M, Peters B, Sette A Immunogenetics. 2019; 72(1-2):57-76.

PMID: 31761977 PMC: 6970984. DOI: 10.1007/s00251-019-01137-6.

Experimental validation of the RATE tool for inferring HLA restrictions of T cell epitopes.

Paul S, Arlehamn C, Schulten V, Westernberg L, Sidney J, Peters B BMC Immunol. 2017; 18(Suppl 1):20.

PMID: 28681704 PMC: 5499093. DOI: 10.1186/s12865-017-0204-1.

The Immune Epitope Database: How Data Are Entered and Retrieved.

Fleri W, Vaughan K, Salimi N, Vita R, Peters B, Sette A J Immunol Res. 2017; 2017:5974574.

PMID: 28634590 PMC: 5467323. DOI: 10.1155/2017/5974574.

Benchmarking B-cell epitope prediction with quantitative dose-response data on antipeptide antibodies: towards novel pharmaceutical product development.

Caoili S Biomed Res Int. 2014; 2014:867905.

PMID: 24949474 PMC: 4037609. DOI: 10.1155/2014/867905.

References

Toseland C, Clayton D, McSparron H, Hemsley S, Blythe M, Paine K . AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res. 2005; 1(1):4. PMC: 1289288. DOI: 10.1186/1745-7580-1-4. View

Sathiamurthy M, Peters B, Bui H, Sidney J, Mokili J, Wilson S . An ontology for immune epitopes: application to the design of a broad scope database of immune reactivities. Immunome Res. 2005; 1(1):2. PMC: 1287064. DOI: 10.1186/1745-7580-1-2. View

Kuiken C, Korber B, Shafer R . HIV sequence databases. AIDS Rev. 2003; 5(1):52-61. PMC: 2613779. View

Lefranc M, Clement O, Kaas Q, Duprat E, Chastellan P, Coelho I . IMGT-Choreography for immunogenetics and immunoinformatics. In Silico Biol. 2005; 5(1):45-60. View

Hornbeck P, Chabra I, Kornhauser J, Skrzypek E, Zhang B . PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation. Proteomics. 2004; 4(6):1551-61. DOI: 10.1002/pmic.200300772. View

Alfarano C, Andrade C, Anthony K, Bahroos N, Bajec M, Bantoft K . The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 2004; 33(Database issue):D418-24. PMC: 540005. DOI: 10.1093/nar/gki051. View

Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B . PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics. 2003; 4:11. PMC: 153503. DOI: 10.1186/1471-2105-4-11. View

Kawai J, Shinagawa A, Shibata K, Yoshino M, Itoh M, Ishii Y . Functional annotation of a full-length mouse cDNA collection. Nature. 2001; 409(6821):685-90. DOI: 10.1038/35055500. View

Krieger C, Zhang P, Mueller L, Wang A, Paley S, Arnaud M . MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2003; 32(Database issue):D438-42. PMC: 308834. DOI: 10.1093/nar/gkh100. View

10.

Schonbach C, Koh J, Sheng X, Wong L, Brusic V . FIMM, a database of functional molecular immunology. Nucleic Acids Res. 1999; 28(1):222-4. PMC: 102489. DOI: 10.1093/nar/28.1.222. View

11.

Berman H, Henrick K, Nakamura H . Announcing the worldwide Protein Data Bank. Nat Struct Biol. 2003; 10(12):980. DOI: 10.1038/nsb1203-980. View

12.

Muller H, Kenny E, Sternberg P . Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol. 2004; 2(11):e309. PMC: 517822. DOI: 10.1371/journal.pbio.0020309. View

13.

Peters B, Sidney J, Bourne P, Bui H, Buus S, Doh G . The design and implementation of the immune epitope database and analysis resource. Immunogenetics. 2005; 57(5):326-36. PMC: 4780685. DOI: 10.1007/s00251-005-0803-5. View

14.

Sathiamurthy M, Hickman H, CAVETT J, Zahoor A, Prilliman K, Metcalf S . Population of the HLA ligand database. Tissue Antigens. 2003; 61(1):12-9. DOI: 10.1034/j.1399-0039.2003.610102.x. View

15.

Lefranc M, Giudicelli V, Kaas Q, Duprat E, Jabado-Michaloud J, Scaviner D . IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res. 2004; 33(Database issue):D593-7. PMC: 540019. DOI: 10.1093/nar/gki065. View

16.

Apweiler R, Bairoch A, Wu C, Barker W, Boeckmann B, Ferro S . UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2003; 32(Database issue):D115-9. PMC: 308865. DOI: 10.1093/nar/gkh131. View

17.

Peters B, Sidney J, Bourne P, Bui H, Buus S, Doh G . The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol. 2005; 3(3):e91. PMC: 1065705. DOI: 10.1371/journal.pbio.0030091. View

18.

Ruepp A, Doudieu O, van den Oever J, Brauner B, Dunger-Kaltenbach I, Fobo G . The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res. 2005; 34(Database issue):D568-71. PMC: 1347437. DOI: 10.1093/nar/gkj074. View

19.

RAMMENSEE H, Bachmann J, Emmerich N, Bachor O, Stevanovic S . SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics. 1999; 50(3-4):213-9. DOI: 10.1007/s002510050595. View

20.

Hu Z, Narayanaswamy M, Ravikumar K, Vijay-Shanker K, Wu C . Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinformatics. 2005; 21(11):2759-65. DOI: 10.1093/bioinformatics/bti390. View