Classification of the universe of immune epitope literature: representation and knowledge gaps

PLoS One. 2009 Sep 14;4(9):e6948. doi: 10.1371/journal.pone.0006948.


Background: A significant fraction of the more than 18 million scientific articles currently indexed in the PubMed database are related to immune responses to various agents, including infectious microbes, autoantigens, allergens, transplants, cancer antigens and others. The Immune Epitope Database (IEDB) is an online repository that catalogs immune epitope reactivity data derived from articles listed in the National Library of Medicine PubMed database. The IEDB is maintained and continually updated by monitoring PubMed for new, potentially relevant references.

Methodology: Herein we detail the classification of all epitope-specific literature in over 100 different immunological domains representing Infectious Diseases and Microbes, Autoimmunity, Allergy, Transplantation and Cancer. The relative number of references in each category reflects past and present areas of research on immune reactivities. In addition to describing the overall landscape of data distribution, this particular characterization of the epitope reference data also allows for the exploration of possible correlations with global disease morbidity and mortality data.

Conclusions/significance: While in most cases diseases associated with high morbidity and mortality rates were amongst the most studied, a number of high impact diseases such as dengue, Schistosoma, HSV-2, B. pertussis and Chlamydia trachoma, were found to have very little coverage. The data analyzed in this fashion represents the first estimate of how reported immunological data corresponds to disease-related morbidity and mortality, and confirms significant discrepancies in the overall research foci versus disease burden, thus identifying important gaps to be pursued by future research. These findings may also provide a justification for redirecting a portion of research funds into some of the underfunded, critical disease areas.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Allergens / chemistry
  • Animals
  • Antigens, Neoplasm / chemistry
  • Chlamydia / metabolism
  • Communicable Diseases / metabolism
  • Computational Biology / methods
  • Databases, Factual
  • Epitopes / chemistry*
  • Humans
  • Immune System*
  • Information Storage and Retrieval
  • Natural Language Processing
  • Neoplasms / metabolism
  • PubMed


  • Allergens
  • Antigens, Neoplasm
  • Epitopes