PubNet: a flexible system for visualizing literature derived networks

Genome Biol. 2005;6(9):R80. doi: 10.1186/gb-2005-6-9-r80. Epub 2005 Aug 16.


We have developed PubNet, a web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual navigation, and topological analysis. PubNet supports the creation of complex networks derived from the contents of individual citations, such as genes, proteins, Protein Data Bank (PDB) IDs, Medical Subject Headings (MeSH) terms, and authors. This feature allows one to, for example, examine a literature derived network of genes based on functional similarity.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Databases, Bibliographic*
  • Databases, Protein
  • Internet*
  • Literature*
  • Medical Subject Headings
  • Periodicals as Topic
  • Research
  • Software