Pubnet Instructions


What is PubNet?

PubNet is a utility that accepts as input up to two PubMed queries, and returns as output a network graph (in multiple image formats) based on user-specified node and edge selection properties. Nodes represent data items associated with publications returned by the queries (such as paper ids, author names, and databank ids), and edges represent instances of shared properties. PubNet can be used to visualize a variety of relationships, such as the degree to which two authors collaborate or the MeSH Term relatedness of publications with PDB ids. The visualization is done with the aid of aiSee.

Generating a graph

  1. Type or paste any Entrez-PubMed query into the blue box labeled "Query 1". See below for further details.
  2. (optional) Type or paste a second query into the yellow textbox.
  3. Choose a Node type and Edge type from the selection boxes at the bottom.
  4. Click Submit.

Interpreting the Graph

Details for interpreting the graph given below.

Node Selection

Edge Types

Tips for Successful Queries

Complexity of PubNet graphs can scale exponentially with the number of nodes. It has been my experience that graphs with more than 1000 nodes are difficult to interpret, and they can take a very long time to load, if they load at all. To get better results, try the following:

Download PubNet Code

The code for PubNet may be downloaded here: PubNet Code