Figure 1

Basic examples. (a) The main page allows for submission of one or two queries. Queries are entered into the blue and yellow text boxes, and parameter options are selected below. Nodes may be defined as author, paper, Protein Data Bank (PDB), Genbank, or Swiss-Prot ID, and edges may be drawn for co-authorship, shared Medical Subject Headings (MeSH) term, or shared location. (b) PubNet connects to PubMed, submits each query separately, and parses the XML results. In this example, only Query1 was submitted, returning four publications. (c) In the output, each paper is represented as a single node. Each pair of nodes that share a common author are linked by an edge. (d) In this example, Query1 and Query2 have each returned three papers, each with MeSH terms and PDB IDs. (e) When nodes are specified as papers and edges specified as shared MeSH terms, papers returned only by Query1 are represented as blue nodes, papers returned only by Query2 are shown in yellow, and papers common to both queries are shown in green. (f) When nodes are specified as PDB IDs and edges specified as shared MeSH terms, each PDB ID from each paper is represented as a node and colored according to the query from which it was derived. A single paper can give rise to multiple nodes, as is the case for Paper3, which contains two PDB identifiers, each of which are represented by a separate node.