Figure 1.

Generating the focused subgraph. Suppose we are searching protein definitions for ubiquitin in the above Biozon subgraph. Each of the two circled nodes corresponds to an entity in which "ubiquitin" appears in its definition field. The set S represents all nodes that will be included in the focused subgraph. These nodes are numbered according to the steps in which they are added to the focused subgraph (see 'Methods'). S₁ is the set of all proteins that match the query term and their neighbors, while S₂ is the set of all non-proteins that match the query term and their protein neighbors. Nodes are included in the subgraph if one of these two criteria is met: (a) A protein whose definition does not contain the search term is included only if it has a neighbor whose definition does contain the search term. (b) A non-protein whose definition does not contain the search term is included only if it has a protein neighbor whose definition does contain the search term.