Nucleic Acids Research, 2006, Vol. 34, Web Server issue W751 Figure 2. Network graphs show relationships between pairs of chemical terms. Clicking on the ‘Graphical View’ link (Figure 1, middle panel) produces a dynamic network graph (upper panel) that shows the interconnectedness of the chemical terms which, in turn, are linked to references (color-coded lines) with the number of co-occurrences labeled in the small circles. This graph displays all the terms from the table (Figure 1, middle panel) that are connected by the number of articles in which they co-occur. The lines and circles are color coded depending on the number of articles: gray, the terms co-occur in 1 article; yellow, co-occurrence in 2–5 articles; pink, co-occurrence in 6–10 articles; green, co-occurrence in >10 articles. Lower panel: magnified region of the cluster of terms that include norepinephrine transporters. for co-occurrences of grouped terms from MEDLINE XML ﬁles and to focus on the general problem of protein–protein interactions. Since we have created a database from the entire set of MEDLINE XML ﬁles, it is anticipated that a variety of other, specialized citation subsets (e.g. cytoskeletal proteins, signal transduction pathways and diseases such as cancer) will be developed that are similar in design to botXminer. It is further anticipated that botXminer will serve as a template for future applications that will mine the entire MEDLINE and other very large sources of biomedical information. ACKNOWLEDGEMENTS We thank Lichun C. Wang for kindly advising us during the initial stages of this effort and for her encouragement. Support for this project was provided to F.J.L. by the Defense Threat Reduction Agency (DTRA; D_X009_04_RD_B) and the Defense Advanced Research Project Agency (DARPA; 05-0-DA-008). This project has been also been funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract N01-CO-12400. Opinions, interpretations, conclusions, and recommendations