Don’s original Web-based one-node search tool is no longer available. I have implemented a simpler version
(3)(
(3) http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/one-node.cgi) in which the investigator starts with a literature that represents a problem to be solved (e.g. Huntington’s disease). Next, the user will be prompted to choose a category of Medical Subject Headings (MeSH) to search within, which encompasses a set of literatures describing entities (or classes of entities) that represent possible approaches or solutions to the problem. (Alternatively, the user can choose the Free Format option, to enter any list of PubMed search queries manually, one on each line.) For example, to search among different classes of drugs according to their molecular mechanism using the MeSH Tree option, the user would drill down from Chemicals and Drugs to Chemical Actions and Uses to Pharmacologic Actions to finally, Molecular Mechanisms of Pharmacological Action [D27.505.519]. This category includes about twenty classes of drugs, including Alkylating Agents [D27.505.519.124], Angiotensin Receptor Antagonists [D27.505.519.162], Antacids [D27.505.519.170], Antifoaming Agents [D27.505.519.178], and so on. Once the user chooses this MeSH term category, the software will carry out a series of two-node searches, each consisting of A = Huntington’s disease
vs C = one of the drug classes. These two-node searches are characterized according to the total number of articles in A and C (and nAC, the intersection of A and C), as well as the total number of B-terms. Finally, the searches are ranked according to
pR, the percentage of B-terms that are predicted to be relevant for meaningful linkage. The two-node search results are all individually stored temporarily by job ID so users can go back without the need to re-run the search each time. Thus, carrying out a one-node search is simply a matter of carrying out a series of two-node searches, one for each MeSH term within the category of interest (
Smalheiser, 2012b). This greatly simplifies the computational issues involved.