Overview

PathBinder is a unique, plant-based tool to explore literature, and to annotate metabolic and regulatory interactions and biomolecules. PathBinder queries the MEDLINE database and retrieves sentences containing two terms of interest, and rank them based on their probability to describe interactions between the two given terms; each sentence is a clickable link pointing to the original online PubMed citation.

Features of PathBinder version 1:

• An API (applications programming interface) to integrate PathBinder into other analysis tools for systems biologists. This API has been used to integrate PathBinder into both FCModeler and MetNetDB
• Hierarchical filters by taxon, morphological context, and/or subcellular location. Specifying a parent will retrieve abstracts containing that parent and its children. Upon retrieval, abstracts are ranked according to a system based on the quality and quantity of the descriptions of the interaction in the literature.
• An extensive set of synonyms which are co-searched when a term is selected. The user does not need to second-guess possible terms for a molecule of interest and do repeated searches.
• A novel "hidden links" tool to identify and explore potential intermediate links in networks. Given biomolecules A and C, which do not co-occur in any sentence in the PubMed abstracts, find biomolecules B that co-occur in sentences both with A and with C.
• A newest feature to extract and rank intearction indicating terms for any give pairs of biomolecules from MEDLINE.

Comments and feedback: Lifeng Zhang zlfpeak@iastate.edu