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; 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.