Mining Biomedical Literature for Molecular Interactions (Muscorian)

Muscorian is a text analysis pipeline for the gathering and analysis of PubMed abstracts to extract assertions on entity-entity using natural language processing (NLP) and statistical co-occurrence of entity terms. Entity terms may refer to protein names or gene names; hence, entity-entity interactions can be gene-gene, gene-protein, or protein-protein interactions. Muscorian also includes the construction and analysis of protein-protein interaction maps. These interaction maps are fundamental for interactomic analysis. However, most of the components used in Muscorian needed individual analysis and benchmarking. This work was initiated in Department of Zoology, The University of Melbourne, Australia, under the financial sponsorship of Cooperative Research Centre for Innovative Dairy Products (Dairy CRC), Australia, as part of my Doctor of Philosophy thesis.