The ever-increasing scientific literature and the exponential growth of large-scale molecular data have prompted active research in biological text mining to facilitate literature-based curation of molecular databases. Meanwhile, systems biology and bioontologies are emerging as critical tools in biological research where complex data in disparate resources are generated, integrated and analyzed. Both rely on literature for data annotation and analysis. The challenges facing us are to develop broadly utilized text mining tools and systems, and to bring together developer and user communities for system development and evaluation. We describe a framework for linking text mining tools with ontology and systems biology, extending from a previously developed text mining resource, iProLINK. We focus on molecular and ontological resources, including genes/proteins, protein-protein interaction (PPI), and Protein Ontology. The framework consists of two major components: a user interface for text mining of PPI from an integrated tool server and software modules to allow text mining outputs to be created, ranked, and used by the community. Use cases are presented for assessing the gaps and making recommendations for future development.