Inference for bio-IE: GENIA meets EKOSS

Information extraction for molecular biology (bioIE) aims to find useful pieces of bio-molecular knowledge (bio-knowledge, hereafter) from natural language expressions in the literature, and to store them in a structured form accessible by computers. One example is protein-protein interaction (PPI) extraction (Bunescu et al., 2004), which has long been a primary task of bio-IE. Usually, a PPI is expressed by a pair of proteins. For example, from the text, “Secretion of TNF was abolished by BHA · · ·,” the following PPI can be extracted: