BioAR: Anaphora Resolution For Relating Protein Names To Proteome Database Entries

The need for associating, or grounding, protein names in the literature with the entries of proteome databases such as Swiss-Prot is well-recognized. The protein names in the biomedical literature show a high degree of morphological and syntactic variations, and various anaphoric expressions including null anaphors. We present a biomedical anaphora resolution system, BioAR, in order to address the variations of protein names and to further associate them with Swiss-Prot entries as the actual entities in the world. The system shows the performance of 59.5% 75.0% precision and 40.7% 56.3% recall, depending on the specific types of anaphoric expressions. We apply BioAR to the protein names in the biological interactions as extracted by our biomedical information extraction system, or BioIE, in order to construct protein pathways automatically.