Comparing Concept Recognizers for Ontology-Based Indexing: MGREP vs. MetaMap

The NCBO is developing a system for automated, ontology-based access to online biomedical resources. The system’s indexing workflow processes the text metadata of diverse resources such as datasets from GEO and ArrayExpress to annotate and index them with concepts from appropriate ontologies... In this paper, we present a comprehensive comparison of two concept recognizers – NIH’s MetaMap and the University of Michigan’s MGREP... Our evaluations demonstrate that MGREP has a clear edge over MetaMap for large-scale applications. Based on our analysis we also suggest areas of potential improvements for MGREP.