OpenDMAP: Open source Direct Memory Access Parser. OpenDMAP is an ontology-driven, rule-based concept analysis and information extraction system. Unlike traditional parsers, OpenDMAP does not have a lexicon that maps from words to all the possible meanings of these words. Rather, each concept is associated with phrasal patterns that are used to recognize that concept. OpenDMAP processes texts to recognize concepts and relationships from a knowledge-base. OpenDMAP uses Protégé knowledge-bases to provide an object model for the possible concepts that might be found in a text. Protégé models concepts as classes that participate in abstraction and packaging hierarchies, and models relationships as class-specific slots.

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  2. Fox, Andrew D.; Baumgartner, William A. Jr.; Johnson, Helen L.; Hunter, Lawrence E.; Slonim, Donna K.: Mining protein-protein interactions from GeneRIFs with OpenDMAP (2010) ioport
  3. Kabiljo, Renata; Clegg, Andrew B.; Shepherd, Adrian J.: A realistic assessment of methods for extracting gene/protein interactions from free text (2009) ioport
  4. Mcintosh, Tara; Curran, James R.: Challenges for automatically extracting molecular interactions from full-text articles (2009) ioport