Will.Whim

A weblog by Will Fitzgerald

OpenDMAP paper

For the few who might be interested: OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression (PDF).

OpenDMAP advances the performance standards for extracting protein-protein interaction predications from the full texts of biomedical research articles. Furthermore, this level of performance appears to generalize to other information extraction tasks, including extracting information about predicates of more than two arguments. The output of the information extraction system is always constructed from elements of an ontology, ensuring that the knowledge representation is grounded with respect to a carefully constructed model of reality. The results of these efforts can be used to increase the efficiency of manual curation efforts and to provide additional features in systems that integrate multiple sources for information extraction. The open source OpenDMAP code library is freely available at http://bionlp.sourceforge.net/

I worked on an early version of this system.

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One response to “OpenDMAP paper

  1. Larry Hunter April 2, 2008 at 5:37 pm

    And if you are *really* interested, we’re having a meeting in Denver on April 16-17 to talk about DMAP approaches. Contact Larry dot Hunter at UCHSC dot EDU for details.

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