We present a comprehensive system to automatically extract and summarize mutation-related information from full-text research papers. The system extraction module is split into subtasks: organism analysis, mutation detection, protein property extraction and full impact analysis, including linking impacts with the causative mutation and the affected protein properties, such as molecular functions, kinetic constants, kinetic values, units of measurements, and physical quantities. The Gene Ontology (GO) is further integrated for the analysis of the detected molecular functions. The output of the presented system is populated to an OWL-DL ontology, which can then be queried to provide structured information. In addition, the performance of the system is evaluated on both external and internal corpora and databases. The results show the reliability of the approaches.

The Open Mutation Miner (OMM) system, including its components and resources, is published under the GNU Affero General Public License v3 (AGPL3) at http://www.semanticsoftware.info/open-mutation-miner.