We are happy to announce the first major public release of our protein mutation impact analysis system, Open Mutation Miner (OMM), together with a new open access publication: Naderi, N., and R. Witte, "Automated extraction and semantic analysis of mutation impacts from the biomedical literature", BMC Genomics, vol. 13, no. Suppl 4, pp. S10, 06/2012.

OMM is the first comprehensive, fully open source system for extracting and analysing mutation-related information from full-text research papers. Novel features not available in other systems include: the detection of various forms of mutation mentions, in particular mutation series, full mutation 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. OMM provides output options in various formats, including populating an OWL ontology, Web service access, structured queries, and interactive use embedded in desktop clients. OMM is robust and scalable: we processed the entire PubMed Open Access Subset (nearly half a million full-text papers) on a standard desktop PC, and larger document sets can be easily processed and indexed on appropriate hardware.