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Semantic Software Lab
Concordia University
Montréal, Canada


First Release of the Open Mutation Miner (OMM) System

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.

Text Mining Assistants in Wikis for Biocuration

Sateli, B., C. Murphy, R. Witte, M. - J. Meurs, and A. Tsang, "Text Mining Assistants in Wikis for Biocuration", 5th International Biocuration Conference, Washington DC, USA : International Society for Biocuration, pp. 126, 04/2012.

OMM Query

OMM Query is our online search interface for an index for full-text research papers from the PMC Open Access Corpus (nearly half a million documents) that have been mined for mutation information with Open Mutation Miner (OMM) and OrganismTagger. It can be accessed using the Mímir query language, combining entity annotations with their features with plain text (see below for some examples).

Note that you can index your own set of documents through OMM and install a local query server, if you want to mine a different set of documents for mutation impact information: all software used in this process is freely available under open source licenses. Besides the web interface, it is also possible to query the Mímir server through a RESTful API.

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