Bioinformatics
Semantic Search for Biological Datasets: A Usability Study on Modes of Querying and Explaining Search Results
Submitted by rene on Tue, 2023-06-13 12:02Towards Semantic Recommendation of Biodiversity Datasets based on Linked Open Data
Submitted by bahar on Thu, 2014-10-23 11:07- Login to post comments
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An Approach to Controlling User Models and Personalization Effects in Recommender Systems
Submitted by rene on Sun, 2013-03-31 08:35Personalized Semantic Assistance for the Curation of Biochemical Literature
Submitted by mj on Mon, 2012-10-15 13:27First 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: "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.
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Mutation Impact Analysis System: Automated Extraction of Protein Mutation Impacts from the Biomedical Literature
Submitted by nona on Thu, 2012-07-05 08:29Automated extraction and semantic analysis of mutation impacts from the biomedical literature
Submitted by nona on Mon, 2012-06-18 07:40Semantic text mining support for lignocellulose research
Submitted by mj on Tue, 2012-05-01 11:44Text Mining Assistants in Wikis for Biocuration
Submitted by mj on Wed, 2012-04-11 17:35- Login to post comments
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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.