Data Integration and Knowledge Management Previous and current research The principal aim of the group is to capture and centralise the knowledge generated by the scientists in the several divisions, and to organise that knowledge in such a way that it is easily mined, browsed and navigated. The group is involved in the following areas: data schema design and technical implementation metadata annotation with respect to experimental data design and implementation of a scientific data portal providing access to data-mining tools (e.g. text-mining)
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'Reflect' used to annotate 'Cell' articles |
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Written by Administrator
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Saturday, 14 November 2009 12:35 |
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Elsevier Pilots New Research Tool ‘Reflect’ In Its Premier Life Science Journal Cell Elsevier announced that our research tool ‘Reflect’, winner of Elsevier’s Grand Challenge 2009, will be piloted on the research articles in the November 12th issue of Cell. The ‘Reflect’ tool identifies the proteins, genes and small molecules mentioned in the Cell articles, and generates pop-up windows containing relevant contextual information, with additional links, about those entities.
find out more: Elsevier press release
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Last Updated on Friday, 05 February 2010 13:06 |
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jClust: A clustering and visualization toolbox. |
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jClust is a user friendly application which provides access to a set of widely used clustering and clique finding algorithms. The toolbox allows applying a range of filtering procedures and is combined with an advanced implementation of the Medusa interactive visualization module. These implemented algorithms are k-Means, Affinity Propagation, Bron-Kerbosch, Restricted Neighborhood Search Cluster Algorithm, Markov Clustering and Spectral Clustering. The supported filtering procedures are 1) haircut, 2) outside-inside, 3) best neighbors and 4) density control operations. The combination of a simple input file format, a set of clustering and filtering algorithms linked together with the visualization tool provides a powerful tool for the exploration and information.
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Reflect: Automated Annotation of Biochemical Terms Reflect allows users to easily highlight the names of all genes, proteins, and small molecules in any web page, typically within one second. Clicking on a highlighted name opens a summary pop-up that provides links to more detailed information. Reflect is freely available at http://reflect.ws. It can also be installed as a plug-in for Firefox or Internet Explorer. 
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ISMB/ECCB 2009  will be held in Stockholm, Sweden, June 27 - July 2. The conference will feature an exciting scientific program including scientific tracks, posters, demonstrations, and featuring ten internationally renowned keynote presenters. Go the ISMB 2009 website |
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We are happy to announce that our Reflect Team is the winner of the Elsevier Grand Challenge!! The competition invited researchers to prototype tools dealing with the ever-increasing amount of online life sciences information. The first and second prize winners were announced at the Experimental Biology conference in New Orleans and chosen from four finalist teams. Each of the four Grand Challenge finalists gave a demonstration of their tool and responded to questions from the panel of judges and an audience of life science researchers. More can be found here: The Elsevier Grand Challenge
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Martini: Finding Enhanced Keywords and Classifying Documents by Comparing Gene Sets |
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We wish to announce Martini (http://martini.embl.de), a new, free service that gives detailed insight into biological function by comparing sets of genes from high-throughput experiments (e.g., siRNA or microarrays). Using Martini is easy: just paste in two sets of genes and Martini automatically finds all PubMed abstracts associated with each gene, and finds biologically relevant keywords in each abstract. Martini then returns keywords that are significantly over-represented in either of the two gene sets.
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OnTheFly server available |
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Automated document-based text tagging, data linking and network generation with OnTheFly
OnTheFly is a web-based java applet application that applies biological named entity recognition with informative popup windows to in Microsoft Word, Microsoft Excel, PDF and plain text files. These files are converted by a commercially available converter into the HTML format and then send to the previously describe Reflect server, which highlights bioentities like genes, proteins and chemical identifiers, and dynamically inserts Java script code to popup a summary window. The latter provides an overview of the most relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to more detailed resources such as literature databases. The bioentities are automatically recognized using the STITCH database dictionaries. By using the STITCH resources, the OnTheFly server can extract the protein-protein, protein-chemical and chemical-chemical networks of recognised genes or proteins that belong to one or even a set of given documents. 
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bioalma launched public Novo|seek server |
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New search site for life science data Bioalma launched novo|seek which is a free information extraction system for searching the published knowledge in biomedical literature. The search engine is based on bioalma's experience of biomedical text analysis technology, like the KnowledgeServer (AKS). Some of the key features are: - Extracts information for key biomedical concepts like diseases, drugs, chemicals compounds, symptoms or genes.
- Highlights relevant biomedical concepts in the text.
- Easy filtering of results.
- Links to relevant external chemical and biological information.
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