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bioinformatics, text mining »

[16 Oct 2009 | No Comment | ]

Recent disease networks studies have demonstrated that the integration of biological knowledge from several sources could lead to biomedical discovery. In this context, it is particularly attractive to connect the dots using the wealth of knowledge in the published literature. In this work we present a web-based open source resource for supporting distributed collaborative annotation efforts. Key assertions are extracted from the literature based on a user query, automatically annotated and mapped to external resources. These annotated extracts can be further corrected and enhanced through user manual intervention via a simple web interface. The results are then converted into Linked Data format.

text mining »

[2 Oct 2009 | No Comment | ]

The Elsevier Grand Challenge came to an end. An the winner is Reflect, a proposal from my ex-colleagues at EMBL, including my dear friend Evangelos, so congratulations to them. Reflect is very well conceived and perfectly implemented, people are already using it, so I think this was the main reason it was the first option for the jury.
A close second was Coraal, probably my favourite in the last stage of the challenge, with its use of semantic technologies and the Exhibit framework for visualization.
Both proposals are quite complementary to our …