IU Chemical Informatics Journal Club

This is a short application note published on Oxford Bioinformatics. The paper described U-Compare, a system based on UIMA(Unstructured Information Management Architecture), and offers out-of-box text mining tools and evaluation platforms. The U-Compare workflow management tool allows easy creation of workflow with drag-and-drops. They also provide a special parallel flow component, with which workflow comparison can be executed. A common task in text mining research is evaluation. U-Compare runs the evaluation process automatically after an execution of a workflow. Results can also be visualized, using various visualization components, even some complex ones. In addition, U-Compare provide programming interfaces (APIs), which allows developers access to workflows via I/O streams. Developers' native tools can be integrated into U-Compare workflow via the APIs.

The paper itself is not very interesting, yet I found that U-Compare and UIMA could be very good tools in bio/chem related text mining project. Right now our research on text mining is project based, and lack of a good platform for everyone to work on. I had tried using other scientific workflow tools such as Taverna, but because those tools are not aiming at text-mining researches, there is also a high barrier. I am planning to install UIMA, U-Compare with other UIMA components locally to facilitate our research in text mining.