The UIMA miRNA detector was a part of UIMA-HPC project at Fraunhofer SCAI. UIMA miRNA detector is a UIMA pipelet and its function is to identify microRNA mentions from free text biomedical literature using text mining techniques. It is now integrated with SCAIView: The knowledge discovery framework. SCAIView is an advanced semantic search engine that addresses questions of interest to general biomedical and life science researchers.
miRNA detector pipelet is developed using Apache UIMA framework within a Java application. The pipelet has two chief components – 1) Collection Reader, and 2) Analysis Engine – Annotator. Collection Reader: The Collection Reader loads the input “.xmi” file into a CAS (Common Annotation Structure) object. Analysis Enginer: This CAS object is then received by the AE (Analysis Engine) component, a UIMA annotator, which detects miRNA mentions, normalizes them and links them to standardized identifier from miRBase.
For example, consider the below given file as the input file for the miRNA detector application.
