NTTMU-SCHEMA BeCalm API in BioCreative V.5

With the emerging of new experimental techniques, there has been a remarkable increase in the amount of available biomedical data. Processing and mining large volumes of data in chemistry has now presented a challenging issue. In order to deal with the challenge, we developed SCHEMA (Spark-based CHEMicAl entity recognizer), a robust and efficient chemical entity recognition system on top of Apache Spark. SCHEMA is developed by following the asynchronous queue design pattern, which has been employed in service-oriented architecture for providing scalable and resilient services. SCHEMA that can retrieve patents in a form of unstructured free text from different websites and recognize chemical named entities described in them. To programmatically interact with SCHEMA, a restful Web application programming interface is provided. By using the custom request tests of the BeCalm (Biomedical annotation metaserver) platform, the test results illustrated that SCHEMA can process 5,000 patients within 5 minutes, indicating an average of only 0.06 second for processing one patent including the data fetch and analysis time.