ality Assurance of Bioinformatics Soware: A Case Study of Testing a Biomedical Text Processing Tool Using Metamorphic Testing∗

Bioinformatics so‰ware plays a very important role in making critical decisions within many areas including medicine and health care. However, most of the research is directed towards developing tools, and liŠle time and e‚ort is spent on testing the so‰ware to assure its quality. In testing, a test oracle is used to determine whether a test is passed or failed during testing, and unfortunately, for much of bioinformatics so‰ware, the exact expected outcomes are not well de€ned. Œus, the main challenge associated with conducting systematic testing on bioinformatics so‰ware is the oracle problem. Metamorphic testing (MT) is a technique used to test programs that face the oracle problem. MT uses metamorphic relations (MRs) to determine whether a test has passed or failed and speci€es how the output should change according to a speci€c change made to the input. In this work, we useMT to test LingPipe, a tool for processing text using computational linguistics, o‰en used in bioinformatics for bio-entity recognition from biomedical literature. First, we identify a set of MRs for testing any bio-entity recognition program. Œen we develop a set of test cases that can be used to test LingPipe’s bio-entity recognition functionality using these MRs. To evaluate the e‚ectiveness of this testing process, we automatically generate a set of faulty versions of LingPipe. According to our analysis of the experimental results, we observe that our MRs can detect the majority of these faulty versions, which shows the utility of this testing technique for quality assurance of bioinformatics so‰ware.