Quality Assurance of Bioinformatics Software: A Case Study of Testing a Biomedical Text Processing Tool Using Metamorphic Testing.

Bioinformatics software plays a very important role in making criticaldecisions within many areas including medicine and health care. However, mostof the research is directed towards developing tools, and little time andeffort is spent on testing the software to assure its quality. In testing, atest oracle is used to determine whether a test is passed or failed duringtesting, and unfortunately, for much of bioinformatics software, the exactexpected outcomes are not well defined. Thus, the main challenge associatedwith conducting systematic testing on bioinformatics software is the oracleproblem.

Metamorphic testing (MT) is a technique used to test programs that face theoracle problem. MT uses metamorphic relations (MRs) to determine whether a testhas passed or failed and specifies how the output should change according to aspecific change made to the input. In this work, we use MT to test LingPipe, atool for processing text using computational linguistics, often used inbioinformatics for bio-entity recognition from biomedical literature.

First, we identify a set of MRs for testing any bio-entity recognitionprogram. Then we develop a set of test cases that can be used to testLingPipe's bio-entity recognition functionality using these MRs. To evaluatethe effectiveness of this testing process, we automatically generate a set offaulty versions of LingPipe. According to our analysis of the experimentalresults, we observe that our MRs can detect the majority of these faultyversions, which shows the utility of this testing technique for qualityassurance of bioinformatics software.