This paper describes a usability evaluation study of an innovative first generation system (Data Dig) designed to retrieve phenotypic data from the large SFARI data set of 2700 families each of which has one child affected with autism spectrum disorder. The usability methods included a cognitive walkthrough and usability testing. Although the subjects were able to learn to use the system, more than 50 usability problems of varying severity were noted. The problems with the greatest frequency resulted from users being unable to understand meanings of variables, filter categories correctly, use the Boolean filter, and correctly interpret the feedback provided by the system. Subjects had difficulty forming a mental model of the organizational system underlying the database. This precluded them from making informed navigation choices while formulating queries. Clinical research informatics is a new and immensely promising discipline. However in its nascent stage, it lacks a stable interaction paradigm to support a range of users on pertinent tasks. This presents great opportunity for researchers to further this science by harnessing the powers of user-centered iterative design.