Exploiting Conceptual Modeling for Searching Genomic Metadata: A Quantitative and Qualitative Empirical Study

Abstract

Providing a common data model for the metadata of several heterogenous genomic data sources is hard, as they do not share any standard or agreed practice for metadata description. Two years ago we managed to discover a subset of common metadata present in most sources and to organize it as a smart genomic conceptual model (GCM); the model has been instrumental to our efforts in the development of a major software pipeline for data integration. More recently, we developed a user-friendly search interface, based on a simplified version of GCM. In this paper, we report our evaluation of the effectiveness of this new user interface. Specifically, we present the results of a compendious empirical study to answer the research question: How well is such a simple interface understood by a standard user? The target of this study is a mixed population, composed by biologists, bioinformaticians and computer scientists. The result of our empirical study shows that the users were successful in producing search queries starting from their natural language description, as they did it with good accuracy and small error rate. The study also shows that most users were generally satisfied; it provides indications on how to improve our search system and how to continue our effort in integration of genomic sources. We are consequently adapting the user interface, that will be soon opened to public use.

GenoSurf: metadata driven semantic search system for integrated genomic datasets

“…Evaluating an integrated platform for the retrieval of genomic data files is a challenging task. We invited about 60 users, expert of the domain but typically at their first encounter with GenoSurf, to evaluate several aspects of our platform (46). We received 40 complete responses; these helped us to assess the usability and usefulness of our system.…”

Model, Integrate, Search... Repeat: A Sound Approach to Building Integrated Repositories of Genomic Data

“…This interface was evaluated by running an extended empirical study whose participants were knowledgeable in Biology and Computer Science. We collected many relevant insights related to the data scouting and extraction habits of different user profiles [9]. The frameworks and tools described in this section are included in a follow-up project, to be exploited for providing biologists and clinicians with a complete data extraction/analysis environment [21] that is: (i) guided by a conversational interface; (ii) equipped with a "marketplace" of ready-to-use best practices; we thus aim to break down the technological barriers that are currently hindering the practical adoption of our systems.…”

Empowering Virus Sequence Research Through Conceptual Modeling

“…Lessons learnt from that experience include the benefits of having: a central fact entity that helps structuring the search; a number of surrounding dimensions capturing organization, biological and experimental conditions to describe the facts; a direct representation of a data structure suitable for conceptually organizing genomic elements and their describing information. a data layout that is easy to learn for first-time users and that helps the answering of practical questions (demonstrated in [4]).…”