Magesh Jayapandian

Making database systems usable

Database researchers have striven to improve the capability of a database in terms of both performance and functionality. We assert that the usability of a database is as important as its capability. In this paper, we study why database systems today are so difficult to use. We identify a set of five pain points and propose a research agenda to address these. In particular, we introduce a presentation data model and recommend direct data manipulation with a schema later approach. We also stress the importance of provenance and of consistency across presentation models.

Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together

Protein interaction data exists in a number of repositories. Each repository has its own data format, molecule identifier and supplementary information. Michigan Molecular Interactions (MiMI) assists scientists searching through this overwhelming amount of protein interaction data. MiMI gathers data from well-known protein interaction databases and deep-merges the information. Utilizing an identity function, molecules that may have different identifiers but represent the same real-world object are merged. Thus, MiMI allows the users to retrieve information from many different databases at once, highlighting complementary and contradictory information. To help scientists judge the usefulness of a piece of data, MiMI tracks the provenance of all data. Finally, a simple yet powerful user interface aids users in their queries, and frees them from the onerous task of knowing the data format or learning a query language. MiMI allows scientists to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI is part of the National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: .

Michigan molecular interactions r2: from interacting proteins to pathways.

Molecular interaction data exists in a number of repositories, each with its own data format, molecule identifier and information coverage. Michigan molecular interactions (MiMI) assists scientists searching through this profusion of molecular interaction data. The original release of MiMI gathered data from well-known protein interaction databases, and deep merged this information while keeping track of provenance. Based on the feedback received from users, MiMI has been completely redesigned. This article describes the resulting MiMI Release 2 (MiMIr2). New functionality includes extension from proteins to genes and to pathways; identification of highlighted sentences in source publications; seamless two-way linkage with Cytoscape; query facilities based on MeSH/GO terms and other concepts; approximate graph matching to find relevant pathways; support for querying in bulk; and a user focus-group driven interface design. MiMI is part of the NIHs; National Center for Integrative Biomedical Informatics (NCIBI) and is publicly available at: http://mimi.ncibi.org.

Automated creation of a forms-based database query interface

Forms-based query interfaces are widely used to access databases today. The design of a forms-based interface is often a key step in the deployment of a database. Each form in such an interface is capable of expressing only a very limited range of queries. Ideally, the set of forms as a whole must be able to express all possible queries that any user may have. Creating an interface that approaches this ideal is surprisingly hard. In this paper, we seek to maximize the ability of a forms-based interface to support queries a user may ask, while bounding both the number of forms and the complexity of any one form. Given a database schema and content we present an automated technique to generate a good set of forms that meet the above desiderata. While a careful analysis of real or expected query workloads are useful in designing the interface, these query sets are often unavailable or hard to obtain prior to the database even being deployed. Hence generating a good set of forms just using the database itself is a challenging yet important problem. Our experimental analysis shows that our techniques can create a reasonable set of forms, one that can express 60--90% of user queries, without any input from the database administrator. Human experts, without support from software such as ours, are often unable to support as high a fraction of user queries.

Expressive query specification through form customization

A form-based query interface is usually the preferred means to provide an unsophisticated user access to a database. Not only is such an interface easy to use, requiring no technical training, but it also requires little or no knowledge of how the data is structured in the database. However, a typical form is static and can express only a very limited set of queries, Without room for change, query specification is limited by the expertise and vision of the interface developer at the time the form was created. If an available form cannot express a desired query, the user is stuck. In this paper, we propose a mechanism to let a user modify an existing form to express the desired query. These modifications are themselves specified through filling forms to create an expression in an underlying form manipulation expression language we define. The technical sophistication required to modify forms is not much greater than form filling. We have developed a form editor that implements this form manipulation language. We have also developed a query generator that modifies the forms original query based on a users changes. We show, by means of a controlled user study, that this tool provides an effective means for specifying complex queries.

Using Delay to Defend Against Database Extraction

For many data providers, the “crown jewels” of their business are the data that they have organized. If someone could copy their entire database, it would be a competitive catastrophe. Yet, a data provider is in the business of providing data, so access to the database cannot be restricted entirely. How is the data provider to permit legitimate access to users who request access to small portions of the database while protecting the database from wholesale copying?