We show that relational algebra calculations for incomplete databases, probabilistic databases, bag semantics and whyprovenance are particular cases of the same general algorithms involving semirings. This further suggests a comprehensive provenance representation that uses semirings of polynomials. We extend these considerations to datalog and semirings of formal power series. We give algorithms for datalog provenance calculation as well as datalog evaluation for incomplete and probabilistic databases. Finally, we show that for some semirings containment of conjunctive queries is the same as for standard set semantics.

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services.

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We study in this paper provenance information for queries with aggregation. Provenance information was studied in the context of various query languages that do not allow for aggregation, and recent work has suggested to capture provenance by annotating the different database tuples with elements of a commutative semiring and propagating the annotations through query evaluation. We show that aggregate queries pose novel challenges rendering this approach inapplicable. Consequently, we propose a new approach, where we annotate with provenance information not just tuples but also the individual values within tuples, using provenance to describe the values computation. We realize this approach in a concrete construction, first for "simple" queries where the aggregation operator is the last one applied, and then for arbitrary (positive) relational algebra queries with aggregation; the latter queries are shown to be more challenging in this context. Finally, we use aggregation to encode queries with difference, and study the semantics obtained for such queries on provenance annotated databases.

We state and solve the query reformulation problem for XML publishing in a general setting that allows mixed (XML and relational) storage for the proprietary data and exploits redundancies (materialized views, indexes and caches) to enhance performance. The correspondence between published and proprietary schemas is specified by views in both directions, and the same algorithm performs rewriting-with-views, compositionwith-views, or the combined effect of both, unifying the Global-As-View and Local-As-View approaches to data integration. We prove a completeness theorem which guarantees that under certain conditions, our algorithm will and a minimal reformulation if one exists. Moreover, we identify conditions when this algorithm achieves optimal complexity bounds. We solve the reformulation problem for constraints by exploiting a reduction to the problem of query reformulation.

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The syntax of comprehensions is very close to the syntax of a number of practical database query languages and is, we believe, a better starting point than first-order logic for the development of database languages. We give an informal account of a language based on comprehension syntax that deals uniformly with a variety of collection types; it also includes pattern matching, variant types and function definition. We show, again informally, how comprehension syntax is a natural fragment of structural recursion, a much more powerful programming paradigm for collection types. We also show that a very small "abstract syntax language" can serve as a basis for the implementation and optimization of comprehension syntax.

Many advanced data management operations (e.g., incremental maintenance, trust assessment, debugging schema mappings, keyword search over databases, or query answering in probabilistic databases), involve computations that look at how a tuple was produced, e.g., to determine its score or existence. This requires answers to queries such as, "Is this data derivable from trusted tuples?"; "What tuples are derived from this relation?"; or "What score should this answer receive, given initial scores of the base tuples?". Such questions can be answered by consulting the provenance of query results.In recent years there has been significant progress on formal models for provenance. However, the issues of provenance storage, maintenance, and querying have not yet been addressed in an application-independent way. In this paper, we adopt the most general formalism for tuple-based provenance, semiring provenance. We develop a query language for provenance, which can express all of the aforementioned types of queries, as well as many more; we propose storage, processing and indexing schemes for data provenance in support of these queries; and we experimentally validate the feasibility of provenance querying and the benefits of our indexing techniques across a variety of application classes and queries.