No abstract

Curated databases in bioinformatics and other disciplines are the result of a great deal of manual annotation, correction and transfer of data from other sources. Provenance information concerning the creation, attribution, or version history of such data is crucial for assessing its integrity and scientific value. General purpose database systems provide little support for tracking provenance, especially when data moves among databases. This paper investigates general-purpose techniques for recording provenance for data that is copied among databases. We describe an approach in which we track the user's actions while browsing source databases and copying data into a curated database, in order to record the user's actions in a convenient, queryable form. We present an implementation of this technique and use it to evaluate the feasibility of database support for provenance management. Our experiments show that although the overhead of a naïve approach is fairly high, it can be decreased to an acceptable level using simple optimizations.

Abstract. Information concerning the origin of data (that is, its provenance) is important in many areas, especially scientific recordkeeping. Currently, provenance information must be maintained explicitly, by added effort of the database maintainer. Since such maintenance is tedious and error-prone, it is desirable to provide support for provenance in the database system itself. In order to provide such support, however, it is important to provide a clear explanation of the behavior and meaning of existing database operations, both queries and updates, with respect to provenance. In this paper we take the view that a query or update implicitly defines a provenance mapping linking components of the output to the originating components in the input. Our key result is that the proposed semantics are expressively complete relative to natural classes of queries that explicitly manipulate provenance.

Provenance, a form of structured metadata designed to record the origin or source of information, can be instrumental in deciding whether information is to be trusted, how it can be integrated with other diverse information sources, and how to establish attribution of information to authors throughout its history. The PROV set of specifications, produced by the World Wide Web Consortium (W3C), is designed to promote the publication of provenance information on the Web, and offers a basis for interoperability across diverse provenance management systems. The PROV provenance model is deliberately generic and domain-agnostic, but extension mechanisms are available and can be exploited for modelling specific domains. This tutorial provides an account of these specifications. Starting from intuitive and informal examples that present idiomatic provenance patterns, it progressively introduces the relational model of provenance along with the constraints model for validation of provenance documents, and concludes with example applications that show the extension points in use.

No abstract

Nominal logic is an extension of first-order logic which provides a simple foundation for formalizing and reasoning about abstract syntax modulo consistent renaming of bound names (that is, α-equivalence). This article investigates logic programming based on nominal logic. This technique is especially well-suited for prototyping type systems, proof theories, operational semantics rules, and other formal systems in which bound names are present. In many cases, nominal logic programs are essentially literal translations of "paper" specifications. As such, nominal logic programming provides an executable specification language for prototyping, communicating, and experimenting with formal systems.We describe some typical nominal logic programs, and develop the model-theoretic, prooftheoretic, and operational semantics of such programs. Besides being of interest for ensuring the correct behavior of implementations, these results provide a rigorous foundation for techniques for analysis and reasoning about nominal logic programs, as we illustrate via two examples.

Cyclone is a type-safe programming language derived from C. The primary design goal of Cyclone is to let programmers control data representation and memory management without sacrificing type-safety. In this paper, we focus on the region-based memory management of Cyclone and its static typing discipline. The design incorporates several advancements, including support for region subtyping and a coherent integration with stack allocation and a garbage collector. To support separate compilation, Cyclone requires programmers to write some explicit region annotations, but a combination of default annotations, local type inference, and a novel treatment of region effects reduces this burden. As a result, we integrate C idioms in a region-based framework. In our experience, porting legacy C to Cyclone has required altering about 8% of the code; of the changes, only 6% (of the 8%) were region annotations.

Cyclone is a type-safe programming language derived from C. The primary design goal of Cyclone is to let programmers control data representation and memory management without sacrificing type-safety. In this paper, we focus on the region-based memory management of Cyclone and its static typing discipline. The design incorporates several advancements, including support for region subtyping and a coherent integration with stack allocation and a garbage collector. To support separate compilation, Cyclone requires programmers to write some explicit region annotations, but a combination of default annotations, local type inference, and a novel treatment of region effects reduces this burden. As a result, we integrate C idioms in a region-based framework. In our experience, porting legacy C to Cyclone has required altering about 8% of the code; of the changes, only 6% (of the 8%) were region annotations.