Natalia Kwasnikowska

A Formal Account of the Open Provenance Model

On the Web, where resources such as documents and data are published, shared, transformed, and republished, provenance is a crucial piece of metadata that would allow users to place their trust in the resources they access. The open provenance model (OPM) is a community data model for provenance that is designed to facilitate the meaningful interchange of provenance information between systems. Underpinning OPM is a notion of directed graph, where nodes represent data products and processes involved in past computations and edges represent dependencies between them; it is complemented by graphical inference rules allowing new dependencies to be derived. Until now, however, the OPM model was a purely syntactical endeavor. The present article extends OPM graphs with an explicit distinction between precise and imprecise edges. Then a formal semantics for the thus enriched OPM graphs is proposed, by viewing OPM graphs as temporal theories on the temporal events represented in the graph. The original OPM inference rules are scrutinized in view of the semantics and found to be sound but incomplete. An extended set of graphical rules is provided and proved to be complete for inference. The article concludes with applications of the formal semantics to inferencing in OPM graphs, operators on OPM graphs, and a formal notion of refinement among OPM graphs.

Mapping the NRC Dataflow Model to the Open Provenance Model

The Open Provenance Model (OPM) has recently been proposed as an exchange framework for workflow provenance information. In this paper we show how the NRC data model for workflow repositories can be mapped to the OPM . Our mapping includes such features as complex data flow in an execution of a workflow; different workflows in the repository that call each other; and the tracking of subvalues of complex data structures in the provenance information. Because the NRC dataflow model has been formally specified, also our mapping can be formally specified; in particular, it can be automated. To facilitate this specification, we present an adapted set-theoretic formalization of the basic OPM .

Petri net + nested relational calculus = dataflow

In this paper we propose a formal, graphical workflow language for dataflows, i.e., workflows where large amounts of complex data are manipulated and the structure of the manipulated data is reflected in the structure of the workflow. It is a common extension of Petri nets, which are responsible for the organization of the processing tasks, and Nested relational calculus, which is a database query language over complex objects, and is responsible for handling collections of data items (in particular, for iteration) and for the typing system. We demonstrate that dataflows constructed in hierarchical manner, according to a set of refinement rules we propose, are sound: initiated with a single token (which may represent a complex scientific data collection) in the input node, terminate with a single token in the output node (which represents the output data collection). In particular they always process all of the input data, leave no ”debris data” behind and the output is always eventually computed.

A formal model of dataflow repositories

Dataflow repositories are databases containing dataflows and their different runs. We propose a formal conceptual data model for such repositories. Our model includes careful formalisations of such features as complex data manipulation, external service calls, subdataflows, and the provenance of output values.

Modeling and storing scientific protocols

We propose an abstract model for scientific protocols, where several atomic operators are proposed for protocol composition We distinguish two different layers associated with scientific protocols: design and implementation, and discuss the mapping between them We illustrate our approach with a representative example and describe ProtocolDB, a scientific protocol repository currently in development Our approach benefits scientists by allowing the archiving of scientific protocols with the collected data sets to constitute a scientific portfolio for the laboratory to query, compare and revise protocols.

Querying an Integrated Complex-Object Dataflow Database

We consider an integrated complex-object dataflow database in which multiple dataflow specifications can be stored, together with multiple executions of these dataflows, including the complex-object data that are involved, and annotations. We focus on dataflow applications frequently encountered in the scientific community, involving the manipulation of data with a complex-object structure combined with service calls, which can be either internal or external. Internal services are dataflows acting as a subprogram of an other dataflow, whereas external services are modeled as functions with a possibly non-deterministic behavior. Dataflow specifications are expressed in a high-level programming language based on the nested relational calculus, the operators of which provide the right “glue” needed to combine different service calls into a complex-object dataflow. All entities involved, whether complex-objects, dataflow executions or dataflow specifications, are first-class citizens of the integrated database: they are all data. We discuss how such dataflow repositories can be queried in a variety of ways, including provenance queries. We show that a modern SQL platform with support for (external) routines and SQL/XML suffices to support all types of dataflow repository queries.