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Register a new userResearch Traceability using Provenance Services for Biomedical Analysis
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Added by
Richard McClatchey
Publication date
2014
fields
Informatics Engineering
and research's language is
English
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We outline the approach being developed in the neuGRID project to use provenance management techniques for the purposes of capturing and preserving the provenance data that emerges in the specification and execution of workflows in biomedical analyses. In the neuGRID project a provenance service has been designed and implemented that is intended to capture, store, retrieve and reconstruct the workflow information needed to facilitate users in conducting user analyses. We describe the architecture of the neuGRID provenance service and discuss how the CRISTAL system from CERN is being adapted to address the requirements of the project and then consider how a generalised approach for provenance management could emerge for more generic application to the (Health)Grid community.
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We outline the approach being developed in the neuGRID project to use provenance management techniques for the purposes of capturing and preserving the provenance data that emerges in the specification and execution of workflows in biomedical analyses. In the neuGRID project a provenance service has been designed and implemented that is intended to capture, store, retrieve and reconstruct the workflow information needed to facilitate users in conducting user analyses. We describe the architecture of the neuGRID provenance service and discuss how the CRISTAL system from CERN is being adapted to address the requirements of the project and then consider how a generalised approach for provenance management could emerge for more generic application to the (Health)Grid community.
Provenance is information recording the source, derivation, or history of some information. Provenance tracking has been studied in a variety of settings; however, although many design points have been explored, the mathematical or semantic foundations of data provenance have received comparatively little attention. In this paper, we argue that dependency analysis techniques familiar from program analysis and program slicing provide a formal foundation for forms of provenance that are intended to show how (part of) the output of a query depends on (parts of) its input. We introduce a semantic characterization of such dependency provenance, show that this form of provenance is not computable, and provide dynamic and static approximation techniques.
As users become confronted with a deluge of provenance data, dedicated techniques are required to make sense of this kind of information. We present Aggregation by Provenance Types, a provenance graph analysis that is capable of generating provenance graph summaries. It proceeds by converting provenance paths up to some length k to attributes, referred to as provenance types, and by grouping nodes that have the same provenance types. The summary also includes numeric values representing the frequency of nodes and edges in the original graph. A quantitative evaluation and a complexity analysis show that this technique is tractable; with small values of k, it can produce useful summaries and can help detect outliers. We illustrate how the generated summaries can further be used for conformance checking and visualization.
Scientific workflow systems increasingly store provenance information about the module executions used to produce a data item, as well as the parameter settings and intermediate data items passed between module executions. However, authors/owners of workflows may wish to keep some of this information confidential. In particular, a module may be proprietary, and users should not be able to infer its behavior by seeing mappings between all data inputs and outputs. The problem we address in this paper is the following: Given a workflow, abstractly modeled by a relation R, a privacy requirement Gamma and costs associated with data. The owner of the workflow decides which data (attributes) to hide, and provides the user with a view R which is the projection of R over attributes which have not been hidden. The goal is to minimize the cost of hidden data while guaranteeing that individual modules are Gamma -private. We call this the secureview problem. We formally define the problem, study its complexity, and offer algorithmic solutions.
Explaining why an answer is in the result of a query or why it is missing from the result is important for many applications including auditing, debugging data and queries, and answering hypothetical questions about data. Both types of questions, i.e., why and why-not provenance, have been studied extensively. In this work, we present the first practical approach for answering such questions for queries with negation (first-order queries). Our approach is based on a rewriting of Datalog rules (called firing rules) that captures successful rule derivations within the context of a Datalog query. We extend this rewriting to support negation and to capture failed derivations that explain missing answers. Given a (why or why-not) provenance question, we compute an explanation, i.e., the part of the provenance that is relevant to answer the question. We introduce optimizations that prune parts of a provenance graph early on if we can determine that they will not be part of the explanation for a given question. We present an implementation that runs on top of a relational database using SQL to compute explanations. Our experiments demonstrate that our approach scales to large instances and significantly outperforms an earlier approach which instantiates the full provenance to compute explanations.
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