Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions

trackr: A Framework for Enhancing Discoverability and Reproducibility of Data Visualizations and Other Artifacts in R

Research is an incremental, iterative process, with new results relying and building upon previous ones. Scientists need to find, retrieve, understand, and verify results in order to confidently extend them, even when the results are their own. We present the trackr framework for organizing, automatically annotating, discovering, and retrieving results. We identify sources of automatically extractable metadata for computational results, and we define an extensible system for organizing, annotating, and searching for results based on these and other metadata. We present an open-source implementation of these concepts for plots, computational artifacts, and woven dynamic reports generated in the R statistical computing language

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources. Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous data stored at different locations. Therefore, we develop a semantic problem solving environment (SPSE) that allows parasitologists to query their lab data integrated with public resources using ontologies. An ontology specifies a common vocabulary and formal relationships among the terms that describe an organism, and experimental data and processes in this case. SPSE supports capturing and querying provenance information, which is metadata on the experimental processes and data recorded for reproducibility, and includes a visual query-processing tool to formulate complex queries without learning the query language syntax. We demonstrate the significance of SPSE in identifying gene knockout targets for T. cruzi. The overall goal of SPSE is to help researchers discover new or existing knowledge that is implicitly present in the data but not always easily detected. Results demonstrate improved usefulness of SPSE over existing lab systems and approaches, and support for complex query design that is otherwise difficult to achieve without the knowledge of query language syntax

A Trichotomy for Regular Trail Queries

Regular path queries (RPQs) are an essential component of graph query languages. Such queries consider a regular expression r and a directed edge-labeled graph G and search for paths in G for which the sequence of labels is in the language of r. In order to avoid having to consider infinitely many paths, some database engines restrict such paths to be trails, that is, they only consider paths without repeated edges. In this paper we consider the evaluation problem for RPQs under trail semantics, in the case where the expression is fixed. We show that, in this setting, there exists a trichotomy. More precisely, the complexity of RPQ evaluation divides the regular languages into the finite languages, the class T_tract (for which the problem is tractable), and the rest. Interestingly, the tractable class in the trichotomy is larger than for the trichotomy for simple paths, discovered by Bagan et al. [Bagan et al., 2013]. In addition to this trichotomy result, we also study characterizations of the tractable class, its expressivity, the recognition problem, closure properties, and show how the decision problem can be extended to the enumeration problem, which is relevant to practice

Algorithms for Provisioning Queries and Analytics

Provisioning is a technique for avoiding repeated expensive computations in what-if analysis. Given a query, an analyst formulates $k$ hypotheticals, each retaining some of the tuples of a database instance, possibly overlapping, and she wishes to answer the query under scenarios, where a scenario is defined by a subset of the hypotheticals that are "turned on". We say that a query admits compact provisioning if given any database instance and any $k$ hypotheticals, one can create a poly-size (in $k$) sketch that can then be used to answer the query under any of the $2^{k}$ possible scenarios without accessing the original instance. In this paper, we focus on provisioning complex queries that combine relational algebra (the logical component), grouping, and statistics/analytics (the numerical component). We first show that queries that compute quantiles or linear regression (as well as simpler queries that compute count and sum/average of positive values) can be compactly provisioned to provide (multiplicative) approximate answers to an arbitrary precision. In contrast, exact provisioning for each of these statistics requires the sketch size to be exponential in $k$. We then establish that for any complex query whose logical component is a positive relational algebra query, as long as the numerical component can be compactly provisioned, the complex query itself can be compactly provisioned. On the other hand, introducing negation or recursion in the logical component again requires the sketch size to be exponential in $k$. While our positive results use algorithms that do not access the original instance after a scenario is known, we prove our lower bounds even for the case when, knowing the scenario, limited access to the instance is allowed