Line C. Pouchard

The Earth System Grid: Supporting the Next Generation of Climate Modeling Research

Understanding the Earths climate system and how it might be changing is a preeminent scientific challenge. Global climate models are used to simulate past, present, and future climates, and experiments are executed continuously on an array of distributed supercomputers. The resulting data archive, spread over several sites, currently contains upwards of 100 TB of simulation data and is growing rapidly. Looking toward mid-decade and beyond, we must anticipate and prepare for distributed climate research data holdings of many petabytes. The Earth System Grid (ESG) is a collaborative interdisciplinary project aimed at addressing the challenge of enabling management, discovery, access, and analysis of these critically important datasets in a distributed and heterogeneous computational environment. The problem is fundamentally a Grid problem. Building upon the Globus toolkit and a variety of other technologies, ESG is developing an environment that addresses authentication, authorization for data access, large-scale data transport and management, services and abstractions for high-performance remote data access, mechanisms for scalable data replication, cataloging with rich semantic and syntactic information, data discovery, distributed monitoring, and Web-based portals for using the system.

Automatic tag recommendation for metadata annotation using probabilistic topic modeling

The increase of the complexity and advancement in ecological and environmental sciences encourages scientists across the world to collect data from multiple places, times, and thematic scales to verify their hypotheses. Accumulated over time, such data not only increases in amount, but also in the diversity of the data sources spread around the world. This poses a huge challenge for scientists who have to manually search for information. To alleviate such problems, ONEMercury has recently been implemented as part of the DataONE project to serve as a portal for accessing environmental and observational data across the globe. ONEMercury harvests metadata from the data hosted by multiple repositories and makes it searchable. However, harvested metadata records sometimes are poorly annotated or lacking meaningful keywords, which could affect effective retrieval. Here, we develop algorithms for automatic annotation of metadata. We transform the problem into a tag recommendation problem with a controlled tag library, and propose two variants of an algorithm for recommending tags. Our experiments on four datasets of environmental science metadata records not only show great promises on the performance of our method, but also shed light on the different natures of the datasets.

An ontology for scientific information in a Grid environment: the earth system Grid

In the emerging world of Grid Computing, shared computational, data, other distributed resources are becoming available to enable scientific advancement through collaborative research and collaboratories. This paper describes the increasing role of ontologies in the context of Grid Computing for obtaining, comparing and analyzing data. We present ontology entities and a declarative model that provide the outline for an ontology of scientific information. Relationships between concepts are also given. The implementation of some concepts described in this ontology is discussed within the context of the Earth System Grid II (ESG)[1].

Multiagent framework for lean manufacturing

We have developed the manufacturing agent-based emulation system as an open framework for design and analysis of discrete manufacturing systems. MABES currently supports the transition from traditional to lean manufacturing in two major functions: analysis of alternative agent-based scheduling and control approaches that can be implemented across the extended enterprise; and real-time collaboration of design teams during manufacturing line design and analysis stages. MABES bases its support for these functions on two system paradigms: distributed agents and synchronous collaboration.

A generalized topic modeling approach for automatic document annotation

Ecological and environmental sciences have become more advanced and complex, requiring observational and experimental data from multiple places, times, and thematic scales to verify their hypotheses. Over time, such data have not only increased in amount, but also in diversity and heterogeneity of the data sources that spread throughout the world. This heterogeneity poses a huge challenge for scientists who have to manually search for desired data. ONEMercury has recently been implemented as part of the DataONE project to alleviate such problems and to serve as a portal for accessing environmental and observational data across the globe. ONEMercury harvests metadata records from multiple archives and repositories, and makes them searchable. However, harvested metadata records sometimes are poorly annotated or lacking meaningful keywords, which could impede effective retrieval. We propose a methodology that learns the annotation from well-annotated collections of metadata records to automatically annotate poorly annotated ones. The problem is first transformed into the tag recommendation problem with a controlled tag library. Then, two variants of an algorithm for automatic tag recommendation are presented. The experiments on four datasets of environmental science metadata records show that our methods perform well and also shed light on the natures of different datasets. We also discuss relevant topics such as using topical coherence to fine-tune parameters and experiments on cross-archive annotation.

A Linked Science investigation: enhancing climate change data discovery with semantic technologies

Linked Science is the practice of inter-connecting scientific assets by publishing, sharing and linking scientific data and processes in end-to-end loosely coupled workflows that allow the sharing and re-use of scientific data. Much of this data does not live in the cloud or on the Web, but rather in multi-institutional data centers that provide tools and add value through quality assurance, validation, curation, dissemination, and analysis of the data. In this paper, we make the case for the use of scientific scenarios in Linked Science. We propose a scenario in river-channel transport that requires biogeochemical experimental data and global climate-simulation model data from many sources. We focus on the use of ontologies—formal machine-readable descriptions of the domain—to facilitate search and discovery of this data. Mercury, developed at Oak Ridge National Laboratory, is a tool for distributed metadata harvesting, search and retrieval. Mercury currently provides uniform access to more than 100,000 metadata records; 30,000 scientists use it each month. We augmented search in Mercury with ontologies, such as the ontologies in the Semantic Web for Earth and Environmental Terminology (SWEET) collection by prototyping a component that provides access to the ontology terms from Mercury. We evaluate the coverage of SWEET for the ORNL Distributed Active Archive Center (ORNL DAAC).

SWEET ontology coverage for earth system sciences

Scientists in the Earth and Environmental Sciences (EES) domain increasingly use ontologies to analyze and integrate their data. For example, the NASA’s SWEET ontologies (Semantic Web for Earth and Environmental Terminology) have become the de facto standard ontologies to represent the EES domain formally (Raskin 2010). Now we must develop principled ways both to evaluate existing ontologies and to ascertain their quality in a quantitative manner. Existing literature describes many potential quality metrics for ontologies. Among these metrics is the coverage metric, which approximates the relevancy of an ontology to a corpus (Yao et al. (PLoS Comput Biol 7(1):e1001055+, 2011)). This paper has three primary contributions to the EES domain: (1) we present an investigation of the applicability of existing coverage techniques for the EES domain; (2) we present a novel expansion of existing techniques that uses thesauri to generate equivalence and subclass axioms automatically; and (3) we present an experiment to establish an upper-bound coverage expectation for the SWEET ontologies against real-world EES corpora from DataONE (Michener et al. (Ecol Inform 11:5–15, 2012)), and a corpus designed from research articles to specifically match the topics covered by the SWEET ontologies. This initial evaluation suggests that the SWEET ontology can accurately represent real corpora within the EES domain.

Data Grid discovery and Semantic Web technologies for the earth sciences

This paper describes scientific data discovery for the earth sciences in the context of data Grids and Grid computing. Requirements and use cases illustrate current challenges due to size, distribution, and minimal annotation of data. Semantics and the characterization of provenance in large data archives are discussed. The targeted community of users is also discussed. Solutions implemented by the Earth System Grid and the National Environment Research Council Data Grid include a prototype ontology, metadata schemas, search mechanisms, and discovery architectures. The use of Semantic Web technologies has facilitated the development of meaningful annotations of data content and opened the door to data discovery in federated systems.

ISO 18629 PSL : A STANDARDISED LANGUAGE FOR SPECIFYING AND EXCHANGING PROCESS INFORMATION

Abstract As enterprise integration increases, developers face increasingly complex problems related to interoperability. When enterprises collaborate, a common frame of reference or at least a common terminology is necessary for human-to-human, human-to-machine, and machine-to-machine communication. Ontology engineering offers a direction towards solving the inter-operability problems brought about by semantic obstacles related to the definitions of business terms and software classes. Ontology engineering is a set of tasks related to the development of ontologies for a particular domain. This paper is aimed at presenting the approach of ISO 18629, i.e. the Process Specification Language (PSL), to this problem. In the first part, the architecture of the standard is described, with the main features of the language. Then, the problems of the interoperability with PSL and the conformance to the standard are presented. The paper ends with an example showing the use of the standard for interoperability.

Data storage and sharing for the long tail of science

Research data infrastructure such as storage must now accommodate new requirements resulting from trends in research data management that require researchers to store their data for the long term and make it available to other researchers. We propose Data Depot, a system and service that provides capabilities for shared space within a group, shared applications, flexible access patterns and ease of transfer at Purdue University. We evaluate Depot as a solution for storing and sharing multi-terabytes of data produced in the long tail of science with a use case in soundscape ecology studies from the Human-Environment Modeling and Analysis Laboratory. We observe that with the capabilities enabled by Data Depot, researchers can easily deploy fine-grained data access control, manage data transfer and sharing, as well as integrate their workflows into a High Performance Computing environment.