Metadata Framework Research Articles

A novel semantic framework for toxicogenomics

Complex biological data stored in bioinformatics databases often require additional knowledge to specify and constrain the values held in a particular database. One method of capturing knowledge within bioinformatics applications and databases is the use of ontologies. Existing ontologies can model components of environmental risk and corresponding events, but cannot synthesize them or describe the broader framework of ideas used to conceptualize and study environmental risk. Environmental Risk Ontology (ERO) aims to synthesize and describe a framework for investigating environmental risk. ERO is intended as a metadata framework for data and literature curation and data mining. In this review, we summarize and describe the basic public databases available for toxicogenomics and present a novel approach that uses a semantic knowledge base — which also organizes the literature in a growing, comprehensive bibliographic database — concerning environmental risk and toxicogenomics.

Construct Ontology-based Enterprise Information Metadata Framework

The standardization and unification of metadata has a significant impact on enterprise’s information integration and sharing. In this paper, information engineering and cluster analysis method is used to define the concepts and relationships of enterprises business meta-data, after that an algorithm is designed to map meta-data to OWL DL ontology and construct ontology-based enterprise information meta-data framework. The proposed framework can unify the definition of enterprise business information and provide a basis for information exchange and system interoperation, as well as provide a premise for knowledge management.

Data error prevention and cleansing: A comprehensive guide for instructors of statistics and their students

The proper analysis of data is predicated on the existence of a data set containing valid responses. There are many sound techniques that should be employed to minimize data errors, and to cleanse data sets. The purpose of this article is to provide instructors and their students with an overview of the mechanics of data capture; the metadata framework; outlier detection and treatment; and contemporary solutions for missing data.

A semantic annotation tool for hydrologic sciences

Semantic annotations are playing an increasingly important role in the world of metadata, more specifically when dealing with semantic heterogeneities between information systems. The need to bring together disparate data sources (in terms of syntax and semantics) so they can be searched simultaneously from a single search environment has become one of the most challenging tasks in developing information systems that span multiple communities as is common in the geosciences. The key problem lies in the legacy information systems, in which, at the time of development, each system used (and continues to use) its own semantic framework to identify variable codes and names, as well as annotating the collected data with metadata. This lack of a common metadata framework as well the uncoordinated use of descriptors and controlled vocabularies has led to a situation in which synonyms and hyponyms abound. Experience has shown that a centralized system with just one vocabulary for all is not feasible. Rather, in order to overcome these discrepancies it is important to realize that heterogeneity is an inevitable aspect of the scientific data world that needs to be accommodated. This paper describes the development and end use of an application that is designed to connect arbitrary variable names to specific concepts in layered search ontology. We will demonstrate the utility of this application through its deployment for the Consortium for the Advancement of Hydrologic Sciences Inc. (CUAHSI) network of testbeds and report on the issues that emerged carrying out variable and concept tagging. These issues concern specificity of a concept, ancillary information needed when identifying proper ontology locations, and multiple appearances of variables at different locations.

Managing a media server content directory in absence of reliable metadata

Content metadata play an important role assisting users to find and access content items of interest. In general, explicit metadata created commercially for traditional media distribution such as TV and packaged content work adequately. However with the proliferation of Internet usage, networked devices, and tools to create, edit, re-distribute, and manage diverse content items, the problem of maintaining reliable metadata in directory services of media servers is very complex. In this paper we analyze existing metadata frameworks used by industry consortia, specifically UPnP (universal plug and play) and DLNA (digital living network alliance) and discuss fundamental problems that cause content directories to be populated with unreliable metadata. We propose alternative methods based on implicit metadata and user-generated tagging that improve availability of reliable metadata.

Theoretical Considerations of Lifecycle Modeling: An Analysis of the Dryad Repository Demonstrating Automatic Metadata Propagation, Inheritance, and Value System Adoption

The Dryad repository is for data supporting published research in the field of evolutionary biology and related disciplines. Dryad development team members seek a theoretical framework to aid communication about metadata issues and plans. This article explores lifecycle modeling as a theoretical framework for understanding metadata in the repository environment. A background discussion reviews the importance of theory, the status of a metadata theory, and lifecycle concepts. An analysis draws examples from the Dryad repository demonstrating automatic propagation, metadata inheritance, and value system adoption, and reports results from a faceted term mapping experiment that included 12 vocabularies and approximately 600 terms. The article also reports selected key findings from a recent survey on the data-sharing attitudes and behaviors of nearly 400 evolutionary biologists. The results confirm the applicability of lifecycle modeling to Dryad's metadata infrastructure. The article concludes that lifecycle modeling provides a theoretical framework that can enhance our understanding of metadata, aid communication about the topic of metadata in the repository environment, and potentially help sustain robust repository development.

Running ahead toward interoperable e-government: The government of Canada metadata framework

The Government of Canada (GoC) has implemented several standardization initiatives toward establishing e-government in order to systematize the capture, description, organization and dissemination of data and information. This study examines the GoC's metadata strategy through the adoption of a Dublin Core (DC)-based metadata scheme toward establishing one unified metadata framework. The study examines the credibility of DC in relation to interoperability, application profiles, and controlled vocabularies and further provides a discussion on the current problems associated with metadata and possible improvements across government agencies in the GoC.

Metadata mapping and reuse in caBIG™

BackgroundThis paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI)'s cancer Biomedical Informatics Grid (caBIG™). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG™ framework or other frameworks that use metadata repositories.ResultsThe Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG™ framework and potentially any framework that uses a metadata repository.ConclusionThis work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG™. This effort contributes to facilitating the development of interoperable systems within caBIG™ as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies.

A net-centric metadata framework for service-oriented environments

The US Department of Defense (DoD) Chief Information Office (CIO) has embarked on an enterprise data management transformation initiative known as the DoD Net-Centric Data Strategy (NCDS). NCDS-related directives require DoD components, such as the United States Air Force (USAF), to describe mission-critical information assets using shared metadata catalogues and metadata registries. To satisfy NCDS requirements, the USAF is transitioning to a service-oriented environment (SOE). The USAF Net-Centric Metadata Framework (NCMF) extends the NCDS notion of metadata and the information assets that it describes in order to support the USAF SOE. The NCMF is implemented in the USAF Metadata Environment (MDE), which enables enterprise-level semantic consistency by linking information asset metadata, service specification metadata, and ontologies. This paper presents the USAF Net-Centric Metadata Framework and its MDE implementation as a practical and potentially reusable approach for achieving semantically interoperable information sharing capability in an enterprise-scale SOE.

Semantic enabled metadata management in PetaShare

We designed a semantic enabled metadata framework using ontology for multi-disciplinary and multi-institutional large-scale scientific data sets in a Data Grid setting. Two main issues are addressed: data integration for semantically and physically heterogeneous distributed knowledge stores, and semantic reasoning for data verification and inference in such a setting. This framework enables data interoperability between otherwise semantically incompatible data sources, cross-domain query capabilities and multi-source knowledge extraction. In this paper, we present the basic system architecture for this framework, as well as an initial implementation. We also analyse a real-life scenario and show integration of our framework into the PetaShare Data Grid where multi-disciplinary data archives are geographically distributed across six research institutions in Louisiana.

The Media Art Notation System: Documenting and Preserving Digital/Media Art

This paper proposes a new approach to conceptualizing digital and media art forms. This theoretical approach will be explored through issues raised in the process of creating a formal declarative model (alternately known as a metadata framework, notation system or ontology) for digital and media art. The approach presented and explored here is intended to inform a better understanding of media art forms and to provide a practical descriptive framework that supports their creation, re-creation, documentation and preservation.

Semantic-based framework for personalised ambient media

The paper proposes a semantic-based metadata framework for personalised interaction with TV media in a connected home context. Our approach allows the current home media centres to go beyond the simple concept of electronic programme guides and to offer the users a personalised media experience in an ambient home environment. The user’s characteristics, preferences and context are used to personalise the user’s experience of viewing and interacting with multimedia content on different heterogeneous devices. The TV-Anytime specification provides the basis for the metadata framework for handling content from IP, digital broadcast, and Blu-ray disc sources.

A general temporal data model and the structured population event history register.

At this time there are 37 demographic surveillance system sites active in sub-Saharan Africa, Asia and Central America, and this number is growing continuously. These sites and other longitudinal population and health research projects generate large quantities of complex temporal data in order to describe, explain and investigate the event histories of individuals and the populations they constitute. This article presents possible solutions to some of the key data management challenges associated with those data. The fundamental components of a temporal system are identified and both they and their relationships to each other are given simple, standardized definitions. Further, a metadata framework is proposed to endow this abstract generalization with specific meaning and to bind the definitions of the data to the data themselves. The result is a temporal data model that is generalized, conceptually tractable, and inherently contains a full description of the primary data it organizes. Individual databases utilizing this temporal data model can be customized to suit the needs of their operators without modifying the underlying design of the database or sacrificing the potential to transparently share compatible subsets of their data with other similar databases. A practical working relational database design based on this general temporal data model is presented and demonstrated. This work has arisen out of experience with demographic surveillance in the developing world, and although the challenges and their solutions are more general, the discussion is organized around applications in demographic surveillance. An appendix contains detailed examples and working prototype databases that implement the examples discussed in the text.

Ontology‐Based Metadata

It is even more remarkable to some of us that up to this point, there has been no thoroughgoing discussion by GIS practitioners and theorists about the epistemology of their subject, the ontology of their objects, and the political commitments embedded in their practices.(Pickles 1997, p. 364) AbstractMetadata are an extant mechanism for conveying ontological information about semantic data. Metadata have the advantage of being institutionally and structurally ensconced in GIS. At present, however, they lack fields to express information beyond the technical and geometric domain. This paper describes a framework for the creation of extended metadata for non‐spatial attributes, with the goal of incorporating ontological context. We use an informatics interpretation of ontology which refers to the total universe of discourse associated with a given attribute (database field). In other words, an ontology is the possible range of meaning offered by an encoded field. Current ontology research in GIScience has focused on data structuring and modelling. Implementation of these schemes demands restructuring of existing relational database models. An alternative is to extend current metadata schemes (e.g. ISO 19115) to include context‐based and tacit information about semantic attributes. Such ontology‐based extended metadata permits data selection and interoperability decisions that are ultimately more defensible. We have developed eight preliminary fields to add to existing metadata frameworks that will enable ontological context to travel with the data. This paper illustrates a preliminary implementation based on the integration of non‐commensurate cadastral data. The results illustrate the value of ontology‐based metadata in highlighting descriptive and substantive differences between similar classification systems. Recognition of semantic heterogeneity is the basis for creating defensible data linkages between multiple datasets. The development of ontology‐based metadata is profoundly different from the current trend to incorporate ontological context at the model level in GIScience. It is pragmatic, however, in that it presents a vehicle for incorporating use‐context with data in a manner that is accessible; requires little re‐engineering; and is intuitively understood by GIS users. Moreover, ontology‐based metadata are a mechanism for addressing Pickles’ (1997) concern about the ontology of spatial objects in GIS.

Integrating information on marine species identification for fishery purposes

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 316:231-238 (2006) - doi:10.3354/meps316231 Integrating information on marine species identification for fishery purposes Jordi Lleonart*, Marc Taconet, Michel Lamboeuf FAO Fisheries Department, Viale delle Terme di Caracalla, 00100 Rome, Italy *Email: jordi.lleonart@fao.org ABSTRACT: Species identification for fishery purposes has been the subject of a major Food and Agriculture Organization (FAO) program since the 1960s. One of the main objectives is to improve catch statistics through accurate species identification. A number of guides (geographical), catalogues (taxonomic) and species synopses have been produced as hard copy, and, more recently, most of these publications have become freely available on the Internet. Species fact sheets are a new electronic product with a database structure integrated in the Fisheries Global Information System (FIGIS). FIGIS interconnects species information with many other types of information related to fisheries (statistics, stocks inventories and assessment reports, fisheries inventories, fishing techniques, fisheries management systems, introduced species, cultured species etc.) and with a wide range of services available from other FAO systems (virtual document library, mapping library, legislation library, scientific abstracts). FIGIS achieves these features thanks to a flexible 3-tier architecture based on open-source software (Java, XML, XSL, HTML), a metadata framework based on international standards, formal institutional partnerships for information sharing, and the exploitation and display of web services. Several gaps in geographical and taxonomical coverage have been determined; these are mainly located in South America and concern several taxa (particularly crustaceans) and some fish families of paramount importance to fisheries. Other species identification tools to address multispecies and ecosystem modeling are also needed. Finally, optimization of the world-wide community efforts in generating and sharing taxonomically related knowledge in a global network is a current challenge calling for an urgent solution. KEY WORDS: FAO · Species identification · Databases Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 316. Online publication date: July 03, 2006 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2006 Inter-Research.

A generic metadata description for hydrodynamic model data

Sharing of data sets between numerical models is considered an important and pressing issue in the modeling community, because of (i) the time consumed to convert data sets and (ii) the need to connect different types of numerical codes to better map inter-connectedness of aquatic domains. One of the reasons for the data sharing problem arises from the lack of sufficient description of the data, or lack of metadata, which is due to the absence of a standardized framework for these metadata sets. This paper describes the development of a metadata framework for hydrodynamic data descriptions using the Geographic Information Metadata, 19115:2003 standard published by the International Standards Organization (ISO). This standard has been chosen not only because of its extent and adequacy to describe geospatial data, but also because of its widespread use and flexibility to extend the coverage. The latter is particularly important, as further extensions of the metadata standard are needed to provide a comprehensive metadata representation of hydrodynamics and their I/O data. In order to enable the community to share and reuse numerical code data sets, however, they need to be published in both human and machine understandable format. One such format is the Web Ontology language (OWL), whose syntax is compliant with the Extensible Markup Language (XML). In this paper, we present an extensive metadata profile using the available elements of ISO 19115:2003 as well as its extension rules. Based on the metadata profile, an explicit specification or ontology for the model data domain has been created using OWL. The use of OWL not only permits flexibility when extending the coverage but also to share data sets as resources across the internet as part of the Semantic Web. We demonstrate the use of the framework using a two-dimensional finite element code and its associated data sets.

The IMDI metadata framework, its current application and future direction

The IMDI Framework offers next to a suitable set of metadata descriptors for language resources, a set of tools and an infrastructure to use these. This paper gives an overview of all these aspects and at the end describes the intentions and hopes for ensuring the interoperability of the IMDI framework within more general ones in development. An evaluation of the current state of the IMDI Framework is presented with an analysis of the benefits and more problematic issues. Finally we describe work on issues of long-term stability for IMDI by linking up to the work done within the ISO TC37/SC4 subcommittee (TC37/SC4).

Scientific Data Management in a Grid Environment

Managing scientific data is by no means a trivial task even in a single site environment with a small number of researchers involved. We discuss some issues concerned with posing well-specified experiments in terms of parameters or instrument settings and the metadata framework that arises from doing so. We are particularly interested in parallel computer simulation experiments, where very large quantities of warehouse-able data are involved, run in a multi-site Grid environment. We consider SQL databases and other framework technologies for manipulating experimental data. Our framework manages the outputs from parallel runs that arise from large cross-products of parameter combinations. Considerable useful experiment planning and analysis can be done with the sparse metadata without fully expanding the parameter cross-products. Extra value can be obtained from simulation output that can subsequently be data-mined. We have particular interests in running large scale Monte Carlo physics model simulations. Finding ourselves overwhelmed by the problems of managing data and compute resources, we have built a prototype tool using Java and MySQL that addresses these issues. We use this example to discuss type-space management and other fundamental ideas for implementing a laboratory information management system.

International Conference on Dublin Core and Metadata Applications 2004

PurposeTo provide an overview of the 2004 International Conference on Dublin Core and Metadata Applications held in Shanghai, China, in October 2004.Design/methodology/approach Outlines the themes of the papers presented in the three plenary paper sessions: Metadata Frameworks, Metadata Users, and Managing & Harvesting Metadata.FindingsFound that one of the most prevailing topics at the conference was interoperability, being the key to ensure the accessibility and sustainability of any effective digital library.Originality/valueProvides a useful summary of a conference of interest to library and information management professionals.

Metadata Broadcasting for Personalized Service: a Practical Solution

As the number of broadcasting channels and programs increases rapidly, the importance of personalized service has been emphasized. In this paper, we propose a practical framework of metadata broadcasting to provide personalized service according to user preferences and various terminal/network conditions. First, we present an overall system architecture of a metadata broadcasting system and then propose several core technologies (particularly in the parts of metadata authoring, metadata encoding, and metadata-based personalized content consumption). For interoperability, the proposed solution is designed to be compliant with the relevant standards of the TV-Anytime Forum, MPEG-7 Systems, and MPEG-2 Systems. Considering a home network environment, we also propose a metadata-based content adaptation scheme. Each component technology has been implemented individually, integrated into an end-to-end prototype broadcasting system, and successfully tested with a set of personalized service scenarios that are also developed in this study.