Giri Palanisamy

Metadata Activities in Biology

The National Biological Information Infrastructure (NBII) has advanced the ability of biological sciences to standardize, share, integrate, and synthesize data by making the metadata program a core of its activities. A series of crosswalks for the main biological metadata specifications enable data providers and international clearinghouses to aggregate and disseminate tens of thousands of metadata records describing petabytes of data records and allow for interoperability. These efforts were accomplished by forming strategic partnerships with key research organizations in the biological and ecological sciences. This paper provides an overview of metadata initiatives undertaken by NBII and the Long Term Ecological Research Network. New efforts to provide better metadata creation and curation tools based on content management systems with semantic mediation for data discovery are presented.

A flexible online metadata editing and management system

Abstract Our team developed a metadata editing and management system employing state of the art XML technologies initially aimed at the environmental sciences but with the potential to be useful across multiple domains. We chose a modular and distributed design for scalability, flexibility, options for customizations, and the possibility to add more functionality at a later stage. The system consists of a desktop design tool that generates code for the actual online editor, a native XML database, and an online user access management application. A Java Swing application that reads an XML schema, the design tool provides the designer with options to combine input fields into online forms with user-friendly tags and determine the flow of input forms. Based on design decisions, the tool generates XForm code for the online metadata editor which is based on the Orbeon XForms engine. The design tool fulfills two requirements: First data entry forms based on a schema are customized at design time and second the tool can generate data entry applications for any valid XML schema without relying on custom information in the schema. A configuration file in the design tool saves custom information generated at design time. Future developments will add functionality to the design tool to integrate help text, tool tips, project specific keyword lists, and thesaurus services. Cascading style sheets customize the look-and-feel of the finished editor. The editor produces XML files in compliance with the original schema, however, a user may save the input into a native XML database at any time independent of validity. The system uses the open source XML database eXist for storage and uses a MySQL relational database and a simple Java Server Faces user interface for file and access management. We chose three levels to distribute administrative responsibilities and handle the common situation of an information manager entering the bulk of the metadata but leave specifics to the actual data provider.

Defining linkages between the GSC and NSF's LTER program: How the Ecological Metadata Language (EML) relates to GCDML and other outcomes

The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML). The LTER is one of the top National Science Foundation (NSF) programs in biology since 1980, representing diverse ecosystems and creating long-term, interdisciplinary research, synthesis of information, and theory. The adoption of EML as the LTER network standard has been key to build network synthesis architectures based on high-quality standardized metadata. EML is the NSF-recognized metadata standard for LTER, and EML is a criteria used to review the LTER program progress. At the workshop, a potential crosswalk between the GCDML and EML was explored. Also, collaboration between the LTER and GSC developers was proposed to join efforts toward a common metadata cataloging designers tool. The community adoption success of a metadata standard depends, among other factors, on the tools and trainings developed to use the standard. LTERs experience in embracing EML may help GSC to achieve similar success. A possible collaboration between LTER and GSC to provide training opportunities for GCDML and the associated tools is being explored. Finally, LTER is investigating EML enhancements to better accommodate genomics data, possibly integrating the GCDML schema into EML. All these action items have been accepted by the LTER contingent, and further collaboration between the GSC and LTER is expected.

Geoscience data curation using a digital object model and open-source frameworks: Provenance applications

We find that software frameworks for digital content management and access may be used for capturing certain data provenance information, particularly for data that has already been created and archived at a repository center. One of the key enabling factors is the abstraction concept of a digital object augmented with semantic relationships. One set of frameworks, Fedora Repository and Drupal CMS with the Islandora connector hold great promise for provenance applications as well as long-term curation of Geoscience datasets.

Department of energy strategic roadmap for Earth system science data integration

The U.S. Department of Energy (DOE) Office of Biological and Environmental Research (BER) Climate and Environmental Sciences Division (CESD) produces a diversity of data, information, software, and model codes across its research and informatics programs and facilities. This information includes raw and reduced observational and instrumentation data, model codes, model-generated results, and integrated data products. Currently, most of these data and information are prepared and shared for program specific activities, corresponding to CESD organization research. A major challenge facing BER CESD is how best to inventory, integrate, and deliver these vast and diverse resources for the purpose of accelerating Earth system science research. This paper provides a concept for a CESD Integrated Data Ecosystem and an initial roadmap for its implementation to address this integration challenge in the “Big Data” domain.

Semantic search integration to climate data

In this paper we present how research projects at Oak Ridge National Laboratory are using Semantic Search capabilities to help scientists perform their research. We will discuss how the Mercury metadata search system, with the help of the semantic search capability, is being used to find, retrieve, and link climate change data.