Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

gauStad, long, MatheR, McfaRl ane, and Shi-Pacific northwest national laboratory, Richland, Washington; golaz and lin-noAA geophysical Fluid dynamics laboratory, Princeton, new Jersey; JenSen, JohnSon, and wiScoMbe-Brookhaven national laboratory,

There is a growing consensus for the need to store and archive digital data, particularly for publicly funded research. Long-term preservation of that data generally requires some form of institutional archive, such as those directed to particular scientific communities of practice. Given that data is often of use to multiple communities of practice, which may have differing norms for data and metadata structure and semantics, effective standards for data and metadata exchange are important factors for users to be able to find and retrieve data. Toolsets that provide a coherent presentation of information across multiple standards are important for data search and access. One such toolset, Mercury, is a open-source metadata harvesting, data discovery, and access system, built for researchers to search for, share and obtain spatiotemporal data used across a range of climate and ecological sciences. Mercury is used across multiple projects to provide a coherent search interface for spatiotemporal data described in any of several metadata formats. Mercury has recently been extended to enable harvesting and distribution of metadata using the Open Archive Initiative Protocol for Metadata Handling (OAI-PMH). In this paper we describe Mercury's capabilities with multiple metadata formats, in general, and, more specifically, the results of our OAI-PMH implementations and the lessons learned.

Mercury is a federated metadata harvesting, search and retrieval tool based on both open source packages and custom software developed at Oak Ridge National Laboratory (ORNL). It was originally developed for the National Aeronautics and Space Administration (NASA), and the consortium now includes funding from NASA, U.S. Geological Survey (USGS), and U.S. Department of Energy (DOE). Mercury is itself a reusable software application which uses a service-oriented architecture (SOA) approach to capturing and managing metadata in support of twelve Earth science projects. Mercury also supports the reuse of metadata by enabling searches across a range of metadata specification and standards including XML, Z39.50, FGDC, Dublin-Core, Darwin-Core, EML, and ISO-19115. It collects metadata and key data from contributing project servers distributed around the world and builds a centralized index. The Mercury search interfaces allows the users to perform simple, fielded, spatial, temporal and other hierarchical searches across these metadata sources. This centralized repository of metadata

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).