Semantic linking of complex properties, monitoring processes and facilities in web-based representations of the environment

Where a virtual representation of the Earth must contain data values observed within the physical Earth system, data models are required that allow the integration of data across the silos of various Earth and environmental sciences domains. Creating a mapping between the well-defined terminologies of these silos is a stubborn problem. This paper presents a generalised ontology for use within Web 3.0 services, which builds on European Commission spatial data infrastructure models. The presented ontology acknowledges that there are many complexities to the description of environmental properties which can be observed within the physical Earth system. The ontology is shown to be flexible and robust enough to describe concepts drawn from a range of Earth science disciplines, including ecology, geochemistry, hydrology and oceanography. This paper also demonstrates the alignment and compatibility of the ontology with existing systems and shows applications in which the ontology may be deployed

Genome-Wide Effects of Selenium and Translational Uncoupling on Transcription in the Termite Gut Symbiont Treponema primitia

When prokaryotic cells acquire mutations, encounter translation-inhibiting substances, or experience adverse environmental conditions that limit their ability to synthesize proteins, transcription can become uncoupled from translation. Such uncoupling is known to suppress transcription of protein-encoding genes in bacteria. Here we show that the trace element selenium controls transcription of the gene for the selenocysteine-utilizing enzyme formate dehydrogenase (fdhF_Sec) through a translation-coupled mechanism in the termite gut symbiont Treponema primitia, a member of the bacterial phylum Spirochaetes. We also evaluated changes in genome-wide transcriptional patterns caused by selenium limitation and by generally uncoupling translation from transcription via antibiotic-mediated inhibition of protein synthesis. We observed that inhibiting protein synthesis in T. primitia influences transcriptional patterns in unexpected ways. In addition to suppressing transcription of certain genes, the expected consequence of inhibiting protein synthesis, we found numerous examples in which transcription of genes and operons is truncated far downstream from putative promoters, is unchanged, or is even stimulated overall. These results indicate that gene regulation in bacteria allows for specific post-initiation transcriptional responses during periods of limited protein synthesis, which may depend both on translational coupling and on unclassified intrinsic elements of protein-encoding genes. A large body of literature demonstrates that the coupling of transcription and translation is a general and essential method by which bacteria regulate gene expression levels. However, the potential role of noncanonical amino acids in regulating transcriptional output via translational control remains, for the most part, undefined. Furthermore, the genome-wide transcriptional state in response to translational decoupling is not well quantified. The results presented here suggest that the noncanonical amino acid selenocysteine is able to tune transcription of an important metabolic gene via translational coupling. Furthermore, a genome-wide analysis reveals that transcriptional decoupling produces a wide-ranging effect and that this effect is not uniform. These results exemplify how growth conditions that impact translational processivity can rapidly feed back on transcriptional productivity of prespecified groups of genes, providing bacteria with an efficient response to environmental changes

Ocean data publication cookbook

This cookbook is an outcome of the 5th session of the SCOR/IODE/MBLWHOI Library Workshop on Data Publication and is posted here by permission of UNESCO.Executive summary: This “Cookbook” has been written for data managers and librarians who are interested in assigning a permanent identifier to a dataset for the purposes of publishing that dataset online and for the citation of that dataset within the scientific literature. A formal publishing process adds value to the dataset for the data originators as well as for future users of the data. Value may be added by providing an indication of the scientific quality and importance of the dataset (as measured through a process of peer review), and by ensuring that the dataset is complete, frozen and has enough supporting metadata and other information to allow it to be used by others. Publishing a dataset also implies a commitment to persistence of the data and allows data producers to obtain academic credit for their work in creating the datasets. One form of persistent identifier is the Digital Object Identifier (DOI). A DOI is a character string (a "digital identifier") used to provide a unique identity of an object such as an electronic document. Metadata about the object is stored in association with the DOI name and this metadata may include a location where the object can be found. The DOI for a document is permanent, whereas its location and other metadata may change. Referring to an online document by its DOI provides more stable linking than simply referring to it by its URL, because if its URL changes, the publisher need only update the metadata for the DOI to link to the new URL. A DOI may be obtained for a variety of objects, including documents, data files and images. The assignment of DOIs to peer-reviewed journal articles has become commonplace. This cookbook provides a step-by-step guide to the data publication process and showcases some best practices for data publication

Lessons from a Marine Spatial Planning data management process for Ireland

Peer-reviewedThis paper presents a framework containing ten components to deliver a data management process for the storage and management of data used for Marine Spatial Planning (MSP) in Ireland. The work includes a data process flow and a recommended solution architecture. The architecture includes a central data catalogue and a spatial storage system. The components of the process are presented to maximise the reuse potential of any dataset within an MSP context. The terms ‘Suitability’ and ‘Readiness’ in the MSP context are offered as both formal and considered assessments of data, as is the applicability of a data stewardship maturity matrix. How data contained in such a storage system can be published externally to potential consumers of these data is also explored. The process presents a means of managing data and metadata to ensure data lineage is optimised by carrying information about the origin of and the processing applied to the data; to evaluate the quality and relevance of geospatial datasets for use in MSP decisions in Ireland. The process was piloted in the National Marine Planning Framework for Ireland in the development of draft map products; feedback from the public consultation is ongoing and not presented

Putting meaning into NETMAR – the open service network for marine environmental data

The open service network for marine environmental data (NETMAR) project uses semantic web technologies in its pilot system which aims to allow users to search, download and integrate satellite, in situ and model data from open ocean and coastal areas. The semantic web is an extension of the fundamental ideas of the World Wide Web, building a web of data through annotation of metadata and data with hyperlinked resources. Within the framework of the NETMAR project, an interconnected semantic web resource was developed to aid in data and web service discovery and to validate Open Geospatial Consortium Web Processing Service orchestration. A second semantic resource was developed to support interoperability of coastal web atlases across jurisdictional boundaries. This paper outlines the approach taken to producing the resource registry used within the NETMAR project and demonstrates the use of these semantic resources to support user interactions with systems. Such interconnected semantic resources allow the increased ability to share and disseminate data through the facilitation of interoperability between data providers. The formal representation of geospatial knowledge to advance geospatial interoperability is a growing research area. Tools and methods such as those outlined in this paper have the potential to support these efforts