Jens Klump

The impact of sediment provenance on barium-based productivity estimates

Abstract Biogenic barium in marine sediments has been suggested to be a reliable proxy of export productivity from the surface ocean and algorithms have been developed to link these properties. However, problems arise when the proposed algorithms are applied to predominantly terrigenous sediments. A major source of error is incorrect estimates of the terrigenous Ba/Al ratio in normative calculations of the amount of biogenic barium in the sediment. Compared to an often used “global average” Ba/Al ratio, much better results can be obtained by estimating the terrigenous Ba/Al ratio from exponential regression of the Ba/Al ratios of surface sediments obtained from continental slope transects. This method has been applied to surface sediments from the Chilean continental slope. The calculated regional terrigenous Ba/Al ratios could be verified with purely terrigenous samples from Chilean rivers. The resulting accumulation rates of biogenic barium on the Chilean continental slope reliably reproduce the regional pattern of primary productivity in the southern Peru–Chile Current, indicating the potential of biogenic barium as a useful (paleo)productivity proxy.

Biogenic barium and the detrital Ba/Al ratio: a comparison of their direct and indirect determination

Biogenic barium concentrations obtained from direct determination by a three-step sequential extraction procedure are compared to those obtained from the widely used indirect normative calculation based on total digestion. A comparison of the biogenic barium from the direct/sequential extraction and the indirect/normative calculation clearly shows that the detrital Ba/Al ratio is the critical factor in the normative approach, and that erroneous assumptions based on this ratio may introduce significant errors to the calculated biogenic barium. Overall, the crustal average Ba/Al ratio of 0.005–0.01 is much higher than our directly determined global average of 0.0037. This would result in an underestimation of the biogenic barium and thus of the primary productivity calculated using the Ba-flux obtained from the normatively calculated Ba record. Using our (Ba/Al)det ratio of ∼0.0037 leads to normatively calculated biogenic barium results that are in reasonable agreement with the biogenic barium from sequential extraction for samples of the Atlantic, Pacific and Indian Ocean. Our directly determined ‘regional’ (Ba/Al)det ratios deviate from those calculated or assumed from hinterland ratios and our global average (Ba/Al)det is lower than the one commonly reported. Therefore, in sediments with a significant terrigenous fraction, the sequential extraction technique is always required.

Making Research Data Repositories Visible: The re3data.org Registry

Researchers require infrastructures that ensure a maximum of accessibility, stability and reliability to facilitate working with and sharing of research data. Such infrastructures are being increasingly summarized under the term Research Data Repositories (RDR). The project re3data.org–Registry of Research Data Repositories–has begun to index research data repositories in 2012 and offers researchers, funding organizations, libraries and publishers an overview of the heterogeneous research data repository landscape. In July 2013 re3data.org lists 400 research data repositories and counting. 288 of these are described in detail using the re3data.org vocabulary. Information icons help researchers to easily identify an adequate repository for the storage and reuse of their data. This article describes the heterogeneous RDR landscape and presents a typology of institutional, disciplinary, multidisciplinary and project-specific RDR. Further the article outlines the features of re3data.org, and shows how this registry helps to identify appropriate repositories for storage and search of research data.

DOI for geoscience data - how early practices shape present perceptions

The first minting of Digital Object Identifiers (DOI) for research data happened in 2004 in the context of the project “Publication and citation of primary scientific data” (STD-DOI). Some of the concepts and perceptions about DOI for data today have their roots in the way this project implemented DOI for research data and the decisions made in those early days still shape the discussion about the use of persistent identifiers for research data today. This project also laid the foundation for a tighter integration of journal publications and data. Promoted by early adopters, such as PANGAEA, DOI registration for data has reached a high level of maturity and has become an integral part of scientific publishing. This paper discusses the fundamental concepts applied in the identification of DOI for research data and how these can be interpreted for alternative and future applications of persistent identifiers for research data.

Charting taxonomic knowledge through ontologies and ranking algorithms

Since the inception of geology as a modern science, paleontologists have described a large number of fossil species. This makes fossilized organisms an important tool in the study of stratigraphy and past environments. Since taxonomic classifications of organisms, and thereby their names, change frequently, the correct application of this tool requires taxonomic expertise in finding correct synonyms for a given species name. Much of this taxonomic information has already been published in journals and books where it is compiled in carefully prepared synonymy lists. Because this information is scattered throughout the paleontological literature, it is difficult to find and sometimes not accessible. Also, taxonomic information in the literature is often difficult to interpret for non-taxonomists looking for taxonomic synonymies as part of their research. The highly formalized structure makes Open Nomenclature synonymy lists ideally suited for computer aided identification of taxonomic synonyms. Because a synonymy list is a list of citations related to a taxon name, its bibliographic nature allows the application of bibliometric techniques to calculate the impact of synonymies and taxonomic concepts. TaxonRank is a ranking algorithm based on bibliometric analysis and Internet page ranking algorithms. TaxonRank uses published synonymy list data stored in TaxonConcept, a taxonomic information system. The basic ranking algorithm has been modified to include a measure of confidence on species identification based on the Open Nomenclature notation used in synonymy list, as well as other synonymy specific criteria. The results of our experiments show that the output of the proposed ranking algorithm gives a good estimate of the impact a published taxonomic concept has on the taxonomic opinions in the geological community. Also, our results show that treating taxonomic synonymies as part of on an ontology is a way to record and manage taxonomic knowledge, and thus contribute to the preservation our scientific heritage.

Representing and publishing physical sample descriptions

Abstract This paper presents a metadata model for physical samples, developed by CSIRO for its role as an allocating agent. The model is essential for connecting various samples to the Web in a systematic manner. It serves as a basis for registering and publishing samples from researchers and laboratories in CSIRO with the International Geo Sample Number (IGSN). The model is simple, extensible and publicly available. We specify how existing controlled vocabularies are incorporated into the model development, and discuss their relevance and limitations. We also describe the mappings between the developed model and existing standards. This is necessary to extend the models adoption across various science domains. The model has been implemented and tested in the context of two large sample repositories in CSIRO. The results demonstrate the effectiveness of the metadata model while maintaining its flexibility to adapt to various sample types.

The design of monitoring and data infrastructures — Applying a forward-thinking reference architecture

Climate Change is an extraordinary challenge for the development of our socioeconomic environment. The compilation of comprehensive knowledge about our physical environment is a key importance for implementing of mitigation strategies. Long-term terrestrial observatories are supporting the systematic monitoring of environmental parameters. They are responsible for data collection, data analysis and subsequently for decision support. Not only the complex structure and the large volume of data streams but also the necessary integration of existing monitoring infrastructures for such observatories imply special technological challenges for todays scientific data and information management. Recent developments of Information and Communication Technology provide important conceptual and technological input for the proper design and implementation of underlying monitoring and data infrastructures. To avoid constantly recurring system developments for such infrastructures, a general and integrated approach for a reference architecture concept is needed.

An Open Source Web Service For Registering And Managing Environmental Samples

Records of environmental samples, such as minerals, soil, rocks, water, air and plants, are distributed across legacy databases, spreadsheets or other proprietary data systems. Sharing and integration of the sample records across the Web requires globally unique identifiers. These identifiers are essential in order to locate samples unambiguously and to manage their associated metadata and data systematically. The International Geo Sample Number (IGSN) is a persistent, globally unique label for identifying environmental samples. IGSN can be resolved to a digital representation of the sample through the Handle system. IGSN names are registered by end-users through allocating agents, which are the institutions acting on behalf of the IGSN registration agency. As an IGSN allocating agent, our goal is to implement a web service based on existing open source tools to streamline the processes of registering IGSNs and for managing and disseminating sample metadata. In this paper, we present our ongoing work onthe design and development of the web service, and its data schema and database model for capturing key aspects of environmental samples. We show how existing controlled vocabularies can be incorporated into the service development to support the metadata registration of different types of samples. The proposed sample registration and curating approach has been trialed in the context of the Capricorn Distal Footprints project on a range of different sample types, varying from water to hard rock samples. The initial results demonstrate the effectiveness of the service while maintaining the flexibility to adapt to various media types, which is critical in the context of a multi-disciplinary project.

TEODOOR - A Spatial Data Infrastructure for terrestrial observation data

Within the TERENO initiative four long-term terrestrial observatories, collecting huge amounts of environmental relevant data are being set up since 2008. In order to manage, describe, exchange and publish these data, the distributed Spatial Data Infrastructure TEODOOR (http://www.tereno.net) has been created. Each institution responsible for an individual observatory set up its own local data infrastructure, which may communicate to each other to exchange data and metadata internally or to the public by OGC-conformal Web services. The TEODOOR data portal serves as a database node to provide scientists and decision makers with reliable and well accessible data and data products. Various tools like hierarchical search or Web-GIS functions allow a deeper insight into the different observatories, test areas and sensor networks. Sensor data can be selected according to the measured parameters, stations and/or time periods, visualized and downloaded according to the common TERENO data policy. Currently, TEODOOR provides free access to data from more than 500 monitoring stations.

Enabling Global Collaboration in the Geosciences: Geoinformatics 2008; Potsdam, Germany, 11–13 June 2008

Scientists are facing an increasing flood of data and information in the Earth sciences from which they try to distill knowledge. The emerging discipline of geoinformatics brings together the tools necessary to create and make accessible the knowledge needed to respond to societys complex challenges, such as climate change, new energy and mineral resources, new sources of water, and protecting environmental and human health. Globalization of geoinformatics-based research and education in support of meeting societal challenges was the theme for the Geoinformatics 2008 conference, which was held at the German Research Centre for Geosciences, in Potsdam, Germany. Participants came from China, France, Germany, Japan, Netherlands, Russia, Switzerland, the United Kingdom, and the United States, representing academic institutions, national research centers, and government agencies.