Margaret O'Brien

Seasonal variability of light availability and utilization in the Sargasso Sea

A 2 year time series of optical, biogeochemical, and physical parameters, taken near the island of Bermuda, is used to evaluate the sources of temporal variability in light availability and utilization in the Sargasso Sea. Integrated assessments of light availability are made by examining the depth of constant percent incident photosynthetically available radiation (%PAR) isolumes. To first order, changes in the depth of %PAR isolumes were caused by physical processes: deep convective mixing in the winter which led to the spring bloom and concurrent shallowing of %PAR depths and the occurrence of anomalous thermohaline water masses during the summer and fall seasons. Spectral light availability variations are assessed using determinations of diffuse attenuation coefficient spectra which illustrate a significant seasonal cycle in colored detrital paniculate and/or dissolved materials that is unrelated to changes in chlorophyll pigment concentrations. Temporal variations in the photosynthetic light utilization index Ψ are used to assess vertically integrated light utilization variations. Values of Ψ are highly variable and show no apparent seasonal pattern which indicates that Ψ is not simply a “biogeochemical constant” Determinations of in situ primary production rates and daily mean PAR fluxes are used to diagnose the relative role of light limitation in determining vertically integrated rates of primary production ∫PP. The mean depth of the light-saturated zone (the vertical region where the daily mean PAR flux was greater than or equal to the saturation irradiance Ik) is only ∼40 m, although more than one half of ∫PP occurred within this zone. Production model results illustrate that accurate predictions of ∫PP are dependent upon rates of light-saturated production rather than upon indices of light limitation. It seems unlikely that significant improvements in simple primary production models will come from the partitioning of the Earths seas into biogeochemical provinces.

The GeoLink Modular Oceanography Ontology

GeoLink is one of the building block projects within EarthCube, a major effort of the National Science Foundation to establish a next-generation knowledge infrastructure for geosciences. As part of this effort, GeoLink aims to improve data retrieval, reuse, and integration of seven geoscience data repositories through the use of ontologies. In this paper, we report on the GeoLink modular ontology, which consists of an interlinked collection of ontology design patterns engineered as the result of a collaborative modeling effort. We explain our design choices, present selected modeling details, and discuss how data integration can be achieved using the patterns while respecting the existing heterogeneity within the participating repositories.

A metadata-driven approach to loading and querying heterogeneous scientific data

Abstract The Ecological Metadata Language is an effective specification for describing data for long-term storage and interpretation. When used in conjunction with a metadata repository such as Metacat, and a metadata editing tool such as Morpho, the Ecological Metadata Language allows a large community of researchers to access and to share their data. Although the Ecological Metadata Language/Morpho/Metacat toolkit provides a rich data documentation mechanism, current methods for retrieving metadata-described data can be laborious and time consuming. Moreover, the structural and semantic heterogeneity of ecological data sets makes the development of custom solutions for integrating and querying these data prohibitively costly for large-scale synthesis. The Data Manager Library leverages the Ecological Metadata Language to provide automated data processing features that allow efficient data access, querying, and manipulation without custom development. The library can be used for many data management tasks and was designed to be immediately useful as well as extensible and easy to incorporate within existing applications. In this paper we describe the motivation for developing the Data Manager Library, provide an overview of its implementation, illustrate ideas for potential use by describing several planned and existing deployments, and describe future work to extend the library.

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.

A Prototype System for Multilingual Data Discovery of International Long-Term Ecological Research (ILTER) Network Data

Shared ecological data have the potential to revolutionize ecological research just as shared genetic sequence data have done for biological research. However, for ecological data to be useful, it must first be discoverable. A broad-scale research topic may require that a researcher be able to locate suitable data from a variety of global, regional and national data providers, which often use different local languages to describe their data. Thus, one of the challenges of international sharing of long-term data is facilitation of multilingual searches. Such searches are hindered by lack of equivalent terms across languages and by uneven application of keywords in ecological metadata. To test whether a thesaurus-based approach to multilingual data searching might be effective, we implemented a prototype web-services-based system for searching International Long-Term Ecological Research Network data repositories. The system builds on the use of a multilingual thesaurus to make searches more complete than would be obtained through search term-translation alone. The resulting system, when coupled to commodity online translation systems, demonstrates the possibility of achieving multilingual searches for ecological data.

Ensuring the quality of data packages in the LTER network data management system

Abstract Considerable data analyses use automated workflows to ingest data from public repositories, and rely on data packages of high structural quality. The Long Term Ecological Research (LTER) Network now screens all packages entering its long-term archive to ensure completeness and quality, and to ascertain that metadata and data are structurally congruent, i.e., that the data typing and formats expressed in metadata agree with that found in data entities. The EML Congruence Checker (ECC) system is a component of the LTER Provenance Aware Synthesis Tracking Architecture (PASTA), and operates on data tables in packages described with Ecological Metadata Language using the EML Data Manager Library, written in Java. Checking is extensible for other data types and customizable via a template. Reports are retained as part of the submitted data package, and summaries here reflect the general usability of LTER data for a variety of purposes. On average in 2015, site-contributed data in the LTER catalog were 95% compliant (valid) with the current suite of checks.

Validation of in-situ inherent optical properties in the Sargasso Sea

In situ inherent optical properties (IOP) determinations from the US JGOFS Bermuda Atlantic Time-Series (BATS) made from 1994 to 1996 are used to develop processing and correction methods for clear natural waters. Upper bound estimates of precision are 0.0066 and 0.0018 m-1 for non-water beam attenuation and absorption coefficient respectively. These are determined by examining the intracruise variability at 190m depth where minimum natural variations exist. The final corrected IOP values show consistent patterns with time, depth and wavelength. A strong correlation is observed between measured beam attenuation and absorption coefficient at 440 nm in the upper 50m. Whereas lower correlation is observed between the scattering coefficient and absorption coefficient. In the upper 50m layer, measured values of a-aw(440) in the upper 50m compare well with chlorophyll-based bio-optical model. However measured values of c-cw(440) and b-bw(440) do not compare well with the modeled values. In particular, the measured b/a(440) shows an inverse relationship compared with estimated b/a(440) ratio in the upper 50m.