Database tools for ecological data integration and synthesis

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.The challenge: 1. To synthesize across research sites syntactically disparate, but thematically similar, data. 2. To efficiently perform cross-site synthesis, using new informatics tools that exploit database component technology. 3. To aid analysis of ecological data through visualization tools that take advantage of informatics-processed data

Facilitating and Improving Environmental Research Data Repository Interoperability

Environmental research data repositories provide much needed services for data preservation and data dissemination to diverse communities with domain specific or programmatic data needs and standards. Due to independent development these repositories serve their communities well, but were developed with different technologies, data models and using different ontologies. Hence, the effectiveness and efficiency of these services can be vastly improved if repositories work together adhering to a shared community platform that focuses on the implementation of agreed upon standards and best practices for curation and dissemination of data. Such a community platform drives forward the convergence of technologies and practices that will advance cross-domain interoperability. It will also facilitate contributions from investigators through standardized and streamlined workflows and provide increased visibility for the role of data managers and the curation services provided by data repositories, beyond preservation infrastructure. Ten specific suggestions for such standardizations are outlined without any suggestions for priority or technical implementation. Although the recommendations are for repositories to implement, they have been chosen specifically with the data provider/data curator and synthesis scientist in mind

Progress in creating a joint research agenda that allows networked long-term socio-ecological research in southern South America : addressing crucial technological and human capacity gaps limiting its application in Chile and Argentina

Since 1980, more than 40 countries have implemented long-term ecological research (LTER) programs, which have shown their power to affect advances in basic science to understand the natural world at meaningful temporal and spatial scales and also help link research with socially relevant outcomes. Recently, a disciplinary paradigmatic shift has integrated the human dimensions of ecosystems, leading to a long-term socio-ecological research (LTSER) framework to address the world's current environmental challenges. A global gap in LTER/LTSER only exists in the latitudinal range of 40–60°S, corresponding to Argentina and Chile's temperate/sub-Antarctic biome. A team of Chilean, Argentine and US researchers has participated in an ongoing dialogue to define not only conceptual, but also practical barriers limiting LTER/LTSER in southern South America. We have found a number of existing long-term research sites and platforms throughout the region, but at the same time it has been concluded an agenda is needed to create and implement further training courses for students, postdoctoral fellows and young scientists, particularly in the areas of data and information management systems. Since LTER/LTSER efforts in Chile and Argentina are incipient, instituting such courses now will enhance human and technical capacity of the natural science and resource community to improve the collection, storage, analysis and dissemination of information in emerging LTER/LTSER platforms. In turn, having this capacity, as well as the ongoing formalization of LTER/LTSER programs at national levels, will allow the enhancement of crucial collaborations and comparisons between long-term research programs within the region and between hemispheres and continents. For Spanish version of the entire article, see Online Supporting Information (Appendix S1).Desde 1980, más de cuarenta países han implementado programas de Investigación Ecológica a Largo Plazo (LTER por sus siglas en inglés), los cuales han mostrado su capacidad para influir sobre los avances en las ciencias básicas que permiten entender el mundo natural en escalas temporales y espaciales significativas, y también ayudar a enfocar la investigación hacia estudios socialmente relevantes. Recientemente, gracias a un cambio de paradigma en la disciplina, se integró también la dimensión humana de los ecosistemas, llevándola a un marco conceptual de Investigación Socio-Ecológica a Largo Plazo (LTSER por sus siglas en inglés) para enfrentar los desafíos medio-ambientales del mundo actual. Existe un vacío global en LTER/LTSER en el rango latitudinal de 40–60°S, correspondiente a los biomas templados/subantárticos de Argentina y Chile. Un equipo de investigadores chilenos, argentinos y estadounidenses ha trabajado por varios años para definir cuáles son la barreras que actualmente limitan la creación de una Red de LTER/LTSER en el sur de Sudamérica, no solamente en términos conceptuales, sino también a nivel práctico. Existe un buen número de sitios de investigación a largo plazo en la región, pero también concluimos que es necesario crear e implementar más cursos de capacitación para estudiantes, investigadores post-doctorales y jóvenes científicos, particularmente en las áreas de sistemas de manejo de datos e información. Considerando que los esfuerzos LTER/LTSER en Chile y Argentina son incipientes, este tipo de cursos podría mejorar la capacidad humana y técnica en la comunidad de las ciencias y los recursos naturales, así como mejorar los procesos de recolección, almacenamiento, análisis y difusión de la información. A su vez, la formalización de cursos de programas LTER/LTSER a nivel nacional para adquirir dicha capacidad de manejo de la información, permitirá un fortalecimiento crucial de las colaboraciones y comparaciones entre programas de investigación a largo plazo dentro de la región, y entre hemisferios y continentes. La versión en castellano del artículo se encuentra disponible en forma digital como Online Supporting Information S1.Fil: Anderson, Chistopher B. University of North Texas. Department of Biological Sciences; Estados UnidosFil: Celis-Diez, Juan Luis. Pontificia Universidad Católica de Valparaíso, Escuela de Agronomía; ChileFil: Bond, Barbara J.H.G. Oregon State University. Andrews Forest Long-Term Ecological Research Site. Department of Forest Ecosystems and Society; Estados UnidosFil: Martínez Pastur, Guillermo José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Cientificas; ArgentinaFil: Little, Christian. Universidad Austral de Chile. Facultad de Ciencias. Instituto de Ciencias de la Tierra y Evolución; Chile. Fundación Centro de los Bosques Nativos FORECOS; ChileFil: Armesto, Juan J. Pontificia Universidad Católica de Valparaíso, Escuela de Agronomía; ChileFil: Ghersa, Claudio Marco. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Austin, Amy Theresa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Schlichter, Tomas Miguel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche. Grupo de Ecología Forestal; ArgentinaFil: Lara, Antonio. Fundación Centro de los Bosques Nativos FORECOS; Chile. Universidad Austral de Chile. Facultad de Ciencias Forestales y Recursos Naturales. Instituto de Silvicultura; ChileFil: Carmona, Martin. Universidad de Chile. Instituto de Ecologıa y Biodiversidad; ChileFil: Chaneton, Enrique Jose. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; Argentina. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Recursos Naturales y Ambiente; ArgentinaFil: Gutierrez, Julio R. Universidad de La Serena. Departamento de Biología. Instituto de Ecología y Biodiversidad. Centro de Estudios Avanzados en Zonas Aridas; ChileFil: Rozzi, Ricardo. Universidad de La Serena. Departamento de Biología. Instituto de Ecología y Biodiversidad; ChileFil: Vanderbilt, Kristin University of New Mexico. Department of Biology. Sevilleta Long-Term Ecological Research Site; Estados UnidosFil: Oyarce, Guillermo University of North Texas. Library and Information Sciences; Estados UnidosFil: Fernandez, Roberto J. University of North Texas, Department of Biological Sciences; Estados Unido

Ground-Truthing Satellite Imagery with Phenological Observations: Visual Observations from Grasslands at the Sevilleta National Wildlife Refuge, New Mexico

Phenology is the study of recurring natural phenomena. The seasonal greening-up and greening-down of dominant vegetation can be used as a predictor for a variety of processes and variables at local to global scales. The use of satellites to monitor land surface phenology is important for understanding local and regional ecosystem variability, identifying change over time, and potentially predicting ecosystem response to short and long-term changes in climate. However, the relationship between how phenology is expressed on the ground and how it is interpreted from satellites is poorly understood because phenological stages do not always correspond well to changes in spectral reflectance. In this study, we explored the relationship between greenness as measured by digital camera, the human eye, and ASTER imagery in two perennial grasslands at the Sevilleta National Wildlife Refuge in central New Mexico

Beyond Discovery: Cross-Platform Application of Ecological Metadata Language in Support of Quality Assurance and Control

Metadata may be generally understood to support discovery and performance of bibliographic functions against a given resource or set of resources. For example, a limited set of basic descriptive metadata can be used to index sets of items, group or otherwise associate similar items through shared metadata values, or to establish means of defining and enforcing relevance or other ranking systems. Within the context of curating research data, descriptive and other types of metadata (notably those defined the CCSDS Reference Model for an Open Archival Information System) may be more broadly applied to administer access and reuse policies, define system requirements, or perform quality assurance and control functions. However, whereas domain repositories such as the Long Term Ecological Research (LTER) Network Data Portal may capitalize on complex metadata schema such as the Ecological Metadata Language (EML) to perform an array of descriptive, technical, provenance, other repository functions, transferring data between these and more general, domain agnostic preservation systems such as university institutional repositories (IR) can result in a loss of features or services when descriptive metadata alone are crosswalked into the (typically Dublin Core) IR metadata schema. By way of exploring methods for maximizing the service and feature potential of complex metadata as harvested form a domain repository for archiving within an IR, a recent collaboration between the University of New Mexico Libraries and the Sevilleta LTER station demonstrates the application of EML at multiple stage in the data lifecycle as a means of performing quality assurance and control functions

LTER Information Management and Collaborative Learning Environments

The need for information management is growing in this age of digital data and information sharing. With growing expectations for data accessibility and needs for data organization, scientific networks face challenges unique to long-term, large-scale scientific endeavors including a recognized gap between skills in information management and the needs – both recognized and unrecognized. Amidst the diversity of tools and technologies available, there are changes in scientific practices to consider that add to the data work in individual investigator’s laboratories and the work involved in supporting collaborative project teams. There are even more profound cultural shifts involved as collaborative systems are developed at multiple, interdependent scales, moving from short-term, single site projects to longer-term, multi-site distributed networks (NSF, 2002, p.15). To support creation and dissemination of knowledge about information management, an NSF supplement proposal was submitted in 2009 to the NSF LTER program office. The request was framed as follows: “We are requesting funds to bring together a group of specialists to 1) define a course of action and guidelines for creating a forum with educational materials on information management and 2) define the research questions we will pursue in a larger proposal.” The idea of initiating an education-oriented information management learning commons grew from collaboration among participants in two networks in the International Long Term Ecological Research Network (ILTER): the US Long Term Ecological Research Program (LTER) and the Finnish Long-Term Socio- Ecological Research (FinLTSER) Network. With Finnish expertise in relevant topics and data managers interested in the commons located at or near Oulu University, the meeting was planned for Oulu University and referred to as ‘the Oulu meeting’. Workshop participants from both networks recognized the need to consider development of some type of life-long, life-wide learning arrangements for information managers. The US Long-Term Ecological Research Network began in 1980. Due to a fortuitous accumulation of insights developed from previous community efforts, of bold visions from charismatic well-placed leaders, of holistic perspectives inherent to ecological science, and of a deep understanding about data matters, data management emerged early on as a required role at each of the U.S. LTER sites. The inclusion of a data manager at a site’s inception can be recognized as a strategic, formative factor. Further, the understanding that ‘data matters’ and that there are new types of work is a message that currently travels informally among ILTER participants. The role and its responsibilities have evolved and broadened in the last decade as is evident in the name change within the US LTER from ‘data manager’ to ‘information manager’ (Baker et al., 2000; Baker and Millerand, 2010). The generation of effective resources to scaffold articulation of and learning about information management roles is, however, at an early stage. This report summarizes start-up efforts in gathering and conceptualizing information about information management (IM) and collaborative learning environments such as a Virtual Learning Commons (VLC). Plans and products are discussed in Section 1; a timeline is given in Section 2 along with a description of initial events. The Oulu meeting activities are detailed in Section 3. Discussion and final thoughts are summarized in Sections 4 and 5, respectively. A list of abbreviations and online links is provided in Appendix 7.1 along with our 2009 proposal, the 2009 LTER All-Scientists Meeting Working Group Reports, and the Oulu meeting agenda

Achieving FAIR Data Principles at the Environmental Data Initiative, the US-LTER Data Repository

The Environmental Data Initiative (EDI) is a continuation and expansion of the original United Stated Long-Term Ecological Research Program (US-LTER) data repository which went into production in 2013. Building on decades of data management experience in LTER, EDI is addressing the challenge of publishing a diverse corpus of research data (Servilla et al. 2016). EDI’s accomplishments span all aspects of the data curation and publication lifecycle, including repository cyberinfrastructure, outreach and training, and enhancements to data documentation methodologies used by the environmental and ecological research communities. EDI is managing almost 43,000 unique data packages and their revisions from a community of nearly 2,300 individual data authors, most of which are contributed by LTER sites, and are openly accessible and documented with rich science metadata in the Ecological Metadata Language (EML) standard. Here we will present how EDI achieves FAIR data principles (Wilkinson et al. 2016, Stall et al. 2017), and report data use metrics as a measure of success. The FAIR principles serve as benchmarks for EDI’s operation and management: the data we curate are Findable because they reside in an open repository, with unique and persistent digital object identifiers (DOIs) and standard metadata indexed as a searchable resource; they are Accessible through industry standard protocols and are, in most cases, under an open-access license (access control is available if required); Interoperability is achieved by archiving data in commonly used file formats, and both metadata and data are machine readable and accessible; rich, high quality science metadata, with automated congruence and completeness checking, render data fit for Reuse in multiple contexts and environments, along with easily generated data provenance to document their lineage. The success of this approach is proven by the number and spatial and temporal extent of recent re-analyses and synthesis efforts of these data. Although formal data citations are not yet common practice, a Google Scholar search reveals over 400 journal articles crediting data re-use through an EDI DOI. However, despite improved data availability, researchers still report that the largest time investment in synthesis projects is discovering, cleaning and combining primary datasets until all data are completely understood and converted to a similar format. Starting with long-term biodiversity observation data EDI is addressing this issue by implementing a pre-harmonization of thematically similar data sets. Positioned between the data author’s specific data format and larger biodiversity data stores or synthesis projects, this approach allows uniform access without the loss of ancillary information. This pre-harmonization step may be accomplished by data managers because the dataset still contains all original information without any aggregation or science question specific decisions for data omission or cleaning. The data are still distributed into distinct datasets allowing for asynchronous updating of long-term observations. The addition of specific and standardized metadata makes them easily discoverable

Team approach to data synthesis: the playbook for creating a centralized, dynamic, and sustainable ANPP database, A

The SGS-LTER research site was established in 1980 by researchers at Colorado State University as part of a network of long-term research sites within the US LTER Network, supported by the National Science Foundation. Scientists within the Natural Resource Ecology Lab, Department of Forest and Rangeland Stewardship, Department of Soil and Crop Sciences, and Biology Department at CSU, California State Fullerton, USDA Agricultural Research Service, University of Northern Colorado, and the University of Wyoming, among others, have contributed to our understanding of the structure and functions of the shortgrass steppe and other diverse ecosystems across the network while maintaining a common mission and sharing expertise, data and infrastructure.Includes bibliographical references.The Grasslands Data Integration (GDI) project has brought together ecologists, information managers and computer scientists to address the interdisciplinary challenges of integrating ANPP data from multiple sources. In this poster we present 1) the necessity to coordinate expertise and information to integrate ANPP data and metadata from five national and international grassland LTER sites, 2) the data model we designed to archive and serve the data, and 3) analysis planned for the future. This collaboration is an example of how professionals with inter-related work experience build a community of experts and a successful data product for the LTER (Baker and Millerand 2007).NSF Canopy Database Project (NSF Grants: DBI-0417311, DBI-0319309), JRN-LTER (NSF Grant: DEB-0080412), KNZ-LTER (NSF Grant: DEB-0218210), SEV-LTER (NSF Grant: DEB-0080529), and SGS-LTER (NSF Grant: DEB-0217631)

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