Data Infrastructures for Estuarine and Coastal Ecological Syntheses
- 444 Downloads
Holistic understanding of estuarine and coastal environments across interacting domains with high-dimensional complexity can profitably be approached through data-centric synthesis studies. Synthesis has been defined as “the inferential process whereby new models are developed from analysis of multiple data sets to explain observed patterns across a range of time and space scales.” Examples include ecological—across ecosystem components or organization levels, spatial—across spatial scales or multiple ecosystems, and temporal—across temporal scales. Though data quantity and volume are increasingly accessible, infrastructures for data sharing, management, and integration remain fractured. Integrating heterogeneous data sets is difficult yet critical. Technological and cultural obstacles hamper finding, accessing, and integrating data to answer scientific and policy questions. To investigate synthesis within the estuarine and coastal science community, we held a workshop at a coastal and estuarine research federation conference and conducted two case studies involving synthesis science. The workshop indicated that data-centric synthesis approaches are valuable for (1) hypothesis testing, (2) baseline monitoring, (3) historical perspectives, and (4) forecasting. Case studies revealed important weaknesses in current data infrastructures and highlighted opportunities for ecological synthesis science. Here, we list requirements for a coastal and estuarine data infrastructure. We model data needs and suggest directions for moving forward. For example, we propose developing community standards, accommodating and integrating big and small data (e.g., sensor feeds and single data sets), and digitizing ‘dark data’ (inaccessible, non-curated, non-archived data potentially destroyed when researchers leave science).
KeywordsSynthesis and integration studies Data Research practices Coastal and estuarine science Informatics Data infrastructure
The authors thank the Coastal and Estuarine Research Federation for supporting their data workshop at the 2013 meeting in San Diego and the workshop participants for providing their input. W. M. Kemp and J. Milliman generously provided their time and information regarding their previous coastal and estuarine ecological syntheses. The authors would like to thank two anonymous reviewers who made comments that significantly improved the manuscript.
- Allinson, Julie. 2006. OAIS as a reference model for repositories: An evaluation. White Rose Research. http://eprints.whiterose.ac.uk/3464/1/Drs-OAIS-evaluation-0.5.pdf. Accessed 28 September 2014.
- Baker, Karen S., Barbara J. Benson, Don L. Henshaw, Darrell Blodgett, John H. Porter, and Susan G. Stafford. 2000. Evolution of a multisite network information system: The LTER information management paradigm. BioScience 50: 963–978. doi: 10.1641/0006-3568(2000)050[0963:EOAMNI]2.0.CO;2.CrossRefGoogle Scholar
- Ball, William P., Damian C. Brady, Maureen T. Brooks, Randal Burns, Benjamin E. Cuker, Dominic M. Di Toro, Thomas F. Gross, W. Michael Kemp, Laura Murray, Rebecca R. Murphy, Eric Perlman, Michael Piasecki, Jeremy M. Testa, and Ilya Zaslavsky. 2008. Prototype system for multidisciplinary shared cyberinfrastructure: Chesapeake Bay Environmental Observatory. Journal of Hydrologic Engineering 13: 960–970. doi: 10.1061/(ASCE)1084-0699(2008)13:10(960)).CrossRefGoogle Scholar
- Baranski, B., T. Deelmann, and B. Schäffer. 2010. Pay-per-use revenue models for geooprocessing services in the cloud. In ISPRS Archives, XXXVIII-4/W13, WebMGS 2010: 1st International Workshop on Pervasive Web Mapping, Geoprocessing and Services, ed. Brovelli, M.A., S. Dragicevic, S. Li, and B. Veenendaal, August 26–27, 2010, Como, Italy: International Society for Photogrammetry and Remote Sensing, 246 pp.Google Scholar
- Barseghian, Derik, Ilkay Altintas, Matthew B. Jones, Daniel Crawl, Nathan Potter, James Gallagher, Peter Cornillon, et al. 2010. Workflows and extensions to the Kepler scientific workflow system to support environmental sensor data access and analysis. Special Issue: Advances in Environmental Information Management 5: 42–50. doi: 10.1016/j.ecoinf.2009.08.008.Google Scholar
- Boudreau, P. R., P. J. F. Geerders, and J. C. Pernetta. 1996. LOICZ data and information system plan. http://loicz.org/imperia/md/content/loicz/print/rsreports/loicz_data.pdf
- Browman, Howard I., Philippe M. Cury, Ray Hilborn, Simon Jennings, Heike K. Lotze, Pamela M. Mace, Steven Murawski, Daniel Pauly, Michael Sissenwine, Konstantinos I. Stergiou, and Dirk Seller. 2004. Perspectives on ecosystem-based approaches to the management of marine resources. Marine Ecology Progress Series 274: 269–303.CrossRefGoogle Scholar
- Bryant, Randal E. 2011. Data-intensive scalable computing for scientific applications. Computing in Science & Engineering 13: 25–33. doi: 10.1109/MCSE.2011.73.
- Callaghan, Sarah, Steve Donegan, Sam Pepler, Mark Thorley, Nathan Cunningham, Peter Kirsch, Linda Ault, Patrick Bell, Rod Bowie, and Adam Leadbetter. 2012. Making data a first class scientific output: Data citation and publication by NERC’s environmental data centres. International Journal of Digital Curation 7: 107–113.CrossRefGoogle Scholar
- Chandras, Christina, Thomas Weaver, Michael Zouberakis, Damian Smedley, Klaus Schughart, Nadia Rosenthal, John M. Hancock, George Kollias, Paul N. Schofield, and Vassilis Aidinis. 2009. Models for financial sustainability of biological databases and resources. Database. doi: 10.1093/database/bap017.Google Scholar
- Codispoti, Louis A., Vince Kelly, Anne E. Thessen, Paty Matrai, Steve Suttles, Victoria Hill, Michael Steele, and Bonnie Light. 2013. Synthesis of primary production in the Arctic Ocean: III. Nitrate and phosphate based estimates of net community production. Progress in Oceanography 110: 126–150.CrossRefGoogle Scholar
- Costello, Mark J., Ward Appeltans, Nicolas Bailly, Walter G. Berendsohn, Yde de Jong, Martin Edwards, Rainer Froese, Falk Huettmann, Wouter Los, Jan Mees, Hendrik Segers, and Frank A. Bisby. 2014. Strategies for the sustainability of online open-access biodiversity databases. Biological Conservation 173: 155–165.CrossRefGoogle Scholar
- Downs, Robert R., and Robert S. Chen. 2013. Towards sustainable stewardship of digital collections of scientific data. http://www.gsdi.org/gsdiconf/gsdi13/papers/130.pdf
- DSWG, Data Sharing Working Group, GEO. 2015. GEOSS data sharing principles post 2015. http://www.earthobservations.org/documents/dswg/Annex%20III%20-%20GEOSS%20Data%20Sharing%20Principles%20Post-2015.pdf
- Duerr, Ruth, Ron Weaver, and Mark A. Parsons. 2010. A new approach to preservation metadata for scientific data—a real world example. In Standard-based data and information systems for earth observation, lecture notes in geoinformation and cartography, 113–125. Berlin Heidelberg: Springer.Google Scholar
- Enke, Neela, Anne E. Thessen, Kerstin Bach, Jörg Bendix, Bernhard Seeger, and Birgit Gemeinholzer. 2012. The user’s view on biodiversity data sharing—investigating facts of acceptance and requirements to realize a sustainable use of research data. Ecological Informatics 11: 25–33.CrossRefGoogle Scholar
- Fiorino, Daniel J. 1995. Making environmental policy. Berkeley: University of California Press.Google Scholar
- Henneken, Edwin A., and Alberto Accomazzi. 2011. Linking to data-effect on citation rates in astronomy. arXiv preprint arXiv:1111.3618.Google Scholar
- Howe, Bill. 2012. Virtual applicances, cloud computing, and reproducible research. Computing in Science & Engineering 14:36. doi: 10.1109/MCSE.2012.62.
- Karasti, Helena, Karen S. Baker, and Eija Halkola. 2006. Enriching the notion of data curation in E-Science: Data managing and information infrastructuring in the Long Term Ecological Research (LTER) network. Computer Supported Cooperative Work (CSCW) 15: 321–358. doi: 10.1007/s10606-006-9023-2.CrossRefGoogle Scholar
- Kelly, Ruth, Mathieu G. Lundy, Frédéric Mineur, Chris Harrod, Christine A. Maggs, Nicolas E. Humphries, David W. Sims, and Neil Reid. 2014. Historical data reveal power-law dispersal patterns of invasive aquatic species. Ecography 37: 581–590. doi: 10.1111/j.1600-0587.2013.00296.x.CrossRefGoogle Scholar
- Kemp, W. Michael, Walter R. Boynton, Jason E. Adolf, Donald F. Boesch, William C. Boicourt, Grace Brush, Jeffrey C. Cornwell, Thomas R. Fisher, Patricia M. Glibert, and Jim D. Hagy. 2005. Eutrophication of Chesapeake Bay: Historical trends and ecological interactions. Marine Ecology Progress Series 303: 1–29.CrossRefGoogle Scholar
- Lookingbill, Todd R., Geoff Sanders, Shawn Carter, Ben Best, Ben J. Longstaff, and Jane M. Hawkey. 2010. Chapter 11: Program design developing a comprehensive data strategy. In Integrating and applying science: a handbook for effective coastal ecosystem assessment, ed. Ben J. Longstaff, Tim J.B. Carruthers, William C. Dennison, Todd R. Lookingbill, Jane M. Hawkey, Jane E. Thomas, E. Caroline Wicks, and Joanna L. Woerner, 167–186. Cambridge: IAN Press.Google Scholar
- Mattmann, Chris, and Jukka Zitting. 2011. Tika in action. Shelter Island: Manning.Google Scholar
- Milliman, John D., Christine Rutkowski and Michel Meybeck, 1995. River discharge to the sea: A global river index. LOICZ Reports and Studies, Netherlands Institute for Sea Research, 125 p.Google Scholar
- Milliman, John D., and Katherine L. Farnsworth. 2013. River discharge to the coastal ocean: a global synthesis. 2nd Edition. Cambridge University Press, 394 pp.Google Scholar
- Morris, Paul J., Maureen A. Kelly, David B. Lowery, James A. Macklin, Robert A. Morris, Donna Tremonte, and Zhimin Wang. 2009. Filtered Push: Annotating distributed data for quality control and fitness for use analysis. American Geophysical Union, Fall Meeting 2009, abstract #IN34B-08.Google Scholar
- Nestler, Angelika, Michael Berglund, Frederik Accoe, Steluta Duta, Dongmei Xue, Pascal Boeckx, and Philip Taylor. 2011. Isotopes for improved management of nitrate pollution in aqueous resources: Review of surface water field studies. Environmental Science and Pollution Research 18: 519–533.CrossRefGoogle Scholar
- PARSE Insight. 2010. Insight into digital preservation of research output in Europe: Case studies report. PARSE.Insight archives. http://www.parse-insight.eu/downloads/PARSE-Insight_D3-3_CaseStudiesReport.pdf. Accessed 29 September 2014.
- Parsons, Mark A. and Ruth Duerr. 2012. Data identifiers, versioning, and micro-citation. AGU 2012 Fall Meeting ePosters. http://fallmeeting.agu.org/2012/files/2012/11/parsons_citation_agu2012.pdf. Accessed 29 September 2014.
- Pernetta, J. C., and J. D. Milliman. 1995. [Eds.] Land-ocean interactions in the coastal zone implementation plan. IGBP Report No. 33, IGBP, Stockholm. 215 pp.Google Scholar
- Piwowar, Heather. 2013. Altmetrics: Value all research products. Nature 493: 159.Google Scholar
- Pritchard, Donald W. 1967. What is an estuary: Physical viewpoint. Estuaries 83: 3–5.Google Scholar
- Probst, Florian, Andrew Gordon, and Ivan Dornelas. 2006. OGC Discussion paper: Ontology-based representation of the OGC observations and measurements model. Institute for Geoinformatics (IFGI) Open Geospatial Consortium 2006. http://seres.uni-muenster.de/o%26m/O%26M_discussion_paper.pdf. Accessed 29 September 2014.
- RDA, Research Data Alliance. 2015. Data Citation Working Group recommendations https://rd-alliance.org/groups/data-citation-wg.html
- Reichman, J.H., and Paul F. Uhlir. 2003. A contractually reconstructed research commons for scientific data in a highly protectionist intellectual property environment. Law and Contemporary Problems 66: 315–462.Google Scholar
- Robbins, Robert J. 2011. Data management for LTER: 1980–2010: A position paper. http://www.nsf.gov/pubs/2012/bio12002/bio12002.pdf. Accessed 29 September 2014.
- Ross, D.A. 1995. Introduction to oceanography. New York: HarperCollins College Publishers.Google Scholar
- Simons, James D., Yuan May, Carollo Cristina, Vega-Cendejas Maru, Shirley Thomas, Maria L.D. Palomares, Roopnarine Peter, Arenas Luis Gerardo Abarca, Ibañez Ana, Holmes Jeff, Schoonard Cristina Mazza, Hertog Rachel, Reed Dave, and Poelen Jorrit. 2013. Building a fisheries trophic interaction database for management and modeling research in the Gulf of Mexico large marine ecosystem. Bulletin of Marine Science 89: 135–160.CrossRefGoogle Scholar
- Taylor, Chris F., Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A. Ball, Pierre-Alain Binz, Molly Bogue, and Tim Booth. 2008. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology 26: 889–896.CrossRefGoogle Scholar
- Thomer, Andrea, Gaurav Vaidya, Robert Guralnick, David Bloom, and Laura Russell. 2012. From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks. ZooKeys 235.Google Scholar
- Thompson, Ernest F. 1926. An introduction to the natural history of the Heathcote Estuary and New Brighton Beach, Canterbury-New Zealand. A study in littoral ecology. Unpublished Ph.D. Thesis, University of Caterbury, Christchurch, New Zealand. 155 pp.Google Scholar
- Thönssen, Barbara. 2010. An enterprise ontology building the bases for automatic metadata generation. In Proceedings of the 4th International Conference on Metadata and Semantic Research, MTSR 1200, 195–210. Madrid: Springer.Google Scholar
- Vafeidis, Athanasios T., Robert J. Nicholls, McFadden Loraine, Richard S.J. Tol, Hinkel Jochen, Spencer Tom, Paul S. Grashoff, Boot Gerben, and Richard J.T. Klein. 2008. A new global coastal database for impact and vulnerability analysis to sea-level rise. Journal of Coastal Research 24: 917–924.Google Scholar
- Vines, Timothy H., Arianne Y.K. Albert, Rose L. Andrew, Florence Débarre, Dan G. Bock, Michelle T. Franklin, Kimberly J. Gilbert, Jean-Sébastien Moore, Sébastien Renaut, and Diana J. Rennison. 2014. The availability of research data declines rapidly with article age. Current Biology 24: 94–97.CrossRefGoogle Scholar
- Weber, Nicholas M., Karen S. Baker, Andrea K. Thomer, Tiffany C. Chao, and Carole L. Palmer. 2012. Value and context in data use: Domain analysis revisited. Proceedings of the American Society for Information Science and Technology 49: 1–10.Google Scholar
- Wheeler, William Henry. 1896. A history of the fens of South Lincolnshire: Being a description of the rivers Witham and Welland and their estuary, and an account of the reclamation, drainage, and enclosure of the fens adjacent thereto. JM Newcombe.Google Scholar
- Williams, P.J.L.B. 2004. Meters, kilograms, seconds but no bomb units. A zero tolerance approach to units. (With apologies to Lynne Truss). Limnology and Oceanography Bulletin 13: 29–32. doi: 10.1002/lob.200413229/epdf.
- WoRMS Editorial Board (2014). World Register of Marine Species. Available from http://www.marinespecies.org at VLIZ. Accessed 1 October 2014.