Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science and data reuse

Patricia A. Soranno, Edward G. Bissell, Kendra S. Cheruvelil, Samuel T. Christel, Sarah M. Collins, C. Emi Fergus, Christopher T. Filstrup, Jean Francois Lapierre, Noah R. Lottig, Samantha K. Oliver, Caren E. Scott, Nicole J. Smith, Scott Stopyak, Shuai Yuan, Mary Tate Bremigan, John A. Downing, Corinna Gries, Emily N. Henry, Nick K. Skaff, Emily H. StanleyCraig A. Stow, Pang Ning Tan, Tyler Wagner, Katherine E. Webster

Research output: Contribution to journalReview articlepeer-review

65 Scopus citations

Abstract

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km2). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

Original languageEnglish (US)
Article number28
JournalGigaScience
Volume4
Issue number1
DOIs
StatePublished - 2015

Bibliographical note

Funding Information:
Support was provided by the National Science Foundation MacroSystems Biology Program in the Emerging Frontiers Division of the Biological Sciences Directorate (EF-1065786 to MSU, EF-1065649 to ISU, and EF-1065818 to UW) and the USDA National Institute of Food and Agriculture, Hatch project 176820. KEW also thanks the STRIVE Programme (2011-W-FS-7) from the Environmental Protection Agency, Ireland, for support. We thank the numerous federal and state agency professionals, tribal agency personnel, non-profit agency personnel, and university principal investigators for providing both public and personal datasets to the LAGOSLIMNO database (listed in Additional file 17). We also thank the national lake survey programs, NSF Long Term Ecological Research (LTER) programs, and citizen monitoring programs that provided data to LAGOS. This is Great Lakes Environmental

Funding Information:
Support was provided by the National Science Foundation MacroSystems Biology Program in the Emerging Frontiers Division of the Biological Sciences Directorate (EF-1065786 to MSU, EF-1065649 to ISU, and EF-1065818 to UW) and the USDA National Institute of Food and Agriculture, Hatch project 176820. KEW also thanks the STRIVE Programme (2011-W-FS-7) from the Environmental Protection Agency, Ireland, for support. We thank the numerous federal and state agency professionals, tribal agency personnel, non-profit agency personnel, and university principal investigators for providing both public and personal datasets to the LAGOSLIMNO database (listed in Additional file 17). We also thank the national lake survey programs, NSF Long Term Ecological Research (LTER) programs, and citizen monitoring programs that provided data to LAGOS. This is Great Lakes Environmental Research Laboratory contribution number 1371. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.

Publisher Copyright:
© 2015 Soranno et al.

Copyright:
Copyright 2017 Elsevier B.V., All rights reserved.

Keywords

  • Data harmonization
  • Data reuse
  • Data sharing
  • Database documentation
  • Ecoinformatics
  • Integrated database
  • LAGOS
  • Landscape limnology
  • Macrosystems ecology
  • Water quality

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