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1. OBIS Infrastructure, Lessons Learned, and Vision for the Future

Author

Eduardo Klein, Ward Appeltans, Pieter Provoost, Hanieh Saeedi, Abigail Benson, Lenore Bajona, Ana Carolina Peralta, and R. Sky Bristol

Subjects
ocean biodiversity, biogeography, research infrastructure, open-access, data and information, science-policy, Science, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

This mini-review paper analyses the achievements of the Ocean Biogeographic Information System (OBIS), as a distributed global data system and as a community of data contributors and users. We highlight some issues and challenges and identify ways OBIS is trying to address these with developing community standards, protocols and best practices, applying new innovative technologies, improving human capacity through training, and establishing beneficial partnerships. With the release of the second generation of OBIS (OBIS 2.0), we now have a more solid foundation to build improved data processing/integration workflows, new data synthesis routines that add value to OBIS data, and new types of products and applications for scientific and decision-making. The future of OBIS will be in working toward an open and inviting process of co-developing OBIS as a global networked open-source data system that will enable the community to organize, document, and contribute analytical codes that interface directly with OBIS, provide analyses, and share results. The main challenges will be in mobilizing and organizing the scientific community to publish richer and high quality data more rapidly in support of developing robust and timely indicators of status and change on Essential Ocean Variables and Essential Biodiversity Variables.

Published
2019
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2. OBIS Infrastructure, Lessons Learned, and Vision for the Future

Author

Ana Carolina Peralta, Ward Appeltans, R. Sky Bristol, Eduardo Klein, Abigail Benson, Hanieh Saeedi, Pieter Provoost, and Lenore Bajona

Subjects
ocean biodiversity, 0106 biological sciences, lcsh:QH1-199.5, 010504 meteorology & atmospheric sciences, Computer science, Interface (Java), Process (engineering), Best practice, data and information, Ocean Engineering, lcsh:General. Including nature conservation, geographical distribution, Aquatic Science, Oceanography, 01 natural sciences, research infrastructure, Community standards, lcsh:Science, biogeography, 0105 earth and related environmental sciences, Water Science and Technology, Global and Planetary Change, 010604 marine biology & hydrobiology, Data science, Ocean Biogeographic Information System, Workflow, Data quality, lcsh:Q, Science policy, open-access, science-policy
Abstract

This mini-review paper analyses the achievements of the Ocean Biogeographic Information System (OBIS), as a distributed global data system and as a community of data contributors and users. We highlight some issues and challenges and identify ways OBIS is trying to address these with developing community standards, protocols and best practices, applying new innovative technologies, improving human capacity through training, and establishing beneficial partnerships. With the release of the second generation of OBIS (OBIS 2.0), we now have a more solid foundation to build improved data processing/integration workflows, new data synthesis routines that add value to OBIS data, and new types of products and applications for scientific and decision-making. The future of OBIS will be in working toward an open and inviting process of co-developing OBIS as a global networked open-source data system that will enable the community to organize, document, and contribute analytical codes that interface directly with OBIS, provide analyses, and share results. The main challenges will be in mobilizing and organizing the scientific community to publish richer and high quality data more rapidly in support of developing robust and timely indicators of status and change on Essential Ocean Variables and Essential Biodiversity Variables.

Published
2019

3. A Conceptual Enterprise Framework for Managing Scientific Data Stewardship

Author

Curt Tilmes, Ge Peng, Edward J. Kearns, Tom Maycock, John J. Bates, R. Sky Bristol, Scott Hausman, Otis B. Brown, and Jeffrey L. Privette

Subjects
Information management, PDCA-cycle, Process management, Geospatial analysis, 010504 meteorology & atmospheric sciences, Information Management, Domain Stewards, User requirements document, computer.software_genre, 01 natural sciences, Article, Open Data, Agency (sociology), Computer Science (miscellaneous), lcsh:Science (General), 0105 earth and related environmental sciences, Government, Scientific Data Stewardship, Information Management, Data Management, Data Quality Management, 05 social sciences, Scientific Data Stewardship, Enterprise Framework, Maturity Matrix, Research Data, Computer Science Applications, Open data, Stewardship, Business, 0509 other social sciences, 050904 information & library sciences, computer, PDCA, lcsh:Q1-390
Abstract

Scientific data stewardship is an important part of long-term preservation and the use/reuse of digital research data. It is critical for ensuring trustworthiness of data, products, and services, which is important for decision-making. Recent U.S. federal government directives and scientific organization guidelines have levied specific requirements, increasing the need for a more formal approach to ensuring that stewardship activities support compliance verification and reporting. However, many science data centers lack an integrated, systematic, and holistic framework to support such efforts. The current business- and process-oriented stewardship frameworks are too costly and lengthy for most data centers to implement. They often do not explicitly address the federal stewardship requirements and/or the uniqueness of geospatial data. This work proposes a data-centric conceptual enterprise framework for managing stewardship activities, based on the philosophy behind the Plan-Do-Check-Act (PDCA) cycle, a proven industrial concept. This framework, which includes the application of maturity assessment models, allows for quantitative evaluation of how organizations manage their stewardship activities and supports informed decision-making for continual improvement towards full compliance with federal, agency, and user requirements.

Published
2018

4. Community for Data Integration 2016 annual report

Author

Norman B. Bliss, Todd M. Preston, Daniel J. Wieferich, Marcia McNiff, Brad Williams, Scott G. Leibowitz, A. Lance Everette, Francis L. Lightsom, Jon J. Amberg, Theresa M. Crimmins, Jeff T. Falgout, Colin Talbert, Sharon Waltman, Rachel T. Bolus, S. Grace McCalla, Eric T. Sundquist, Randall J. Hunt, Leslie Hsu, Nancy J. Hoebelheinrich, Marc H. Weber, Jake F. Weltzin, Roy Sando, Roland J. Viger, Benjamin M. Sleeter, Andrew R. Bock, Kevin D. Henry, John C. Nelson, Paul S. Earle, Katherine J. Chase, Jason Sherba, Michael N. Fienen, Michelle R. Guy, Jeanne M. Jones, Rusty Griffin, Jeffrey T. Morisette, Dana M. Infante, Vivian B. Hutchison, R. Lee Marsh, Richard A. Erickson, Richard P. Signell, Tamar Norkin, Tim Kern, Drew A. Ignizio, Alyssa Rosemartin, Madison L. Langseth, Catherine S. Jarnevich, John L. Faundeen, Lisamarie Windham-Myers, and R. Sky Bristol

Subjects
Geography, business.industry, Environmental resource management, Annual report, computer.software_genre, business, computer, Data integration
Published
2017

5. Grand challenges for integrated USGS science — A workshop report

Author

Nedal T. Nassar, Carl D. Shapiro, Toni Lyn Morelli, Adam J. Terando, Karen E. Jenni, Michael J. Focazio, Sasha C. Reed, Suzette A. Morman, Donald E. Tillitt, Edward G. Stets, Jordan S. Read, Jake F. Weltzin, Jill S. Baron, R. Sky Bristol, Julio L. Betancourt, Leslie Hsu, John W. Haines, Terry L. Sohl, Timothy R. Newman, Michael A. Tischler, Martin B. Goldhaber, Christian E. Zimmerman, Paul C.D. Milly, Richard A. Smith, Victor F. Labson, Mary Cantrill, Kevin D. Lafferty, Patricia L. Toccalino, Ward E. Sanford, Kristin A. Ludwig, Mark P. Waldrop, Paul E. Exter, Anne Wein, David J. Wald, Lauren E. Hay, and Andrea C. Ostroff

Subjects
Engineering, business.industry, Library science, business, Grand Challenges
Published
2017

6. SemantEco: A semantically powered modular architecture for integrating distributed environmental and ecological data

Author

Deborah L. McGuinness, Evan W. Patton, Linyun Fu, F. Joshua Dein, A. Patrice Seyed, Ping Wang, and R. Sky Bristol

Subjects
Knowledge management, Computer Networks and Communications, business.industry, Computer science, Environmental pollution, Linked data, Modular design, Ontology (information science), Resource (project management), Hardware and Architecture, Environmental monitoring, Semantic technology, Ecosystem, Use case, Water quality, Architecture, business, Semantic Web, Software
Abstract

We aim to inform the development of decision support tools for resource managers who need to examine large complex ecosystems and make recommendations in the face of many tradeoffs and conflicting drivers. We take a semantic technology approach, leveraging background ontologies and the growing body of linked open data. In previous work, we designed and implemented a semantically enabled environmental monitoring framework called SemantEco and used it to build a water quality portal named SemantAqua. Our previous system included foundational ontologies to support environmental regulation violations and relevant human health effects. In this work, we discuss SemantEco’s new architecture that supports modular extensions and makes it easier to support additional domains. Our enhanced framework includes foundational ontologies to support modeling of wildlife observation and wildlife health impacts, thereby enabling deeper and broader support for more holistically examining the effects of environmental pollution on ecosystems. We conclude with a discussion of how, through the application of semantic technologies, modular designs will make it easier for resource managers to bring in new sources of data to support more complex use cases.

Published
2014

8. Dam Removal Information Portal (DRIP)—A map-based resource linking scientific studies and associated geospatial information about dam removals

Author

Jonathan A. Warrick, Laura S. Craig, Daniel J. Wieferich, Jeffrey J. Duda, Vivian B. Hutchison, J. Ryan Bellmore, Katherine M. Vittum, and R. Sky Bristol

Subjects
Resource (biology), Geospatial analysis, business.industry, Dam removal, Environmental resource management, Environmental science, business, computer.software_genre, computer
Published
2016

9. Community for Data Integration 2015 annual report

Author

Heather S. Henkel, Katherine E. Wesenberg, Tim Kern, Ra'ad A. Saleh, Jennifer Carlino, David L. Govoni, Vivian B. Hutchison, Anthony L. Everette, Stan W. Smith, Daniel Buscombe, Joshua Bradley, Daniel J. Wieferich, Roland J. Viger, Jeffrey J. Duda, John L. Long, Tabitha A. Graves, J. Ryan Bellmore, Luke Winslow, Daniella D. Birch, R. Sky Bristol, Michelle M. Greenwood, Frances L. Lightsom, Jonathan A. Warrick, Rynn M. Lamb, Madison L. Langseth, Jennifer Lacey, Michelle Y. Chang, Christopher E. Soulard, and Brenda K. Jones

Subjects
Geography, business.industry, Environmental resource management, Annual report, business, computer.software_genre, computer, Data integration
Published
2016

10. Community for Data Integration 2014 annual report

Author

Eric C. Wood, Michelle R. Guy, Joseph W. Long, Michelle Y. Chang, Ryan Longhenry, Pamela L. Fuller, Tim Kern, Heather S. Henkel, Frances L. Lightsom, Craig Conzelmann, Joshua Bradley, Stan W. Smith, Robert H. Diehl, Laura E. Ellison, Janice M. Gordon, Anthony L. Everette, David L. Govoni, Paul S. Earle, Roland J. Viger, Daniella D. Birch, R. Sky Bristol, Todd M. Preston, Katherine E. Wesenberg, Jennifer Carlino, Madison L. Langseth, and Vivian B. Hutchison

Subjects
Geography, business.industry, Environmental resource management, Annual report, computer.software_genre, business, computer, Data integration
Published
2015

11. U.S. Geological Survey core science systems strategy: characterizing, synthesizing, and understanding the critical zone through a modular science framework

Author

Brian E. McCallum, R. Sky Bristol, Nathaniel L. Booth, Barbara S. Poore, Dean B. Gesch, Jay E. Diffendorfer, Suzette A. Morman, Roland J. Viger, Nina Burkardt, Ned H. Euliss, Richard P. Signell, and David M. Miller

Subjects
Engineering, business.industry, Systems science, Core (graph theory), Geological survey, Systems engineering, Critical zone, Modular design, business
Published
2013

12. Towards semantically-enabled exploration and analysis of environmental ecosystems

Author

Linyun Fu, Deborah L. McGuinness, Evan W. Patton, F. Joshua Dein, R. Sky Bristol, and Ping Wang

Subjects
Class (computer programming), Decision support system, Knowledge management, Resource (project management), Computer science, business.industry, Semantic technology, Environmental pollution, Linked data, Ontology (information science), business, Semantic Web
Abstract

We aim to inform the development of decision support tools for resource managers who need to examine large complex ecosystems and make recommendations in the face of many tradeoffs and conflicting drivers. We take a semantic technology approach, leveraging background ontologies and the growing body of open linked data. In previous work, we designed and implemented a semantically-enabled environmental monitoring framework called SemantEco and used it to build a water quality portal named SemantAqua. In this work, we significantly extend SemantEco to include knowledge required to support resource decisions concerning fish and wildlife species and their habitats. Our previous system included foundational ontologies to support environmental regulation violations and relevant human health effects. Our enhanced framework includes foundational ontologies to support modeling of wildlife observation and wildlife health impacts, thereby enabling deeper and broader support for more holistically examining the effects of environmental pollution on ecosystems. Our results include a refactored and expanded version of the SemantEco portal. Additionally the updated system is now compatible with the emerging best in class Extensible Observation Ontology (OBOE). A wider range of relevant data has been integrated, focusing on additions concerning wildlife health related to exposure to contaminants. The resulting system stores and exposes provenance concerning the source of the data, how it was used, and also the rationale for choosing the data. In this paper, we describe the system, highlight its research contributions, and describe current and envisioned usage.

Published
2012

13. Science strategy for Core Science Systems in the U.S. Geological Survey, 2013-2023

Author

Nina Burkardt, Dean B. Gesch, Suzette A. Morman, Nathaniel L. Booth, Roland J. Viger, David M. Miller, Brian E. McCallum, R. Sky Bristol, Barbara S. Poore, Jay E. Diffendorfer, Ned H. Euliss, and Richard P. Signell

Subjects
Systems science, Core (graph theory), Geological survey, Environmental science, Engineering ethics
Published
2012

15. U.S. Geological Survey Science for the Wyoming Landscape Conservation Initiative-2010 Annual Report

Author

Matthew J. Kauffman, Sarah L. Shafer, Daniel J. Manier, Kirk A. Miller, Stephen S. Germaine, Katharine Foster, M.L. Clark, David Smith, Spencer Schell, Robert R. McDougal, Zachary H. Bowen, Laura R.H. Biewick, Douglas A. Keinath, Jay E. Diffendorfer, Lisa L. Stillings, Anna D. Chalfoun, Natasha B. Carr, Michele L.W. Tuttle, Steven L. Garman, Collin G. Homer, R. Sky Bristol, Jessica Montag, Patrick J. Anderson, Cameron L. Aldridge, Cynthia P. Melcher, Timothy J. Assal, Steven W. Blecker, Gregory K. Boughton, Geneva W. Chong, Christopher J. Potter, JoAnn M. Holloway, Bradley C. Fedy, Anna B. Wilson, and Natalie Latysh

Subjects
Geography, Geological survey, Landscape conservation, Annual report, Archaeology
Published
2011

16. U.S. Geological Survey Science for the Wyoming Landscape Conservation Initiative-2009 Annual Report

Author

Michele L.W. Tuttle, Anna D. Chalfoun, Daniel J. Manier, Steven W. Blecker, Spencer Schell, Richard I. Grauch, Cameron L. Aldridge, Patrick J. Anderson, Jessica Montag, Zachary H. Bowen, Timothy J. Assal, R. Sky Bristol, Cynthia P. Melcher, Douglas A. Keinath, Collin G. Homer, Stephen S. Germaine, Robert R. McDougal, Steven L. Garman, Sarah L. Shafer, Lisa L. Stillings, Anna B. Wilson, Natalie Latysh, Natasha B. Carr, James E. Diffendorfer, Laura R.H. Biewick, Kirk A. Miller, Hall Sawyer, Constance J. Nutt, David Smith, Bradley C. Fedy, Matthew J. Kauffman, Christopher J. Potter, JoAnn M. Holloway, and Geneva W. Chong

Subjects
Geological survey, Environmental science, Landscape conservation, Annual report, Archaeology
Published
2010

17. U.S. Geological Survey Science for the Wyoming Landscape Conservation Initiative - 2008 Annual Report

Author

Collin G. Homer, Anna B. Wilson, Matthew J. Kauffman, Richard I. Grauch, Cameron L. Aldridge, Jay E. Diffendorfer, Daniel J. Manier, David Smith, Stephen S. Germaine, Michael J. Sweat, Zachary H. Bowen, Hall Sawyer, Bradley C. Fedy, Patrick J. Anderson, Steven L. Garman, Christopher J. Potter, Timothy J. Assal, Jessica Montag, Lori Anne Baer, Cynthia P. Melcher, Constance J. Nutt, R. Sky Bristol, Natasha B. Carr, Kirk A. Miller, Geneva W. Chong, and Natalie Latysh

Subjects
business.industry, Environmental resource management, Geological survey, Environmental science, Forestry, Landscape conservation, Annual report, business
Published
2009

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