Informatics and Data Management Publications from NCEAS

The NCEAS Informatics team collaborate globally on new data management and informatics developments to support synthetic research and  foster open, robust, and reproducible science. The team includes: Mark Schildhauer, Matthew B. Jones, Christopher Jones, Jing Tao, and Ben Leinfelder. Below is a listing of the publications they have co-authored:

Informatics publications by NCEAS
 

Schematic of the sample application of the SST Comparison procedure.Barseghian, Derik; Altintas, Ilkay; Jones, Matthew B.; Crawl, Daniel; Potter, Nathan; Gallagher, James; Cornillon, Peter; Schildhauer, Mark; Borer, Elizabeth T.; Seabloom, Eric W.; and Hosseini, Parviez R. 2010. Workflows and Extensions to the Kepler Scientific Workflow System to Support Environmental Sensor Data Access and Analysis. Ecological Informatics 5(1): 42–50.

Borer, Elizabeth T.; Seabloom, Eric; Jones, Matthew B.; and Schildhauer, Mark P.. 2009. Some simple guidelines for effective data management. 48. Bulletin of the Ecological Society of America. Bulletin of the Ecological Society of America. Apr:205-214.

Bowers, Shawn; Madin, Joshua S.; and Schildhauer, Mark P. 2010. Owlifier: Creating OWL-DL Ontologies from Simple Spreadsheet-Based Knowledge Descriptions. Ecological Informatics 5(1): 19–25.

Fegraus, Eric H.; Andelman, Sandy J.; and Jones, Matthew B.. 2005. Maximizing the value of ecological data with structured metadata: An introduction to Ecological Metadata Language (EML) and principles for metadata creation. 48. Bulletin of the Ecological Society of America. Bulletin of the Ecological Society of America. 86(3):158-168.

Gamon, John A.; Rahman, Faiz; Dungan, Jennifer L.; Schildhauer, Mark P.; and Huemmrich, Karl F.. 2006. Spectral network (SpecNet) - what is it and why do we need it?. 229. Remote Sensing of Environment. Remote Sensing of Environment. 103:227-235.

Jones, Christopher; Blanchette, Carol A.; Brooke, Matthew; Harris, John; Jones, Matthew B.; and Schildhauer, Mark P.. 2007. A metadata-driven framework for generating field data entry interfaces in ecology. 2710. Ecological Informatics. Ecological Informatics. 2(3):270-278.

Jones, Matthew B.. 2007. Meta-information systems and ontologies: A special feature from ISEI'06. 2710. Ecological Informatics. Ecological Informatics. 2 (3):193-194.

Jones, Matthew B.; Berkley, Chad; Bojilova, Jivka; and Schildhauer, Mark P.. 2001. Managing scientific metadata.3786. IEEE Internet Computing. IEEE Internet Computing. 5(5):59-68.

Jones, Matthew B.; Schildhauer, Mark P.; Reichman, O. J.; and Bowers, Shawn. 2006. The new bioinformatics: Integrating ecological data from the gene to the biosphere. 32. Annual Review of Ecology Evolution and Systematics. Annual Review of Ecology Evolution and Systematics. 37:519-544.

Lamanna, Christine; Blonder, Benjamin; Violle, Cyrille; Kraft, Nathan J. B.; Sandel, Brody; Šímová, Irena;. Donoghue, John C, II; Svenning, Jens-Christian; McGill, Brian J.; Boyle, Brad; Buzzard, Vanessa; Dolins, Steven; Jørgensen, Peter M.; Marcuse-Kubitza, Aaron; Morueta-Holme, Naia; Peet, Robert K.; Piel, William H.; Regetz, James; Schildhauer, Mark; Spencer, Nick; Thiers, Barbara; Wiser, Susan K.; and Enquist, Brian J.. 2014. Functional trait space and the latitudinal diversity gradienta. Proceedings of the National Academy of Sciences, 111(38) doi:10.1073/pnas.1317722111.

Leinfelder, Ben; Bowers, Shawn; O'Brien, Margaret O.; Jones, Matthew B.; Schildhauer, Mark. 2011. Using semantic metadata for discovery and integration of heterogeneous ecological data.Proceedings of the Environmental Information Management Conference (EIM 2011) (pp. 92-97).

Leinfelder, Ben; Tao, Jing; Costa, Duane; Jones, Matthew B.; Servilla, Mark; O'Brien, Margaret; and Burt, Chad. 2010. A metadata-driven approach to loading and querying heterogeneous scientific data. 2710. Ecological Informatics. Ecological Informatics. 5(1).

Ludaescher, Bertram; Altintas, Ilkay; Berkley, Chad; Higgins, Dan; Jaeger-Frank, Efrat; Jones, Matthew B.; Lee, Edward A.; Tao, Jing; and Zhao, Yang. 2006. Scientific workflow management and the Kepler system. 65. Concurrency and Computation-Practice & Experience. 18:1039-1065.

Madin, Joshua S.; Bowers, Shawn; Schildhauer, Mark P.; and Jones, Matthew B.. 2008. Advancing ecological research with ontologies. 243. Trends in Ecology and Evolution. Trends in Ecology & Evolution. 23(3)

Madin, Joshua S.; Bowers, Shawn; Schildhauer, Mark P.; Krivov, Serguei; Pennington, Deana D.; and Villa, Ferdinando. 2007. An ontology for describing and synthesizing ecological observation data. 2706. Ecological Economics. Ecological Informatics. 2:279-296.

Michener, William K. and Jones, Matthew B.. 2012. Ecoinformatics: Supporting ecology as a data-intensive science. 243. Trends in Ecology and Evolution. Trends in Ecology and Evolution. 27(2):85-93.

Mitchener, William K.; Beach, James H.; Jones, Matthew B.; Ludaescher, Bertram; Pennington, Deana D.; Pereira, Ricardo S.; Rajasekar, Arcot; and Schildhauer, Mark P.. 2007. A knowledge environment for the biodiversity and ecological sciences. 130. Journal of Intelligent Information Systems. Journal of Intelligent Information Systems. 29:111-126.

Morueta-Holme, Naia; Enquist, Brian J; McGill, Brian J; Boyle, Brad; Jørgensen, Peter M.; Ott, Jeffrey E.; Peet, Robert K.; Šímová, Irena; Sloat, Lindsey L.; Thiers, Barbara; Violle, Cyrille; Wiser, Susan K.; Dolins, Steven; Donoghue II, John C.; Kraft, Nathan J. B.; Regetz, Jim; Schildhauer, Mark; Spencer, Nick; and Svenning, Jens-Christian. 2013. Habitat Area and Climate Stability Determine Geographical Variation in Plant Species Range Sizes. Ecology Letters 16(12): 1446–1454.

Pennington, Deana D.; Athanasiadis, I. N.; Bowers, Shawn; Krivov, Serguei; Madin, Joshua S.; Schildhauer, Mark P.; and Villa, Ferdinando. 2008. Indirectly driven knowledge modeling in ecology. 123. International Journal of Metadata, Semantics and Ontologies. International Journal of Metadata, Semantics and Ontologies. 3(3):210-225.

Pennington, Deana D.; Michener, William K.; Katz, Samantha; Downey, Laura; and Schildhauer, Mark P.. 2008. Transforming scientists through technical education - a view from the trenches. 64. Computing in Science & Engineering. Computing in Science & Engineering. 10(5):28-33.

Queenborough, Simon A; Cooke, Ira R.; and Schildhauer, Mark P. 2010. Do We Need an EcoBank? The Ecology of Data-Sharing. Bulletin of the British Ecological Society 41(3): 33–35.

Reichman, O. J.; Jones, Matthew B.; and Schildhauer, Mark P.. 2011. Challenges and opportunities of open data in ecology. 8182. Science. Science. 331:703-705.

Schildhauer, Mark P. 1998.Virtual working groups at NCEAS: Using the web to facilitate scientific collaboration. Data and Information Management in the Ecological Sciences: A Resource Guide: 79.

Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve;  Beaman, Reed;  Blum, Stanley;  Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil;  Endresen, Dag; Gandolfo, Maria Alejandra;  Hanner, Robert;  Janning, Alyssa;  Krishtalka, Leonard;  Matsunaga, Andréa;  Midford, Peter; Morrison, Norman;  Tuama, Éamonn Ó.;  Schildhauer, Mark;  Smith, Barry; Stucky, Brian J.;  Thomer, Andrea;  Wieczorek, John;  Whitacre, Jamie; and Wooley, John. 2014. Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies. PloS One 9(3): e89606.