Data platforms in integrative biodiversity research

Ecological Informatics

Volumn 11, Issue , 2012, Pages 1-4

  Bendix, Jörg ^a   Nieschulze, Jens ^b   Michener, William K ^c  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84865170982     PISSN: 15749541     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecoinf.2012.04.001     Document Type: Editorial

References (56)

1. Arzberger P., Schroeder P., Beaulieu A., Bowker G., Casey K., Laaksonen L., Moorman D., Uhlir P., Wouters P. An international framework to promote access to data. Science 2004, 303:1777-1778.
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nature Genetics 2000, 25:25-29.
3. Bach K., Schäfer D., Enke N., Seeger B., Gemeinholzer B., Bendix J. A comparative evaluation of technical solutions for long-term data repositories in integrative biodiversity research. Ecological Informatics 2012, 10.1016/j.ecoinf.2011.11.008.
4. Balmford A., Crane P., Dobson A., Green R.E., Mace G.M. The 2010 challenge: data availability, information needs and extraterrestrial insights. Philosophical Transactions of the Royal Society of London, Series B 2005, 360:221-228.
5. Beck E. German research programs, related to the understanding and conservation of biodiversity as an example of the impact of the Convention of Rio on an industrial nation. Lyonia 2004, 6:7-18.
6. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Research 2008, 36:D25-D30.
7. Bisby F.A. The quiet revolution: biodiversity informatics and the internet. Science 2000, 289:2309-2312.
8. Bowker G.C. Biodiversity data diversity. Social Studies of Science 2000, 30:643-683.
9. Butchart S.H.M., Walpole M., Collen B., van Strien A., Scharlemann J.P.W., Almond R.E.A., Baillie J.E.M., Bomhard B., Brown C., Bruno J., Carpenter K.E., Carr G.M., Chanson J., Chenery A.M., Csirke J., Davidson N.C., Dentener F., Foster M., Galli A., Galloway J.N., Genovesi P., Gregory R.D., Hockings M., Kapos V., Lamarque J.F., Leverington F., Loh J., McGeoch M.A., McRae L., Minasyan A., Morcillo M.H., Oldfield T.E.E., Pauly D., Quader S., Revenga C., Sauer J.R., Skolnik B., Spear D., Stanwell-Smith D., Stuart S.N., Symes A., Tierney M., Tyrell T.D., Vie J.C., Watson R. Global biodiversity: indicators of recent declines. Science 2010, 328:1164-1168.
10. Canhos V.P., Souza S., Giovanni R., Canhos D.A.L. Global biodiversity informatics: setting the scene for a "New World" of ecological modeling. Biodiversity Informatics 2004, 1:1-13.
11. Carusi C., Reimer T. Virtual Research Environment Collaborative Landscape Study http://www.jisc.ac.uk/media/documents/publications/vrelandscapereport.pdf.
12. Daltio J., Bauzer Medeiros C. Aondê: an ontology Web service for interoperability across biodiversity applications. Information Systems 2008, 33:724-753.
13. Easterbrook P.J., Matthews D.R. Fate of research studies. Journal of the Royal Society of Medicine 1992, 85:71-79.
14. Edwards J.L., Lane M.A., Nielsen E.S. Interoperability of biodiversity databases: biodiversity information on every desktop. Science 2000, 289:2312-2314.
15. Enke N., Thessen A., Bach K., Bendix J., Seeger B., Gemeinholzer B. The user's view on biodiversity data sharing - investigating facts of acceptance and requirements to realize a sustainable use of research data. Ecological Informatics 2012, 10.1016/j.ecoinf.2012.03.004.
16. Fegraus E.H., Andelman S., Jones M.B., Schildhauer M. Maximizing the value of ecological data with structured metadata: an introduction to ecological metadata language (EML) and principles for metadata creation. Bulletin of the Ecological Society of America 2005, 86:158-168.
17. Feijen M., Horstmann W., Manghi P., Robinson M., Russell R. DRIVER: building the network for accessing digital repositories across Europe. Ariadne 2007, 53:1-10.
18. Fischer M., Bossdorf O., Gockel S., Hansel F., Hemp A., Hessenmoller D., Korte G., Nieschulze J., Pfeiffer S., Prati D., Renner S., Schoning I., Schumacher U., Wells K., Buscot F., Kalko E.K.V., Linsenmair K.E., Schulze E.-D., Weisser W.W. Implementing large-scale and long-term functional biodiversity research: the biodiversity exploratories. Basic and Applied Ecology 2010, 11:473-485. 10.1016/j.baae.2010.07.009.
19. Flemonsa P., Guralnick R., Krieger J., Ranipeta A., Neufeld D. A web-based GIS tool for exploring the world's biodiversity: the Global Biodiversity Information Facility Mapping and Analysis Portal Application (GBIF-MAPA). Ecological Informatics 2007, 2:49-60.
20. Frawley W., Piatetsky-Shapiro G., Matheus C. Knowledge discovery in databases: an overview. AI Magazine 1992, 13:57-70.
21. Froese R. Ten years of FishBase. EC Fisheries Cooperation Bulletin 2001, 14:13.
22. Godfray H.C.J., Clark B.R., Kitching I.J., Mayo S.J., Scoble M.J. The web and the structure of taxonomy. Systematic Biology 2007, 56:943-955.
23. Guralnick R.P., Hill A.W., Lane M. Towards a collaborative, global infrastructure for biodiversity assessment. Ecology Letters 2007, 10:663-672.
24. Hernández Ernst V., Poigné A., Los W. LifeWatch - a large-scale eScience infrastructure to assist in understanding and managing our planet's biodiversity. Geophysical Research Abstracts 2010, 12. EGU2010-15218.
25. Jones M.B., Schildhauer M.P., Reichman O.J., Bowers S. The new bioinformatics: integrating ecological data from the gene to the biosphere. Annual Review of Ecology, Evolution, and Systematics 2006, 37:519-544.
26. Kahn S.D. On the future of genomic data. Science 2011, 331:728-729.
27. Klump J. Digitale Forschungsdaten. Nestor Handbuch: Eine kleine Enzyklopädie der digitalen Langzeitarchivierung, Boizenburg (Germany) 2010, 104-115. (http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0008-20100305375). H. Neuroth, A. Oßwald, R. Scheffel, S. Strathmann, K. Huth (Eds.).
28. Kottmann R., Gray T., Murphy S., Kagan L., Kravitz S., Lombardot T., Field D., Glöckner F.O. A standard MIGS/MIMS compliant XML schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS 2008, 12:115-121.
29. Krishtalka L., Humphrey P.S. Can natural history museums capture the future?. BioScience 2000, 50:611-617.
30. La Sorte F.A., Jetz W. Avian distributions under climate change: towards improved projections. Journal of Experimental Biology 2010, 213:862-869.
31. Laporte M.-A., Mougenot I., Garnier E. ThesauForm - Traits: a web based collaborative tool to develop a thesaurus for plant functional diversity research. Ecological Informatics 2012, ECOINF-D-11-00057R1.
32. Lotz T., Nieschulze J., Bendix J., Dobbermann M., König-Ries B. Diverse or uniform? - intercomparison of two major German project databases for interdisciplinary collaborative functional biodiversity research. Ecological Informatics 2012, 10.1016/j.ecoinf.2011.11.004.
33. MacKenzie C., Laskey K., McCabe F., Brown P., Metz R. Reference model for Service Oriented Architecture 1.0. Architecture 2006, http://docs.oasis-open.org/soa-rm/v1.0/. Retrieved from http://docs.oasis-open.org/soa-rm/v1.0/soa-rm.pdf.
34. Madin J., Bowers S., Schildhauer M., Krivov S., Pennington D., Villa F. An ontology for describing and synthesizing ecological observation data. Ecological Informatics 2007, 2:279-296.
35. Marris E. UN body will assess ecosystems and biodiversity. Nature 2010, 465:859.
36. Michener W.K. Meta-information concepts for ecological data management. Ecological Informatics 2006, 1:3-7.
37. Michener W.K., Brunt J.W., Helly J.J., Kirchner T.B., Stafford S.G. Non-geospatial metadata for the ecological sciences. Ecological Applications 1997, 7:330-342.
38. Michener W., Vieglais D., Vision T., Kunze J., Cruse P., Janee G. DataONE: Data Observation Network for Earth - preserving data and enabling innovation in the biological and environmental science. D-Lib Magazine 2011, 17(1/2).
39. Michener W.K., Allard S., Budden A., Cook R.B., Douglass K., Frame M., Kelling S., Koskela R., Tenopir C., Vieglais D.A. Participatory design of DataONE - enabling cyberinfrastructure for the biological and environmental sciences. Ecological Informatics 2012, 10.1016/j.ecoinf.2011.08.007.
40. Moonen A.-C., Bàrberi P. Functional biodiversity: an agroecosystem approach. Agriculture, Ecosystems & Environment 2008, 127:7-21.
41. Overpeck J.T., Meehl G.A., Bony S., Easterlin D.R. Climate data challenges in the 21st century. Science 2011, 331:700-702.
42. Page R.D.M. Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Briefings in Bioinformatics 2008, 9:345-354.
43. Papazoglou M. Extending the service-oriented architecture. Business Integration Journal 2005, 7:18-21.
44. Pereira H.M., Cooper H.D. Towards the global monitoring of biodiversity change. Trends in Ecology & Evolution 2006, 21:123-129.
45. Pereira H.M., Leadley P.W., Proença V., Alkemade R., Scharlemann J.P.W., Fernandez-Manjarrés J.-F., Araújo M.B., Balvanera P., Biggs R., Cheung W.W.L., Chini L., Cooper H.D., Gilman E.L., Guénette S., Hurtt G.C., Huntington H.P., Mace G.M., Oberdorff T., Revenga C., Rodrigues R., Scholes R.J., Sumaila U.R., Walpole M. Scenarios for global biodiversity in the 21st century. Science 2010, 330:1496-1501.
46. Porter J.H. Scientific databases. Ecological Data: Design, Management and Processing 2000, 48-69. Blackwell Science, Oxford, Oxford. W.K. Michener, J. Brunt (Eds.).
47. Reichman O.J., Jones M.B., Schildhauer M.P. Challenges and opportunities of open data in ecology. Science 2011, 331:703-705.
48. Sakar I.N. Biodiversity informatics: organizing and linking information across the spectrum of life. Briefings in Bioinformatics 2007, 8:347-357.
49. Sala O.E., Chapin F.S., Armesto J.J., Berlow E., Bloomfileld J., Dirzo R., Huber-Sanwald E., Huenneke L.F., Jackson R.B., Kinzig A., Leemans R., Lodge D.M., Mooney H.A., Oesterheld M., Poff N.L., Sykes M.T., Walker B.H., Walker M., Wall D.H. Biodiversity - global biodiversity scenarios for the year 2100. Science 2000, 287:1770-1774.
50. Scholes R.J., Mace G.M., Turner W., Geller G.N., Jürgens N., Larigauderie A., Muchoney D., Walther B.A., Mooney H.A. Toward a global biodiversity observing system. Science 2008, 321:1044-1045.
51. Shanmughavel P. An overview on biodiversity information in databases. Bioinformation 2007, 1:367-369.
52. Soberón J., Peterson A.T. Monitoring biodiversity loss with primary species-occurrence data: toward national-level indicators for the 2010 target of the convention on biological diversity. Ambio 2009, 38:29-34.
53. Torres R.S., Medeiros C.B., Hallerman E.A., Gonçalves M.A., Fox E.A. Integrating image and spatial data for biodiversity information management. Technical Report IC-04-012 2004, Inst. de Comp., Univ. Estadual de Campinas, Brazil, 14 pp.
54. Torres R.S., Bauzer Medei C., Gonçalves M.A., Fox E.A. A digital library framework for biodiversity information systems. International Journal on Digital Libraries 2006, 6:3-17.
55. Vision T. Open data and the social contract of scientific publishing. BioScience 2010, 60:330-331.
56. Vogt L. The future role of bio-ontologies for developing a general data standard in biology: chance and challenge for zoo-morphology. Zoomorphology 2009, 128:201-217.