An infrastructure-oriented approach for supporting biodiversity research

Ecological Informatics

Volumn 26, Issue P2, 2015, Pages 162-172

  Candela, Leonardo ^a   Castelli, Donatella ^a   Coro, Gianpaolo ^a   Lelii, Lucio ^a   Mangiacrapa, Francesco ^a   Marioli, Valentina ^a   Pagano, Pasquale ^a  

^a ISTI CNR   (Italy)

Author keywords

Data integration; Data processing; Data sharing; Species occurrence data

Indexed keywords

BIODIVERSITY; DATA MANAGEMENT; DATA PROCESSING; DATABASE; INFORMATION SYSTEM; INFRASTRUCTURE; INTERNET; SPATIAL DISTRIBUTION; SPECIES OCCURRENCE;

EID: 84926447800     PISSN: 15749541     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecoinf.2014.07.006     Document Type: Article

References (53)

1. Amaral R., Badia R.M., Blanquer I., Braga-Neto R., Candela L., Castelli D., Flann C., De Giovanni R., Gray W.A., Jones A., Lezzi D., Pagano P., Perez-Canhos V., Quevedo F., Rafanell R., Rebello V., Sousa-Baena M., Torres E. Supporting Biodiversity Studies with the EUBrazilOpenBio Hybrid Data Infrastructure. Concurrency and Computation: Practice and Experience 2014, (n/a, n/a).
2. Ankerst M., Breunig M.M., Kriegel H.-P., Sander J. OPTICS: ordering points to identify the clustering structure. Proceedings of the 1999 ACM SIGMOD International Conference on Management of Data 1999, 49-60. ACM Press.
3. Assante M., Candela L., Castelli D., Pagano P. The D4Science research-oriented social networking facilities. ERCIM News 2014, 96:44-45. (January).
4. 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. Ecol. Inform. 2012, 11:16-24.
5. Bendix J., Nieschulze J., Michener W.K. Data platforms in integrative biodiversity research. Ecol. Inform. 2012, 11:1-4.
6. Borgman C. The conundrum of sharing research data. J. Am. Soc. Inf. Sci. Technol. 2011, 1-40.
7. Boulton G., Campbell P., Collins B., Elias P., Hall D.W., Laurie G., O'Neill O., Rawlins M., Thornton D.J., Vallance P., Walport M. Science as an Open Enterprise. Tech. rep. 2012, The Royal Society, (June).
8. Breunig M.M., Kriegel H.-P., Ng R.T., Sander J. LOF: identifying density-based local outliers. SIGMOD Rec. 2000, 29(2):93-104. (May). 10.1145/335191.335388.
9. Candela L., Castelli D., Pagano P. gCube: a service-oriented application framework on the grid. ERCIM News 2008, 72:48-49. (October).
10. Candela L., Castelli D., Pagano P. D4Science: an e-infrastructure for supporting virtual research environments. Post-proceedings of the 5th Italian Research Conference on Digital Libraries - IRCDL 2009 2009, 166-169. DELOS: an Association for Digital Libraries. M. Agosti, F. Esposito, C. Thanos (Eds.).
11. Candela L., Castelli D., Pagano P. Making virtual research environments in the cloud a reality: the gCube approach. ERCIM News 2010, 83:32-33. (October).
12. Candela L., Castelli D., Coro G., Pagano P., Sinibaldi F. Species Distribution Modeling in the Cloud. Concurrency and Computation: Practice and Experience 2013, 10.1002/cpe.3030.
13. Candela L., Castelli D., Pagano P. Virtual research environments: an overview and a research agenda. CODATA Data Sci. J. 2013, 12:GRDI75-GRDI81.
14. Candela L., De Faveri F., Lelli L., Mangiacrapa F., Marioli V., Pagano P. Accessing biodiversity databases: a domain specific query language and a unifying data model. Technical Report 2014-TR-26 2014, Istituto di Scienza e Tecnologie dell'Informazione A. Faedo, CNR.
15. Clark T., Martin S., Liefeld T. Globally distributed object identification for biological knowledgebases. Brief. Bioinform. 2004, 5(1):59-70.
16. Constable H., Guralnick R., Wieczorek J., Spencer C., Peterson A.T., The VertNet Steering Committee Vertnet: a new model for biodiversity data sharing. PLoS Biol. 2010, 8(2):e1000309. (02, URL).
17. Coro G., Pagano P., Ellenbroek A. Combining simulated expert knowledge with neural networks to produce ecological niche models for Latimeria chalumnae. Ecol. Model. 2013, 268(0):55-63. (URL http://www.sciencedirect.com/science/article/pii/S0304380013003980).
18. Coro G., Candela L., Pagano P., Italiano A., Liccardo L. Parallelising the execution of native data mining algorithms for computational biology. Concurrency and Computation: Practice and Experience 2014, (submitted for publication).
19. Costello M.J. Motivating online publication of data. Bioscience 2009, 59(5):418-427.
20. Cumming G.S., Gaidet N., Ndlovu M. Towards a unification of movement ecology and biogeography: conceptual framework and a case study on Afrotropical ducks. J. Biogeogr. 2012, 39(8):1401-1411.
21. D4Science.org D4Science Hybrid Data Infrastructure URL. http://www.d4science.org.
22. Diepenbroek M., Grobe H., Reinke M., Schindler U., Schlitzer R., Sieger R., Wefer G. Pangaea - an information system for environmental sciences. Comput. Geosci. 2002, 28(10):1201-1210. (URL http://www.sciencedirect.com/science/article/pii/S0098300402000390).
23. Edwards J.L., Lane M.A., Nielsen E.S. Interoperability of biodiversity databases: biodiversity information on every desktop. Science 2000, 289(5488):2312-2314.
24. Ellenbroek A., Pagano P. EA-CoP validation. D3.4 iMarine Project Report 2012.
25. 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. Ecol. Inform. 2012, 11:25-33.
26. Ester M., Kriegel H., Sander J., Xu X. A density-based algorithm for discovering clusters in large spatial databases with noise. Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining 1996, 226-231. AAAI Press.
27. Foster I., Zhao Y., Raicu I., Lu S. Cloud Computing and Grid Computing 360-Degree Compared. Grid Computing Environments Workshop, 2008. GCE '08 2008, 1-10.
28. Global Biodiversity Information Facility GBIF Strategic Plan 2012-2016: Seizing the Future URL. http://links.gbif.org/sp20122016.pdf.
29. Goddard A., Wilson N., Cryer P., Yamashita G. Data hosting infrastructure for primary biodiversity data. BMC Bioinforma. 2011, 12(Suppl. 5):S5.
30. Graham C.H., Ferrier S., Huettman F., Moritz C., Peterson A.T. New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol. Evol. 2004, 19(9):497-503.
31. Graham C.H., Elith J., Hijmans R.J., Guisan A., Townsend Peterson A., Loiselle B.A. The influence of spatial errors in species occurrence data used in distribution models. J. Appl. Ecol. 2008, 45(1):239-247.
32. Grassle J. The Ocean Biogeographic Information System (OBIS): an on-line, worldwide atlas for accessing, modeling and mapping marine biological data in a multidimensional geographic context. Oceanography 2000, 13(3):5-7.
33. Gray J., Szalay A.S., Thakar A.R., Stoughton C., Vandenberg J. Online scientific data curation, publication, and archiving. Technical Report MSR-TR-2002-74 2002, Microsoft Research, (July).
34. Hey T., Tansley S., Tolle K. The Fourth Paradigm: Data-intensive Scientific Discovery 2009, Microsoft Research.
35. Jetz W., McPherson J.M., Guralnick R.P. Integrating biodiversity distribution knowledge: toward a global map of life. Trends Ecol. Evol. 2012, 27(3):151-159.
36. Jolliffe I. Principal Component Analysis 2005, Wiley Online Library.
37. Jones A.C., White R.J., Orme E.R. Identifying and relating biological concepts in the catalogue of life. J. Biomed. Semant. 2011, 2(7).
38. Lenzerini M. Data integration: a theoretical perspective. PODS '02: Proceedings of the Twenty-first ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems 2002, 233-246. ACM Press, New York, NY, USA.
39. Levenshtein V. Binary codes capable of correcting deletions, insertions and reversals. Sov. Phys. Dokl. 1966, 10:707-710.
40. MacLeod C. Habitat representativeness score (HRS): a novel concept for objectively assessing the suitability of survey coverage for modelling the distribution of marine species. J. Mar. Biol. Assoc. U. K. 2010, 90(07):1269-1277.
41. MacQueen J., et al. Some methods for classification and analysis of multivariate observations. Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probability 1967, vol. 1:14. Elsevier, California, USA.
42. Meng C. Biological information standards. Bull. Assoc. Inf. Sci. Technol. 2004, 30(2). (December/January, n/a).
43. Michener W.K., Jones M.B. Ecoinformatics: supporting ecology as a data-intensive science. Trends Ecol. Evol. 2012, 27(2):85-93.
44. 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. Ecol. Inform. 2012, 11:5-15.
45. Pelleg D., Moore A. X-means: extending k-means with efficient estimation of the number of clusters. Proceedings of the Seventeenth International Conference on Machine Learning 2000, 727-734. Morgan Kaufmann, San Francisco.
46. Peterson A.T., Knapp S., Guralnick R., Sobern J., Holder M.T. The big questions for biodiversity informatics. Syst. Biodivers. 2010, 8(2):159-168. 10.1080/14772001003739369.
47. Roberts D., Moritz T. A framework for publishing primary biodiversity data. BMC Bioinforma. 2011, 12:I1.
48. TDWG Access to Biological Collections Data - ABCD. Version 2.06 URL. http://www.tdwg.org/activities/abcd/.
49. TDWG TAPIR - TDWG Access Protocol for Information Retrieval. Version 1.0 URL. http://www.tdwg.org/activities/abcd/.
50. True S. Planning the future of the World Geodetic System 1984. Position Location and Navigation Symposium, 2004 2004, 639-648. PLANS 2004, (April).
51. Vanden Berghe E., Bailly N., Coro G., Fiorellato F., Aldemita C., Ellenbroek A., Pagano P. BiOnym: a flexible workflow approach to taxon name matching. Technical Report 2014-TR-22 2014, Istituto di Scienza e Tecnologie dell'Informazione A. Faedo, CNR.
52. Wieczorek J., Bloom D., Guralnick R., Blum S., Döring M., Robertson R.D.T., Vieglais D. Darwin Core: an evolving community-developed biodiversity data standard. PLoS One 2012, 7(1).
53. Wiederhold G. Mediators in the architecture of future information systems. Computer 1992, 25(3):38-49.