Toward a knowledge infrastructure for traits-based ecological risk assessment

Integrated Environmental Assessment and Management

Volumn 7, Issue 2, 2011, Pages 209-215

  Baird, Donald J ^a   Baker, Christopher J O ^b   Brua, Robert B ^c   Hajibabaei, Mehrdad ^e   McNicol, Kearon ^d   Pascoe, Timothy J ^c   de Zwart, Dick ^f  

^a UNIVERSITY OF NEW BRUNSWICK   (Canada)

^b UNIVERSITY OF NEW BRUNSWICK   (Canada)

^c ENVIRONMENT CANADA   (Canada)

^d FRESHWATER BIOLOGICAL ASSOCIATION   (United Kingdom)

^e UNIVERSITY OF GUELPH   (Canada)

^f NATIONAL INSTITUTE FOR PUBLIC HEALTH AND THE ENVIRONMENT   (Netherlands)

Author keywords

Ecological risk assesssment; Knowledge infrastructure; Traits

Indexed keywords

ARTICLE; ECOLOGY; METHODOLOGY; RISK ASSESSMENT;

ECOLOGY; RISK ASSESSMENT;

EID: 79961069208     PISSN: 15513793     EISSN: None     Source Type: Journal    
DOI: 10.1002/ieam.129     Document Type: Article

References (42)

1. Andelman SJ, Bowles CM, Willig MR, Waide RB. 2004. Understanding environmental complexity through a distributed knowledge network. Bioscience 54:240-246.
2. Baird DJ, Rubach MN, Van den Brink PJ. 2008. Trait-based ecological risk assessment (TERA): The new frontier? Integr Environ Assess Manag 4:2-3.
3. Baird DJ, Van den Brink PJ. 2007. Using biological traits to predict species sensitivity to toxic substances. Ecotoxicol Environ Saf 67:296-301.
4. Baker CJO, Cheung K-H. 2007. Semantic web: Revolutionizing knowledge discovery in the life sciences. New York (NY): Springer. 465 p.
5. Baker CJO, Kanagasabai R, Ang WT, Veeramani A, Low H-S, Wenk MR. 2008. Towards ontology-driven navigation of the lipid bibliosphere. BMC Bioinf 9 (Suppl 1): S5.
6. Bêche L, Statzner B. 2009. Richness gradients of stream invertebrates across the USA: taxonomy- and trait-based approaches. Biodivers Conserv 18:3909- 3930.
7. Birney E, Hudson TJ, Green ED, Gunter C, Eddy S, Rogers J, Harris JR, Ehrlich SD, Apweiler R, Austin CP. 2009. Pre-publication data sharing. Nature 461:168- 170.
8. Boulton A, Piégay H, Sanders M. 2008. Turbulence and train wrecks: using knowledge strategies to the enhance application of integrative river science to effective river management. In: Brierley GJ, Fryirs KA. editors. River futures: an integrative scientific approach to river repair. Washington (DC): Island. p 28-36.
9. Chandras C, Weaver T, Zouberakis M, Smedley D, Schugart K, Rosenthal N, Hancock JM, Kollias G, Schofield PN, Aidinis V. 2009. Models for financial sustainability of biological databases and resources [Internet]. Database (2009) 2009: article ID bap017; doi:10.1093/database/bap017
10. Chen Z, Gangopadhyay A, Holden SH, Karabatis G, McGuire MP. 2007. Semantic integration of government data for water quality management. Gov Info Q 24:716-735.
11. Clark & Parsia LLC. 2010. Pellet: OWL 2 Reasoner for Java. [Accessed 2010 July 19]. Available from: clarkparsia.com/pellet.
12. Culp J, Armanini DG, Dunbar MJ, Orlofske JM, Poff NL, Pollard AI, Yates AG, Hose GC. 2011. Incorporating traits in aquatic biomonitoring to enhance causal diagnosis and prediction. Integrated Environmental Assessment and Management 7:187-197.
13. Doms A, Schroeder M. 2005. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 33(Web Server issue): W783-W786 DOI: 10.1093/nar/gki470
14. Field D, Sansone SA, Collis A, Booth T, Dukes P, Gregurick SK, Kennedy K, Kolar P, Kolker E, Maxon M, et al. 2009. 'Omics data sharing. Science 326:234-236.
15. Glover DM, Chandler CL, Doney SC, Buesseler KO, Heimerdinger G, Bishop JKB, Flierl GR. 2006. The US JGOFS data management experience. Deep-Sea Res II 53:793-802.
16. Gruber TP. 1993. A translation approach to portable ontology specifications. Knowledge Acquisition 5:199-220.
17. Guttmacher AE, Nabel EG, Collins FS. 2009. Why data-sharing policies matter. Proc Natl Acad Sci USA 106:16894.
18. Hajibabaei M, Singer GAC, Hebert PDN, Hickey DA. 2007. DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet 23:167-172.
19. Heino J, Virkkala R, Tiovonen H. 2008. Climate change ad freshwater biodiversity: Detected patterns, future trends and adaptations in northern regions. Biol Rev 84:39-54.
20. Micheli F, Halpern BS. 2005. Low functional redundancy in coastal marine reserves. Ecol Lett 8:391-400.
21. National Centre for Biomedical Ontolog. 2010. Bioportal. [Accessed 2010 July 19]. Available from: bioportal.bioontology.org. Nelson B. 2009. Empty archives. Nature 461:160-163.
22. Organisation for Economic Co-Operation and Development (OECD). 2007. OECD principles and guidelines for access to research data from public funding. Paris (FR): OECD. 24 p.
23. Pascoe TJ, Kralidis T, Cree J, Baird DJ. 2006. BugML: Implementing XML standards for sharing and interoperability of aquatic biomonitoring data [abstract]. p6 5th International Conference on Ecological Informatics, 2006 Dec 4-6; Santa Barbara (CA).
24. Piwowar HA, Day RS, Fridsma DB. 2007. Sharing detailed research data is associated with increased citation rate. PLos ONE 2:e208. DOI: 10.1371/journal.pone.0000308.
25. Poff NL, Olden JD, Vieira NKM, Finn DS, Simmons MP, Kondratieff BC. 2006. Functional trait niches of North American lotic insects: traits-based ecological applications in light of phylogenetic relationships. J North Am Benth Soc 25:730-755.
26. Rajapakse M, Kanagasabai R, Ang WT, Veeramani A, Schreiber MJ, Baker CJO. 2008. Ontology-centric knowledge integration & navigation of the dengue literature. J Biomed Inform 41:806-815.
27. Rubach MN, Baird DJ, Van den Brink PJ. 2010. A new method for ranking modespecific sensitivity of freshwater arthropods to insecticides and its relationship to biological traits. Environ Toxicol Chem 29:476-487.
28. Rubach MN, Ashauer R, Buchwalter DB, De Lange HJ, Hamer M, Preuss TG, Töpke K, Maund SJ. 2011. Framework for traits-based assessment in ecotoxicology. Integrated Environmental Assessment and Management 7:172-186.
29. Schofield PN, Bubela T, Weaver T, Portilla L, Brown SD, Hancock JM, Einhorn D, Tocchini-Valentini G, Hrabe de Angelis M, Rosenthal N. 2009. Post-publication sharing of data and tools. Nature 461:171-173.
30. Smedley D, Swetz MA, Wostencroft K, Proctor G, Zouberakis M, Bard J, Hancock JM, Schofield P. 2008. Solutions for data integration in functional genomics: A critical assessment and case study. Brief Bioinform 9:532-544.
31. Statzner B, Bêche L. 2010. Can biological invretebrate traits resolve effects of multiple stressors on running water ecosystems. Freshwater Biol 55 (Suppl 1): 80-119.
32. Statzner B, Bonada N, Dolédec S. 2007. Conservation of taxonomic and biological trait diversity of European stream macroinvertebrates communities: A case for a collective public database. Biodiversity Conserv 16:3609-3632.
33. Statzner B, Dolédec S, Hugueny B. 2004. Biological trait composition of European stream invertebrate communities: Assessing the effects of various trait filter types. Ecography 27:470-488.
34. Stanford Centre for Biomedical Sciences. 2010. Protégé. [Accessed 2010 July 19]. Avaliable from: protege.stanford.edu.
35. Tautz D, Arctander P, Minelli A, Thomas RH, Vogler AP. 2003. A plea for DNA taxonomy. Trends Ecol Evol 18:70-74.
36. University at Buffalo. 2010. International conference on biomedical ontology. [Accessed 2010 July 19]. Available from: icbo.buffalo.edu.
37. Usseglio-Polatera P, Bournaud M, Richoux P, Tachet H. 2000. Biomonitoring through biological traits of benthic macroinvertebrates: How to use species trait databases? Hydrobiologia 422/423:153-162.
38. Van Den Brink PJ, Alexander AC, Desrosiers M, Goedkoop W, Goethals PLM, LiessM, Dyer S. 2011. Traits-based approaches in bioassessment and ecological risk assessment: strengths, weaknesses, opportunities and threats. Integrated Environmental Assessment and Management 7:198-208.
39. Whitlock MC, McPeek MA, Rausher MD, Rieseberg L, Moore AJ. 2010. Data archiving. Am Nat 172:145-146.
40. Willig MR, Kaufman DM, Stevens RD. 2003. Latitudinal gradients of biodiversity: pattern, process, scale and synthesis. Annu Rev Ecol Syst 34:273-309.
41. Witte R, Kappler T, Baker CJO. 2007. Enhanced semantic access to the protein engineering literature using ontologies populated by text mining. Int J Bioinf Res Appl 3.
42. Wolstencroft K, Stevens R, Haarslev V. 2007. Applying OWL reasoning to genomic data. In: Basker CO, Cheung K-H, editors. Semantic web: Revolutionizing knowledge discovery in the life sciences. New York (NY): Springer Verlag. p 225-248.