Advancing ecological research with ontologies

Trends in Ecology and Evolution

Volumn 23, Issue 3, 2008, Pages 159-168

  Madin, Joshua S ^a,b   Bowers, Shawn ^c   Schildhauer, Mark P ^a   Jones, Matthew B ^a  

^a NATIONAL CENTER FOR ECOLOGICAL ANALYSIS AND SYNTHESIS   (United States)

^b MACQUARIE UNIVERSITY   (Australia)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGY; RESEARCH; TERMINOLOGY;

ECOLOGY; NOMENCLATURE; RESEARCH; REVIEW;

ECOLOGY; RESEARCH; TERMINOLOGY AS TOPIC;

EID: 40049110106     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2007.11.007     Document Type: Review

References (67)

1. Grimm V., and Wissel C. Babel, or the ecological stability discussions: an inventory and analysis of terminology and a guide for avoiding confusion. Oecologia 109 (1997) 323-334
2. Callicott J., et al. Current normative concepts in conservation. Conserv. Biol. 13 (1999) 22-35
3. Pimm S.L. The complexity and stability of ecosystems. Nature 307 (1984) 321-326
4. Jax K. Ecological units: definitions and applications. Q. Rev. Biol. 81 (2006) 237-257
5. Lehman C.L., and Tilman D. Biodiversity, stability, productivity in competitive communities. Am. Nat. 156 (2000) 534-552
6. Madin J., et al. An ontology for describing and synthesizing ecological observation data. Int. J. Ecol. Informatics 2 (2007) 279-296
7. Worm B., et al. Impacts of biodiversity loss on ocean ecosystem services. Science 314 (2006) 787-790
8. Graham C.H., et al. New developments in museum-based informatics and applications in biodiversity analysis. Trends Ecol. Evol. 19 (2004) 497-503
9. Kerr J.T., et al. The macroecological contribution to global change solutions. Science 316 (2007) 1581-1584
10. Scheiner S.M., and Willig M.R. Developing unified theories in ecology as exemplified with diversity gradients. Am. Nat. 166 (2005) 458-469
11. Pickett S., et al. Ecological Understanding: The Nature of Theory and The Theory of Nature (1994), Academic Press
12. Jax K., et al. The self-identity of ecological units. Oikos 82 (1998) 253-264
13. Parr C.S., and Cummings M. Data sharing in ecology and evolution. Trends Ecol. Evol. 20 (2005) 362-363
14. Fegraus E., et al. Maximizing the value of ecological data with structured metadata: an introduction to Ecological Metadata Language (EML) and principles for metadata creation. Bull. Ecol. Soc. Am. 86 (2005) 158-168
15. Jones M.B., et al. The new bioinformatics: integrating ecological data from the gene to the biosphere. Annu. Rev. Ecol. Evol. Syst. 37 (2006) 519-544
16. Michener W.K., et al. Non-geospatial metadata for the ecological sciences. Ecol. Appl. 7 (1997) 330-342
17. Grossman D.A., and Frieder O. Information Retrieval: Algorithms and Heuristics. 2nd edn (2004), Springer
18. Bard J.B.L., and Rhee S.Y. Ontologies in biology: design, applications, and future challenges. Nat. Rev. Genet. 5 (2004) 213-221
19. Ashburner M., et al. Gene ontology: tool for the unification of biology. Nat. Genet. 25 (2000) 25-29
20. Soldatova L.N., and King R.D. Are the current ontologies in biology good ontologies?. Nat. Biotechnol. 23 (2005) 1095-1098
21. Smith B., et al. Relations in biomedical ontologies. Genome Biol. 6 (2005) R46
22. Baader F., et al. The Description Logic Handbook: Theory, Implementation, and Applications (2003), Cambridge University Press
23. Kelly J. The Essence of Logic (1996), Prentice Hall
24. Guarino N. Formal ontology, concept analysis, and knowledge representation. Int. J. Hum. Comput. Stud. 43 (1995) 625-640
25. Chandrasekaran B., et al. What are ontologies, and why do we need them?. IEEE Intell. Syst. 14 (1999) 20-26
26. Sowa J.F. Knowledge Representation: Logical, Philosophical, and Computational Foundations (2000), Brooks Cole
27. Schuh R.T. The Linnaean system and its 250-year persistence. Bot. Rev. 69 (2003) 59-78
28. Kennedy, J. et al. (2005) Scientific names are ambiguous as identifiers for biological taxa: their context and definition are required for accurate data integration. In Proceedings of the 2nd International Workshop on Data Integration in the Life Sciences, Springer Lecture Notes in Computer Science (Vol. 3615), pp. 80-95, Springer
29. Smith B. Objects and their environments: from Aristotle to ecological ontology. In: Frank A., et al. (Ed). The Life and Motion of Socio-Economic Units (2001), Taylor and Francis 79-97
30. McGuinness, D.L. and Van Harmelen, F. (2004) OWL Web ontology language overview. W3C Recommendation (http://www.w3.org/TR/owl-features)
31. Berners-Lee T., et al. The semantic web: a new form of web content that is meaningful to computers will unleash a revolution of new possibilities. Sci. Am. 284 (2001) 34-43
32. Borgida A. Description logics in data management. IEEE Trans. Knowl. Data Eng. 7 (1995) 671-682
33. Ludäscher B., et al. Model-based mediation with domain maps. Proceedings of the 17th International Conference on Data Engineering (2001), IEEE Computer Society 81-90
34. Bowers S., et al. On integrating scientific resources through semantic registration. Proceedings of the 16th International Conference on Scientific and Statistical Database Management (2004), IEEE Computer Society 349-352
35. Haas L.M., et al. Data integration through database federation. IBM Syst. J. 41 (2002) 578-596
36. Costanza R., et al. The value of the world's ecosystem services and natural capital. Nature 387 (1997) 253-260
37. Williams R.J., et al. Ontologies for ecoinformatics. J. Web Sem. 4 (2006) 237-242
38. Yoon I., et al. Interactive 3D visualization of highly connected ecological networks on the WWW. In: Haddad H., et al. (Ed). Proceedings of the 2005 ACM Symposium on Applied Computing (2005), ACM Press 1207-1212
39. Fox P., et al. Semantically-enabled large-scale science data repositories. In: Cruz I., et al. (Ed). Proceedings of the International Semantic Web Conference, Lecture Notes in Computer Science 4273 (2006), Springer 792-805
40. Gruber T.R., and Olsen G.R. An ontology for engineering mathematics. In: Doyle J., et al. (Ed). Proceedings of the 4th International Conference on Principles of Knowledge Representation and Reasoning (1994), Morgan Kaufmann 258-269
41. Gangemi A., et al. Sweetening ontologies with DOLCE. Knowledge Engineering and Knowledge Management, Lecture Notes in Computer Science Vol. 2473 (2002), Springer 166-181
42. Smith B., and Varzi A. The niche. Nous 33 (1999) 198-222
43. Smith B., and Varzi A. The formal structure of ecological contexts. In: Bouquet P., et al. (Ed). Modeling and Using Contexts: Proceedings of the 2nd International Interdisciplinary Conference (1999), Springer 339-351
44. Keet C.M. Factors affecting ontology development in ecology. In: Ludäscher B., and Raschid L. (Eds). Data Integration in the Life Sciences, Lecture Notes in Computer Science (2005), Springer 46-62
45. Mabee P.M., et al. Phenotype ontologies: the bridge between genomics and evolution. Trends Ecol. Evol. 22 (2007) 345-350
46. Brilhante V. An ontology for quantities in ecology. Proceedings of the Brazilian Symposium on Artificial Intelligence, Lecture Notes in Artificial Intelligence Vol. 3171 (2004), Springer 144-153
47. Schentz H., and Mirtl M. MORIS: a universal information system for environmental monitoring. In: Schimak G.P., et al. (Ed). Environmental Software Systems (2003), Springer 60-68
48. Doerr, M. (2001) Semantic problems of thesaurus mapping. J. Digital Information 1, article 52 (http://hdl.handle.net/2249.2/jodi-35)
49. Jones M.B., et al. Managing scientific metadata. IEEE Internet Comput. 5 (2001) 59-68
50. Ludäscher B., et al. Scientific workflow management and the Kepler system. Concurr. Comp. Pract. E 18 (2006) 1039-1065
51. Berkley C., et al. Incorporating semantics in scientific workflow authoring. In: Frew J. (Ed). Proceedings of the 17th International Conference on Scientific and Statistical Databases (2005), Lawrence Berkeley Laboratory 75-78
52. Thompson J., et al. Frontiers of ecology. Bioscience 51 (2001) 15-24
53. Greene J., et al. Complexity in ecology and conservation: mathematical, statistical, and computational challenges. Bioscience 55 (2005) 501-510
54. Chen P.P. The entity-relationship model - toward a unified view of data. ACM Trans. Database Syst. 1 (1976) 9-36
55. Hammer J., and McLeod D. On the resolution of representational diversity in multidatabase systems. In: Elmagarmid A.K., et al. (Ed). Management of Heterogeneous and Autonomous Database Systems (1998), Morgan Kaufmann 91-118
56. Sachs J., et al. Using the semantic web to support ecoinformatics. In: Honavar V., and Finin T. (Eds). Proceedings of the AAAI Fall Symposium on the Semantic Web for Collaborative Knowledge Acquisition (2006), AAAI Press 56-61
57. Stuckenschmidt H., et al. Index structures and algorithms for querying distributed RDF repositories. In: Feldman S., et al. (Ed). Proceedings of the International Conference on World Wide Web (2004), ACM Press 631-639
58. Moldovan D.I., and Mihalcea R. Using WordNet and lexical operators to improve Internet searchers. IEEE Internet Comput. 4 (2000) 34-43
59. Jarvelin K., et al. ExpansionTool: concept-based query expansion and construction. Inform. Retrieval 4 (2001) 231-255
60. Voorhees E.M. Query expansion using lexical-semantic relations. In: Croft W.B., and van Rijsbergen C.J. (Eds). Proceedings of the 17th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval (1994), Springer 61-69
61. Bowers S., and Ludäscher B. An ontology-driven framework for data transformation in scientific workflows. In: Rahm E. (Ed). Data Integration in the Life Sciences, Springer Lecture Notes in Computer Science (2004), Springer 1-16
62. Guarino N., and Welty C.A. Evaluating ontological decisions with OntoClean. Commun. ACM 45 (2002) 61-65
63. Rector A., et al. OWL pizzas: practical experience of teaching OWL-DL: common errors and common patterns. Engineering Knowledge in the Age of the SemanticWeb Vol. 3257 (2004), Springer 63-81
64. Pinto H.S., and Martins J.P. Ontologies: how can they be built?. Knowl. Inf. Syst. 6 (2004) 441-464
65. Wand Y., et al. An ontological analysis of the relationship construct in conceptual modeling. ACM Trans. Database Syst. 24 (1999) 494-528
66. Winston M.E., et al. A taxonomy of part-whole relations. Cogn. Sci. 11 (1987) 417-444
67. Smith B. Mereotopology: a theory of parts and boundaries. Data Knowl. Eng. 20 (1996) 287-303