BrainFrame: A knowledge visualization system for the neurosciences

Proceedings of SPIE - The International Society for Optical Engineering

Volumn 7243, Issue , 2009, Pages

  Barnes, Steven J ^a,b   Shaw, Chris D ^b  

^a SIMON FRASER UNIVERSITY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Biology; Knowledge management; Knowledge visualization; Neuroinformatics; Neuroscience; Ontology; Reasoning

Indexed keywords

COMPUTING SPEED; DATA STORAGES; EXPERIMENTAL DATUM; EXPERIMENTAL TECHNIQUES; HUMAN NERVOUS SYSTEMS; KNOWLEDGE BASE; KNOWLEDGE VISUALIZATION; MANAGEMENT TECHNIQUES; NEUROINFORMATICS; NEUROSCIENCE; REASONING; RUN-TIME;

INDUSTRIAL MANAGEMENT; KNOWLEDGE BASED SYSTEMS; KNOWLEDGE MANAGEMENT; ONTOLOGY; VISUALIZATION;

DATA VISUALIZATION;

EID: 62249087132     PISSN: 0277786X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1117/12.812290     Document Type: Conference Paper

References (40)

1. Post-conference web site for "Digital Biology: The Emerging Paradigm," http://www.bisti.nih.gov/2003-meeting/.
2. Bota, M., and Swanson, L. W., "Online workbenches for neural network connections," J. Comp. Neurol. 500, 807-814 (2007).
3. Tversky, A., and Kahneman, D. "Judgment under uncertainty: heuristics and biases," Science 185, 1124-1131 (1974).
4. Mcalister, F. A., Clark, H. D., Van Walraven, C., Straus, S. E., Lawson, F. M. E., Moher, D., and Mulrow, C. D., "The medical review article revisited: has the science improved?" Ann. Intern. Med. 131, 947-951 (1999).
5. Scoville, W. B., and Milner, B., "Loss of recent memory after bilateral hippocampal lesions," J. Neurol. Neurosurg. Psychiatry, 20, 11-21 (1957).
6. Andreassen, H. K., Bujnowska-Fedak, M. M., Chronaki, C. E., Dumitru, R. C., Pudule, I., Santana, S., Voss, H., and Wynn, R., "European citizens' use of E-health services: A study of seven countries," B. M.C. Pub. Health 7 53 (2007).
7. Ascoli, G. A., "Mobilizing the base of neuroscience data: The case of neuronal morphologies," Nat. Rev. Neurosci. 7, 318-324 (2006).
8. Van Horn, J. D., and Gazzaniga, M. S., "Maximizing information content in shared and archived neuroimaging studies of human cognition." In Koslow, S. H., and Subramaniam, S. (eds.), [Databasing the Brain], John Wiley & Sons Inc., Canada, 449-458 (2005).
9. Gardner, D., "Neurodatabase.org: networking the microelectrode. " Nat. Neurosci. 7, 486-487 (2004).
10. Koslow, S. H., and Subramaniam, S. (eds.), [Databasing the Brain], John Wiley & Sons Inc., Canada, (2005).
11. Gupta, A., Ludascher, B., Grethe, J. S., and Martone, M. E. "Towards a formalization of disease-specific ontologies for neuroinformatics," Neural Netw. 16, 1277-1292 (2003).
12. Gene Ontology Consortium, "Creating the gene ontology resource: design and implementation," Genome Research, 11, 1425-1433 (2002).
13. National Library Of Medicine "UMLS documentation" (2003).
14. Martone, M. E., Gupta, A., and Ellisman, M. H., "E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains," Nat. Neurosci. 7, 467-472 (2004).
15. "Cell Centred Database," http://ccdb.ucsd.edu/CCD-BWebSite/ index.html.
16. "Biomedical Informatics Research Network," http://-www.nbirn. net/.
17. Nielsen, F. A., "Bibliography on Neuroinformatics: Neuroscience Tenninology." http://hendrix.ei.dtu.dk/staff/fnielsen/bib/ Nielsen2001BibNeuroinformatics/node11.html (2007).
18. Kashyap, V., and Hongsermeier, T., "Can semantic web technologies enable translational medicine?" In Baker, C. J. O., and Cheung, K. (eds.), [Semantic web: Revolutionizing knowledge discovery in the life sciences.] Springer Science and Business Media, New York, 249-279 (2007).
19. Bowden, D. M., and Martin, R. F. "NeuroNames brain hierarchy," Neuroimage 2, 63-83 (1995).
20. Hole, W. T., and Srinivasan, S. "Adding NeuroNames to the UMLS metathesaurus," Neuroinformatics 1, 61-63 (2003).
21. "Brainlnfo," http://braininfo.rprc.washington.edu/me-numain. html.
22. Gardner, D., Abato, M., Knuth, K. H., and Robert, A. " Neuroinformatics for neurophysiology: the role, design, and use of databases," In Koslow, S. H. and Subramaniam, S. (eds.), [Databasing the Brain.], John Wiley & Sons Inc., Canada, 47-67 (2005).
23. Zhang, W., Zhang, Y., Zheng, H., Zhang, C., Xiong, W., Olyarchuk, J. G., Walker, M., Xu, W., Zhao, M., Zhao, S., Zhou, Z., and Wei, L., "SYNDB: a synapse protein database based on synapse ontology." Nucleic Acids Res. 35 D737-D741 (2007).
24. Williams, J., and Andersen, W., "Bringing ontology to the gene ontology." Comparative Functional Genomics 4, 90-93 (2003).
25. The Protégé Ontology Editor and Knowledge Acquisition System," http://protege.stanford.edu/.
26. "Jess: The Rule Engine for the Java Platform," http://www.jessrules.com/.
27. Kalfoglou, Y., and Schorlemmer, M. "Ontology mapping: the state of the art," The Knowledge Engineering Review 18, 1-31 (2003).
28. "Allen Institute for Brain Science," http://www.alien- institute.org/default.htm.
29. "Brainmaps.org,". http://brainmaps.org/.
30. Burkhard, R. http://www.knowledge-visualization.org/(2007).
31. Fox, P., Mcguiness, D., Middleton, D., Cinquini, L., Darnell, J. A., Garcia, J., West, P., Benedict, J., and Solomon, S. "Semantically-enabled large-scale science data repositories," In Cruz, I. (ed.), [ISWC 2006, LNCS 4273], 792-805 (2006).
32. "Jena: A Semantic Web Framework for Java," http://iena. sourceforge.net/.
33. "Processing 1.0 Beta", http:/yprocessing.org/.
34. Ahlers, J., and Weimer, H., "Challenges in interactive visualization for knowledge management," Proceedings of the Sixth International Conference on Information Visualization (2002).
35. Squire, L. R., Roberts, J. L., Spitzer, N. C., Zigmond, M. J., McConnell, S. K., and Bloom, F. E., [Fundamental Neuroscience, Second Edition], Academic Press, San Diego (2003).
36. Kandel, E. R., Schwartz, J. H., and Jessell, T. M., [Principles of Neural Science, Fourth Edition] McGraw-Hill, USA (2000).
37. "The digital object identifier system," http://doi.org/.
38. "International ISBN agency," http://www.isbn-international.org/ .
39. Crasto, C. J., and Shepherd, G. M., "Managing knowledge in neuroscience," Methods Mol. Biol. 401, 3-21 (2007).
40. Crasto, C. J., Marenco, L. N., Migliore, M., Mao, B., Nadkarni, P. M., Miller, P., and Shepherd, G. M., "Text mining neuroscience journal articles to populate neuroscience databases," Neuroinformatics 1, 215-237 (2003).