An ontology-driven knowledge environment for subcellular neuroanatomy

CEUR Workshop Proceedings

Volumn 258, Issue , 2007, Pages

  Fong, Lisa L ^a   Larson, Stephen D ^a   Gupta, Amarnath ^b   Condit, Christopher ^b   Bug, William J ^c   Chen, Li ^b   West, Ruth ^a   Lamont, Stephan ^a   Terada, Masako ^a   Martone, Maryann E ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c DREXEL UNIVERSITY COLLEGE OF MEDICINE   (United States)

Author keywords

Data integration; Database; Descriptive logic; Nervous system; Protege; Reasoning; Rules based logic; Upper level ontology

Indexed keywords

COMPUTATIONAL MODEL; DESCRIPTIVE LOGIC; HIGH-RESOLUTION MICROSCOPY; INTRICATE STRUCTURES; KNOWLEDGE ENVIRONMENT; PROTEGE; REASONING; RULES-BASED LOGIC;

BIRDS; CELLS; DATA INTEGRATION; DATABASE SYSTEMS; KNOWLEDGE BASED SYSTEMS; NEUROLOGY; QUERY PROCESSING;

NEURONS;

EID: 80053067036     PISSN: 16130073     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (24)

1. Astakhov, V., Gupta, A., Santini, A., Grethe, J. S.: Data Integration in the Biomedical Informatics Research Network (BIRN). DILS 2005: 317-320, 2005
2. Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome Biol. 6(2):R21, 2005.
3. Bota M, Dong HW, Swanson LW Brain architecture management system. Neuroinformatics. 3:15-48, 2005.
4. Bowden DM, Dubach M.F. (2003) NeuroNames 2002. Neuroinformatics. 1(1):43-59.
5. Chen, L., Martone, M.E., Gupta, A., Fong, L., Wong-Barnum, M. (2006). OntoQuest: Exploring Ontological Data Made Easy, Abstract, Very Large Databases Conference. 1183-1186.
6. Cuenca Grau, C, Parsia, B, and Sirin, E (2005) Combining OWL Ontologies Using E-Connections. Journal of Web Semantics. 4:1, 42 pp.
7. Gene Ontology Consortium (2002). Creating the gene ontology resource: design and implementation. Genome Research, 11, 1425-1433.
8. Grenon P, Smith B, Goldberg L. (2004) Biodynamic ontology: applying BFO in the biomedical domain. Stud Health Technol Inform. 102: 20-38.
9. Gupta, A., Ludascher, B., Martone, M., Rajasekar, A., Ross, E., Qian, X., Santini, S., He, H. and Zaslavsky, I. (2003) BIRN-M: A Semantic Mediator for Solving Real-World Neuroscience Problems. Proceedings of SIGMOD, June 9-12, 2003, San Diego, CA,
10. Huerta, M., Koslow, S.H., Leshner, A. I. (1993) The Human Brain Project: an international resource. TINS 16: 436-438.
11. Hunter, P. J. and Borg, T. K. (2003) Integration from proteins to organs: the Physiome Project. Nat Rev Mol Cell Biol, 4: 237-243.
12. Larson SD, Martone ME, Rule-Based Reasoning With A Multi-Scale Neuroanatomical Ontology. OWL: Experiences and Directions workshop 2007, submitted
13. Lein ES, Hawrylycz MJ, Ao N, Ayres M et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445: 168-176.
14. Lucie V, Forster F, Baumeister W. Structural studies by electron tomography: from cells to molecules. Annu Rev Biochem. 74:833-65, 2005.
15. Martin, RF, Mejino, JL Jr, Bowden, DM, Brinkley, JF 3rd, Rosse, C. (2001) Foundational model of neuroanatomy: implications for the Human Brain Project. Proc AMIA Symp 438-42.
16. Martone ME, Zhang S, Gupta A., Qian X, He H, Price D.L., Wong M., Santini S, Ellisman MH. The cell-centered database: a database for multiscale structural and protein localization data from light and electron microscopy. Neuroinformatics. 1:379-95, 2003
17. Mechouche, A, Golbreich, Gibaud, B. Towards an hybrid system for annotating brain MRI images. OWL ED 2006.
18. Migliore M, Shepherd GM Opinion: an integrated approach to classifying neuronal phenotypes. Nat Rev Neurosci. 2005 Oct;6(10):810-8.
19. Perkins, G., Renken, C, Martone, M. E., Young, S. J., Ellisman, M. and Frey, T. (1997) Electron tomography of neuronal mitochondria: three-dimensional structure and organization of cristae and membrane contacts. J Struct Biol, 119: 260-272.
20. Peters, A. L., Palay, S. and Webster, H. d. F. (1991) The fine structure of the nervous system. New York: Harper and Row.
21. Rector, A, Rogers, J, Bittner T. (2006) Granularity, scale and collectivity: when size does and does not matter. Journal of Biomedical Informatics (Special issue: Biomedical ontologies). 39:3, p333.
22. Rosse C, Kumar A, Mejino JLV Jr, Cook DL, Detwiler LT, Smith B. (2005). A strategy for improving and integrating biomedical ontologies. AMIA 2005 Symposium Proceedings, 639-643.
23. Smith B, Ceusters W, Klagges B., Kohler J, Kumar A, Lomax J., Mungall C, Neuhaus F, Rector AL, Rosse C. (2005) Genome Biol. 2005;6(5):R46
24. Zhang, W, Zhang, Y, Zheng, H, Zhang, C, Xiong, W, Olyarchuk, JG, Walker, M, Xu, W, Zhao, M, Zhao, S, Zhou, Z, Wei, L. (2007) SynDB: a Synapse protein DataBase based on synapse ontology. Nucleic Acids Res. 35: D737-41.