Towards a formalization of disease-specific ontologies for neuroinformatics

Neural Networks

Volumn 16, Issue 9, 2003, Pages 1277-1292

  Gupta, Amarnath ^a   Ludäscher, Bertram ^a   Grethe, Jeffrey S ^b   Martone, Maryann E ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Logic Model; Neuruoinformatics; Ontology; Parkinson's disease; Semantic

Indexed keywords

BIOCOMMUNICATIONS; CALCULATIONS; IMAGE ANALYSIS; NEUROLOGY;

DISEASE MAPS;

NEURAL NETWORKS;

ALZHEIMER DISEASE; ARTICLE; METAPHYSICS; MODEL; NEUROINFORMATICS; NEUROLOGIC DISEASE; NEUROSCIENCE; PARKINSON DISEASE; PRIORITY JOURNAL; SCHIZOPHRENIA; SEMANTICS;

EID: 0242468090     PISSN: 08936080     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neunet.2003.07.008     Document Type: Article

References (39)

1. Abiteboul S., Hull R., Vianu V. Foundations of databases. 1995;Addison-Wesley, Reading, MA.
2. Artale A., Franconi E., Guarino N., Pazzi L. Part-whole relations in object-centered systems: an overview. Data and Knowledge Engineering. 20:(3):1996;347-383.
3. Baader F., Calvanese D., McGuinness D., Nardi D., Patel-Schneider P. The description logic handbook - theory, implementation and applications. 2003;Cambridge University Press, Cambridge.
4. Baral C. Knowledge representation, reasoning and declarative problem solving. 2003;Cambridge University Press, Cambridge.
5. Beal M. Experimental models of Parkinson's disease. Nature Reviews Neuroscience. 2:(5):2001;325-334.
6. BIRN-CC (2003). Parkinson's disease map. http://www.nbirn.net/Projects/ CoordinatingCenter/PDM/.
7. Bondarenko A., Dung P., Kowalski R., Toni F. An abstract, argumentation - theoretic approach to default reasoning. Artificial Intelligence. 93:(4):1997;63-101.
8. Bota, M (2001). Neural homologies: Principles, databases and modeling. Unpublished doctoral dissertation, University of Southern California. (http://brancusi.usc.edu/thesis_bota.pdf) .
9. Bota M., Arbib M.A. The neurohomology database. Neurocomputing. 38-40:2001;1627-1631.
10. Brewka G., Dix J. Knowledge representation with logic programs. 2nd ed Handbook of philosophical logic. Vol. 6:2003;Oxford University Press, Oxford.
11. Buchanan B.G., Shortliffe H. Rule-based expert systems: The MYCIN experiments of the Stanford heuristic programming project. 1984;Addison-Wesley, Reading, MA.
12. Chen W., Kifer M., Warren D.S. HILOG: A foundation for higher-order logic programming. Journal of Logic Programming. 15:(3):1993;187-230.
13. Dix J. Semantics of logic programs: their intuitions and formal properties. An overview. Fuhrmann A., Rott H. Logic, action and information - Essays on logic in philosophy and artificial intelligence. 2003;241-327 De Gruyter, Berlin.
14. Dung P.M. On the acceptability of arguments and its fundamental role in nonmonotonic reasoning, logic programming and n -person games. Artificial Intelligence. 77:1995;321-357.
15. Gardner D., Xiao Y., Abato M., Knuth K., Gardner E. BrainML and GENIE: neuroinformatics schemas for neuroscience data sharing. Society for Neuroscience Abstracts. Vol. 28:2002.
16. Gelfond M., Lifschitz V. The stable model semantics for logic programming. Kowalski R.A., Bowen K. Proceedings of the Fifth International Conference on Logic Programming. 1988;1070-1080 The MIT Press, Cambridge, MA.
17. Creating the gene ontology resource: design and implementation. Genome Research. 11:2002;1425-1433.
18. Goedert M. Alpha-synuclein and neurodegenerative diseases. Nature Reviews Neuroscience. 2:2001;492-501.
19. Gruber T. A translation approach to portable ontologies. Knowledge Acquisition. 5:(2):1993;199-220.
20. Guarino N., Giaretta P. Ontologies and knowledge bases: towards a terminological clarification. Mars N. Towards very large knowledge bases. 1995;25-32 IOS Press, Amsterdam. http://ontology.ip.rm.cnr.it/Papers/KBKS95.pdf.
21. Guninger M., Lee J. Ontology applications and design. Communications of the ACM. 45:(2):2002;39-41.
22. Gupta A., Ludäscher B., Martone M.E. Knowledge-based integration of neuroscience data sources. 12th International Conference on Scientific and Statistical Database Management (SSDBM). 2000;IEEE Computer Society, Berlin. pp. 39-52.
23. Jagadish H.V., Al-Khalifa S., Chapman A., Lakshmanan L.V.S., Nierman A., Paparizos S., Patel J.M., Srivastava D., Wiwatwattana N., Wu Y., Yu C. Timber: a native xml database. The VLDB Journal. 11:(4):2002;274-291.
24. Kahle P.J., Haass C., Kretzschmar H.A., Neumann M. Structure/function of α-synuclein in health and disease: rational development of animal models for parkinson's and related diseases. Journal of Neurochemistry. 82:2002;449-457.
25. Karp P.D. An ontology for biological function based on molecular interactions. Bioinformatics. 16:2000;269-285.
26. Karp P., Ouzounis P., Paley S. HinCyc: a knowledge base of the complete genome and metabolic pathways of H. influenzae. Fourth International Conference on Intelligent Systems for Molecular Biology. Vol. 4:1996;. pp. 116-124.
27. Karp P., Riley M., Paley S., Pellegrini-Toole A., Krummenacker M. EcoCyc: encyclopedia of the Escherichia coli genes and metabolism. Nucleic Acids Research. 27:1999;55-58.
28. Karp P., Riley M., Saier M., Paulsen I., Pellegrini-Toole A. The ecocyc and metacyc databases. Nucleic Acids Research. 28:2000;56-59.
29. Kifer M., Lausen G., Wu J. Logical foundations of object-oriented and frame-based languages. Journal of the ACM. 42:(4):1995;741-843.
30. Ludäscher B., Gupta A., Martone M.E. Model-based mediation with domain maps. 17th International Conference on Data Engineering (ICDE). 2001;IEEE Computer Society, Heidelberg, Germany. pp. 81-90.
31. Ludäscher B., Gupta A., Martone M.E. A model-based mediator system for scientific data management. Critchlow T., Lacroix Z. Bioinformatics: Managing scientific data. 2003;Morgan Kaufmann, Los Altos.
32. National Library of Medicine (2003). UMLS documentation. http://www.nlm.nih.gov/research/umls/UMLSDOC_2003AA.pdf .
33. Rector A. Description logics in medical informatics. Baader F., Calvanese D., McGuinness D., Nardi D., Patel-Schneider P. The description logic handbook - theory, implementation and applications. 2003;Cambridge University Press, Cambridge.
34. Reiter R. A logic for default reasoning. Artificial Intelligence. 13:(1/2):1980;81-132.
35. Sagonas K., Swift T., Warren D. XSB as an efficient deductive database engine. ACM SIGMOD International Conference on Management of Data, San Jose, CA. 1994;. pp. 442-453.
36. Stevens R., Goble C., Paton N., Bechhofer S., Ng G., Baker P., Brass A. Complex query formulation over diverse information sources in TAMBIS. In Workshop on Computation of Biochemical Pathways and Genetic Networks. 1999;European Media Lab (EML). pp. 83-88.
37. Swanson L.W. Brain maps: Structure of the rat brain. 2nd ed :1998;Elsevier, Amsterdam.
38. Van Gelder A., Ross K., Schlipf J.S. The well-founded semantics for general logic programs. Journal of the ACM. 38:(3):1991;620-650.
39. Williams J., Andersen W. Bringing ontology to the gene ontology. Comparative Functional Genomics. 4:2003;90-93.