A Platform Based on the Multi-dimensional Data Model for Analysis of Bio-Molecular Structures

A platform called AnMol for supporting analytical applications over structural data of large biomolecules is described. The term "biomolecular structure" has various connotations and different representations. AnMol reduces these representations into graph structures. Each of these graphs are then stored as one or more vectors in a database. Vectors encapsulate structural features of these graphs. Structural queries like similarity and substructure are transformed into spatial constructs like distance and containment within regions. Query results are based on inexact matches. A refinement mechanism is supported for increasing accuracy of the results. Design and implementation issues of AnMol including schema structure and performance results are discussed in this paper.

[1]  D. Cook,et al.  Graph-based hierarchical conceptual clustering , 2002 .

[2]  Himanshu Agrawal,et al.  Vectorization of Structure to Index Graph Databases , 2002, ISDB.

[3]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[4]  D.J. Cook,et al.  Structural mining of molecular biology data , 2001, IEEE Engineering in Medicine and Biology Magazine.

[5]  Jignesh M. Patel,et al.  Searching on the Secondary Structure of Protein Sequences , 2002, VLDB.

[6]  C. V. Ramamoorthy,et al.  Knowledge and Data Engineering , 1989, IEEE Trans. Knowl. Data Eng..

[7]  Kaizhong Zhang,et al.  Finding Patterns in Three-Dimensional Graphs: Algorithms and Applications to Scientific Data Mining , 2002, IEEE Trans. Knowl. Data Eng..

[8]  Yehezkel Lamdan,et al.  Geometric Hashing: A General And Efficient Model-based Recognition Scheme , 1988, [1988 Proceedings] Second International Conference on Computer Vision.

[9]  Dennis Shasha,et al.  New techniques for extracting features from protein sequences , 2001, IBM Syst. J..

[10]  Emden R. Gansner,et al.  An open graph visualization system and its applications to software engineering , 2000 .

[11]  Dennis Shasha,et al.  GraphGrep: A fast and universal method for querying graphs , 2002, Object recognition supported by user interaction for service robots.

[12]  Ruth Nussinov,et al.  Multiple Structural Alignment and Core Detection by Geometric Hashing , 1999, ISMB.