Bio-medical Ontologies Maintenance and Change Management

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328 M.T. Hoque, M. Chetty, and A. Sattar Absolute encoding [34, 42, 77−79] replaces the direct coordinate presentation with letters representing directions with respect to the lattice structure. The permitted moves for absolute encoding are: f (forward), l (left), r (right), b (back), u (up) and d (down) (see Fig. 9), while u and d indicate +z and –z direction respectively. A conformation c in 2D with n residues could be { } 1 n− c ∈ f , l, r, b while in 3D it would be { } 1 n− c ∈ f , l, r, b, u, d . Alternatively, in relative encoding the move direction is defined relative to the direction of the previous move as shown in Fig. 10, rather than relative to the axis defined by the lattice. These moves are lattice automorphic [34], with the initial move always expressed by F (forward). A conformation c of n residues in 2D and 3D could then be { } 2 n− ∈ F, L, R { } 2 n− ∈ F, L, R, U, D c and c , respectively. Relative encoding (Fig. 10) was developed with a view to improving presentation over absolute encoding with pivot mutation being represented as the single locus or character alteration of a chromosome as shown in Fig. 11. (a) (b) Fig. 11. (a) Single mutation at residue number 6 (red colour) using absolute encoding using changes in genotype and in the corresponding phenotype is not a pivot rotation (b) Single mutation at residue 6 using relative coding results in true pivot rotation (a) (b) (c) Fig. 12. The cross-exchange indicated by the dotted contour in the identical conformations (a) and (b) result conformation in (c), which can also be constructed from (a) or (b) by applying mutation (i.e. pivot rotation) at residue number 5. Hence, the crossover can result equivalent to the mutation operation for identical parents.
Genetic Algorithm in Ab Initio Protein Structure Prediction 329 It is clear that the coordinates of a rotating object change so direct coordinate presentation is inherently isomorphic. Moreover as shown in Fig. 13 and Fig. 14, absolute and relative encodings are also isomorphic. Thus, a non-isomorphic encoding algorithm is essentially proposed in [76] by assigning a fixed directions for a growing chain based upon the first occurrences of the move in a particular dimension. The direction from first residue towards the second is marked ‘1’ and the reverse is marked ‘2’, which defines the complete move in 1-dimension. The first occurrence of a direction perpendicular to the 1-dimension is marked as ‘3’ and the reverse as ‘4’, which completes the moves in 2-dimensions. The first occurrence of the move perpendicular to the plane formed by ‘1’ and ‘3’ moves is marked as ‘5’ and the reverse as ‘6’, which finally defines the moves in 3-dimensions. Fig. 13. Absolute encoding is isomorphic. For six directions, namely +x, -x, +y, -y, +z and - z, 24 ( = 6 × 4) different genotypes are possible for a given 3D conformation. Fig. 14. Relative encoding is isomorphic. Four variations shown in 3D by rotating around axis formed by 1-2 connecting line, but no variation achieved by the change in direction (x or y or z). 4.4 Domain Knowledge Based Heuristic Despite the aforementioned improvements, PSP remains an intractable problem because during the search, the solution becomes phenotypically more compact,
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Amandeep S. Sidhu and Tharam S. Dil
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Amandeep S. Sidhu and Tharam S. Dil
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Preface The molecular biology commu
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Preface VII biomedical systems, and
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X Contents Mining Clinical, Immunol
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2 A.S. Sidhu, M. Bellgard, and T.S.
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Towards Bioinformatics Resourceomes
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2 The New Waves Towards Bioinformat
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2.4 Semantic Web Towards Bioinforma
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A Summary of Genomic Databases: Ove
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Appendix A Summary of Genomic Datab
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Protein Data Integration Problem Am
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Protein Data Integration Problem 57
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Fig. 3. Class Hierarchy of Protein
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Bio-medical Ontologies Maintenance
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TextToOnto (Maedche and Volz 2001)
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Extraction of Constraints from Biol
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Classifying Patterns in Bioinformat
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Mining Clinical, Immunological, and
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Substructure Analysis of Metabolic
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entry compound relation subtype com
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Running Time 4500 4000 3500 3000 25
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6 Conclusion Substructure Analysis
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266 J.Y. Chen, S. Taduri, and F. Ll
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Bio-medical Ontologies Maintenance and Change Management

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