DataStorage » History » Version 1
Anonymous, 10/05/2007 09:34 PM
| 1 | 1 | Anonymous | = Data Storage = |
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| 2 | 1 | Anonymous | |
| 3 | 1 | Anonymous | This page describes the design of the database that is/will be used in order to store all necessary pieces information that are obtained from the "stand-alone" ProCKSI application (see [wiki:DataStandardisation]). |
| 4 | 1 | Anonymous | |
| 5 | 1 | Anonymous | == Database Design for the (static) Protein Multivers == |
| 6 | 1 | Anonymous | [attachment:ProteinMultiverseDataBase.png] |
| 7 | 1 | Anonymous | |
| 8 | 1 | Anonymous | '''Explenation of the database design''': |
| 9 | 1 | Anonymous | * There are multiple similarity comparison ''Methods'': e.g. USM, MaxCMO, DaliLite, ... |
| 10 | 1 | Anonymous | * There are multiple similarity ''Measures'': e.g. Z-score, TM-score, Number of Alignments, ... |
| 11 | 1 | Anonymous | * Some ''Methods'' produce ''Measures'' with the same name, but not necessarily the same meaning: e.g. DaliLite/Z, TMalign/Z, ...[[br]] |
| 12 | 1 | Anonymous | Thus, a ''!MethodMeasures'' relation is necessary. |
| 13 | 1 | Anonymous | |
| 14 | 1 | Anonymous | * Each ''Method'' can have multiple (different) ''Parameters'': e.g. USM/Compressor, USM/Equation, ... |
| 15 | 1 | Anonymous | * Each ''Method'' can have multiple (different) ''!ParameterOptions'': USM/Compressor/bzip, USM/Compressor/gzip, ... |
| 16 | 1 | Anonymous | * A "!ParameterSet" is used to calculate the ''Similarity'' of ''!StructurePairs''. It is a collection of specific ''!ParameterSetOptions''. If a ''Method'' does not use any parameters, it is not included in the ''!ParameterSet'', but accessible via the ''!MethodMeasure'' relation. |
| 17 | 1 | Anonymous | |
| 18 | 1 | Anonymous | * The ''!StructurePairs'' relation holds all possible combinations of ''Structures'', and a link to a further ''Results'' file in XML format. This file may contain results for multiple ''!StructurePairs'', e.g. alignments, matrices, etc. |
| 19 | 1 | Anonymous | * Each ''Structure'' is uniquely determined by its PDB code, model and chain. (Domains are not taken into accout yet.) The location of the PDB file is given and a link to a further ''Results'' file in XML format. This file may contain additional information for multiple ''Structures'', e.g. sequence, secondary structure, experimental resolution, ... |
| 20 | 1 | Anonymous | |
| 21 | 1 | Anonymous | * Each ''Structure'' is extended by further classifiction information from ''CATH'' and ''SCOP''. |