DataStorage » History » Version 1

Anonymous, 10/05/2007 09:34 PM

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= Data Storage =
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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]).
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== Database Design for the (static) Protein Multivers ==
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[attachment:ProteinMultiverseDataBase.png]
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'''Explenation of the database design''':
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 * There are multiple similarity comparison ''Methods'': e.g. USM, MaxCMO, DaliLite, ...
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 * There are multiple similarity ''Measures'': e.g. Z-score, TM-score, Number of Alignments, ...
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 * Some ''Methods'' produce ''Measures'' with the same name, but not necessarily the same meaning: e.g. DaliLite/Z, TMalign/Z, ...[[br]]
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 Thus, a ''!MethodMeasures'' relation is necessary.
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 * Each ''Method'' can have multiple (different) ''Parameters'': e.g. USM/Compressor, USM/Equation, ...
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 * Each ''Method'' can have multiple (different) ''!ParameterOptions'': USM/Compressor/bzip, USM/Compressor/gzip, ...
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 * 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.
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 * 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.
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 * 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, ...
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 * Each ''Structure'' is extended by further classifiction information from ''CATH'' and ''SCOP''.