ProCKSI

= Data Storage =

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 ''core'' application (see [wiki:DataStandardisation]).

== Database Design for the (static) Protein Multiverse Multivers ==
[[Image(ProteinMultiverseDataBase.png)]]

'''Explenation of the database design''':
* There are multiple similarity comparison ''Methods'': e.g. USM, MaxCMO, DaliLite, ...
* There are multiple similarity ''Measures'': e.g. Z-score, TM-score, Number of Alignments, ...
* Some ''Methods'' produce ''Measures'' with the same name, but not necessarily the same meaning: e.g. DaliLite/Z, TMalign/Z, ...[[br]]
Thus, a ''!MethodMeasures'' relation is necessary.

* Each ''Method'' can have multiple (different) ''Parameters'': e.g. USM/Compressor, USM/Equation, ...
* Each ''Method'' can have multiple (different) ''!ParameterOptions'': USM/Compressor/bzip, USM/Compressor/gzip, ...
* 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.

* 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.
* 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, ...

* Each ''Structure'' is extended by further classifiction information from ''CATH'' and ''SCOP''.

== Extended Database Design for the (static) Protein Multiverse ==

[[Image(ProteinMultiverseDataBaseExt.png)]]

This proposal for an extended database design for the (static) Protein Multiverse aims to include not only ''Comparisons'' but also ''Transformations'' (following the latest development of the I/O specificaitions for the ProCKSI "stand-alone" ''core'' application):
* A ''Transformation'' is a process that derives ONE (main) ''Result'' from ONE single input file.[[br]]
__Example__: The transformation of ''Structure'', ''Tree'', ''!SimilarityMatrix'', etc., using a certain ''Method'' with a certain ''!ParameterSet'', produces a contact map, a tree, ...
* A ''Comparison'' is a process that derives ONE (main) ''Result'' from TWO input files. [[br]]
__Example__ The comparison of ''Structures'', ''Trees'', etc., using a ''Method'' with a certain ''!ParameterSet'', produces a similarity value and an alignment
* A ''Composition'' is a process that derives ONE (main) ''Result'' from SEVERAL input files. [[br]]
__Example__ The composition of ''!SimilarityMatrices'', ''Trees'', using a ''Method'' with a certain ''!ParameterSet'', produces a consensus similarity matrix, a consensus tree, ...