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Data Conversion in MACiE

This section describes the processes involed in converting the flat RDFile version of MACiE into the MySQL version of MACiE.

All data is entered into MACiE in ISIS/Base, and then converted into the MySQL format. This conversion not only transforms the ISIS RDFile into a MySQL database, it also performs a number of validation checks:

  1. Are there any residues that are annotated as a spectator, but which have reactant function?
  2. Are there any residues that are annotated as a reactant, but which do not have any reactant functions? This is subject to a list of special cases, e.g. Ser70 in M0002 steps 2 and 4 in which it isn't acting itself, but it is covalently attached to the reacting species, these special cases need catching.
  3. All residues should have a location of function
  4. All residues should have a function. Note, if a residue is only annotated with a location of function and as a spectator (i.e. no other function) it should be listed as not active in the database, not have a blank function. This annotation of "Not Active" is handled by the conversion process, and does not need to be incorporated into the ISIS/Base annotation.
  5. Are any rxn files that are present in the SQL MACiE tables also present in the file directories?
  6. Are any gif files for the reactions in the SQL MACiE also present in the file directories? If the answer to this question is affermative, then the gif files are copied accross to the web directories.
  7. Are all the compound gifs required for the MACiE overall reactants and products present in the file directories? If the answer to this question is affermative, then the gif files are copied accross to the web directories.
  8. Are all the MACiE entries with metal cofactors annotated also to be found in Metal-MACiE?
  9. Are there any reaction steps with blank mechanisms or mechanismComponents?
  10. Are there any reaction steps with blank bond changes (both atom1 and atom2)?

Before the new public version of MACiE is released and frozen, all of these checks must have been sucessfully passed. As we build a deeper and more detailed understanding of enzymes and their catalytic mechanisms, these checks will become more sophisticated and detailed. It is worth noting at this stage that all the checks require a human to sign off on them.

Conversion of MACiE from ISIS to MySQL also updates and/or creates the version statistics an the catalytic propensities of the residues, as well as compiling the various statistics images that are required by the MACiE Database. This is also the point at which the overall RXN files are created. We also capture any changes between versions of the database at this point.

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