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Load into a database

It is not necessary to load UniProt into a database (the code works also when just using UniProt XML files). However it is a possibility provided by this project. This has the advantage that queries can be formulated across all of UniProt.

There are two possibilities how to load into a database.

  1. from the IDE,
  2. from the command line, using a jar file

1) Load from IDE:

  1. Make sure you have access to a MySQL installation, create an empty new database there, make sure you have write permissions
  2. Update the configuration in src/main/resources/database.properties to match your configuration
  3. Run LoadMissing.java (ideally over-night, by next morning you will have a populated database)

2) Load from a jar file

An executable jar file can be compiled with mvn package. You can run this jar file and pass in the DB configuration as a command line parameter (see LoadMissing.java as the main class).

Default: Load all of Swiss-Prot

The default functionality provided here is to load all Swiss-Prot entries into the database (see the LoadMissing.java class). Currently these includes about 550k UniProt entries. The process to load all these files takes about 8 hours on a typical database server.