iRefIndex Release Process

From irefindex
Revision as of 15:17, 6 March 2009 by PaulBoddie (talk | contribs) (Added file upload information.)

The release process consists of the following activities:

  1. Build the database - see iRefIndex Build Process for details.
  2. Generate output files and statistics - see iRefIndex Output and Statistics for details.
  3. Test the output.
  4. Post the output files, statistics and release information.

Testing the Output

  • Checking for errors and log messages
  • Web services
  • Spot checks
  • Counting XML tags
  • Validation
  • Parsing the final output files - see iRefIndex MITAB Parser for details.

Posting the Output Files

The output files themselves are made available on the iRefIndex FTP site as described on the iRefIndex information page. This involves making a directory in the following local location:


For example, for the iRefIndex 3.0 release, the following directory hierarchy is created:

mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab

The data files are then copied into this new directory. For example:

cp /home/irefindex/output/*.zip /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab/

A README file should be placed in the directory containing a link to the format description. For example:

Please see

The symbolic link indicating the location of the current release needs to be updated. For iRefIndex 3.0 this is done as follows:

cd /biotek/proteas/ftp/irefindex/data
rm current
ln -s archive/release_3.0 current

Finally, the release file must be updated to indicate the current release number. For iRefIndex 3.0 this contains the following text:


Optional/Experimental Output Files

Additional PSI-MI-XML files may be made available within the release directory within a subdirectory created as follows (for iRefIndex 3.0):

mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi25xml

(Instructions on copying these files will be added in future.)

A README file should be placed in the directory with the following form:

Please see

(This directory contains a sample of iRefIndex data in PSI-MI 2.5 XML format for testing purposes only)