GFF3 Validation

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The GFF3 Validator tool has both a command-line and an online version. It is structured as a core module that is responsible for validation. A module extension generates a online interface. The command-line script directly uses the core validation module. The online CGI script uses the extension module and provides an online interface.

The code base: $WORMBASE/utils/gff3_validator/

An online installation is available at brie3:

http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

As described in the GFF3 conversion section, GFF3 format requires feature types to come from an ontology. As of this writing, the SOFA ontology is used. The two most recent releases of SOFA are available in CVS. Please note that there is recent discussion about transitioning to use of SO instead of SOFA for the GFF3 format. If such transition occurs, the code needs to be updated to take this into account.

The core of the code base is the validator module, GFF3::Validator. In order to install a command-line version of the validator, make this module available to your Perl scripts (add to @INC path by using PERL5LIB, installing globally, etc.) and use the validate_gff3.pl script and validate_gff3.cfg config file. The config file needs to be customized for the installation and contains instructions. The main configuration requirement is setting up a MySQL database and a temporary directory where the validator can write to. Please refer to the config file for further requirements.

The validator code base contains a second module, GFF3::Online, which provides an online interface to the GFF3::Validator. In order to install a web-based version of the validator, make both GFF3::Validator and GFF3::Online available to your Perl scripts. Install the validate_gff3_online script into Apache's CGI script directory and adjust pointer to validate_gff3_online.cfg config file and customize the config file for the installation. The config file contains instructions. Also, please note that the config file points to the validate_gff3.cfg config file. Both config files need to be customized and functional for the online version.

With every release of the code base, a software package is created.

The current and previous packages: brie3:/usr/local/wormbase/html/validate_gff3_online/Validator-Files-*.tar.gz

A web-based version of the application is maintained at Wormbase on brie3 (see above). The online version of the validator points to the documentation and the current software package. The locations of these files are configured using the config file.