GoOboScanner is a console application to translate Gene Ontology Obo-files ( into SQL-code suitable to load the code directly into a database. Supported databases are SQLite (, PostgreSQL ( and MySQL (

General usage


Just download the Zip archiv and execute the binary for your platform. GoOboScanner is provided both in source code and in binary format for different platforms. Currently the binaries for the following platforms are part of the download: Win32, Linux-32 and 64-bit, Solaris-sparc, and Mac-OSX-universal. If a binary for your platform is not available or the provided binary does not work due to some C-library incompatibilities you can compile the application easily yourself using the GCC-compiler. As the source code GoOboScanner.c does not depend on any external library it should compile easily using the command "gcc GoOboScanner.c -o GoOboScanner". The resulting binaries might be copied somewhere in your PATH and be used directly without any further installation.


The GoOboScanner applicationd needs two arguments for converting your GeneOntology-files into database data. At first the name of the GeneOntoloy-file which should be scanned and secondly the name of a table prefix which should preceed all tablenames with this prefix. This allows to store results of different GeneOntology-files in the same database. A sample inovaction might be the following:

$ GoOboScanner--Windows-x86.exe  --infile gene_ontology.obo --prefix sep09 > sep09.sql

the code in sep09.sql can be used to fill the database. If you don't need a prefix use `--prefix none'.

Usage with SQLite

The SQL-code can be directly piped into the SQLite console application like here:

$ GoOboScanner-Linux-x86 --infile gene_ontology.obo --prefix sep09 | sqlite3 go.sqlite3
$ GoOboScanner-Linux-x86 --infile gene_ontology-sep08.obo --prefix sep08 | sqlite3 go.sqlite3

Usage with MySQL

The MySQL command line client can be used to import the data into a certain database. It is recommended to do the following steps in the mysql-shell:

mysql> connect godb;
mysql> set autocommit=0;
mysql> source /path/to/sep09.sql;

this will import your data into the database you are currently connected.

Usage with PostgreSQL

The psql command line application can be used to import the data into the database you invoke psql for importing the data into sampledb like so:

$ psql godb -U youruserid -f /path/to/sep09.sql


GoOboScanner is provided under a BSD-like license (see License.txt). In short this means that you can do anything you want with the source code as long as you retain our copyright-notice.


GoOboScanner is part of the Bioscanners project at Sourceforge: For reporting bugs and suggestions the project maintainer can be reached by email using dgroth(at)gmx(dot)de.