The Sequence Ontology - Developers

News

March 2011 SOBA workshop presented at GMOD Spring Training.
Feb 11th 2011 The CVS repository on sourceforge is back online after the hacking incident.
January 2011 SO presented at Synthetic Biology Workshop.
December 2010 10Gen Data Set v1.04 available.

December 2010 GVF Specification v1.04 available.

November 2010 Release 2.4.4 available.

September 2010 A standard variation file format for human genome sequences in Genome Biology.
August 2010 'Toward a Richer Representation of Sequence Variation in the Sequence Ontology' with Mike Bada accepted by AIMM Workshop.

June 2010 Release 2.4.3 available.

May 2010 SOBA paper available from Nucleic Acids Research.

April 2010 Release 2.4.2 available.

March 2010 New SO paper out: 'Evolution of the Sequence Ontology terms and relationships' in the Journal of Biomedical Informatics. A pre-print of this paper is available here.

February 2010: Sequence Ontology Bioinformatics Analysis (SOBA) is available. Genome annotations in GFF3 can be uploaded and analysed.

2009 December Release 2.4.1 available.

2009 October Release 2.4 available.

2009 July SO presented at the International Conference of Biomedical Ontology.

2009 June Chris Conley -Undergrad from BYU joins SO for the summer

2009 May Graduate student, John Naylor joins SO.

2009 February 22: A new SO related paper Quantitative Measures for the Management and Comparison of Annotated Genomes K Eilbeck et. al.

2009 January 4-6: SO represented at the RNA Ontology consortium meeting in Cambridge UK.

2008 December 1: A paper from the BioSapiens project describing protein features in SO is published. The Protein Feature Ontology: A tool for the unification of protein feature annotations. GA Reeves et. al.

Download SO Data & Software via Anonymous CVS

The SO CVS repository can be checked out through anonymous (pserver) CVS with the following instruction set. The module you wish to check out must be specified as the modulename. When prompted for a password for anonymous, simply press the Enter key.

cvs -d:pserver:anonymous@song.cvs.sourceforge.net:/cvsroot/song login cvs -d:pserver:anonymous@song.cvs.sourceforge.net:/cvsroot/song co modulename

Updates from within the module's directory do not need the -d parameter.

You can check out the following modules. Note that capitalization is significant!

ontology	The sequence ontology in OBO format
software	Perl modules and scripts for using SO to manage genome annotation.
so-home	The html, css, perl and javascript source for the SO website

Please note that although we do our best not to check in malfunctioning software, the CVS versions of these packages are cutting edge and hence not guaranteed to be bug free. Always be careful when using these packages!

You can also browse the SO CVS repository to find particular files or to view the change history.

Developer CVS Access via SSH

Only project developers can access the CVS tree via this method. SSH1 must be installed on your client machine. Substitute module_name and developer_name with the proper values. Enter your site password when prompted.

export CVS_RSH=ssh cvs -z3 -d:ext:developer_name@song.cvs.sourceforge.net:/cvsroot/song co module_name