The Sequence Ontology - SO Compliant Software

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.

Here you will find a list of tools that work with SO data or with SO compliant annotations.

GO Perl: A set of perl modules for parsing, manipulating and exporting ontologies.
Comparative Genomics Library (CGL): A Perl library designed for comparative analysis of genomic data. This library uses annotations marked up with Chaos-XML.
BioPerl: A Perl library that deals with a wide array of biological data including GFF3 and Chado genome annotations.
Apollo: A genome annotation viewer and editor that was developed as a collaboration between the Berkeley Drosophila Genome Project and The Sanger Institute.
The Generic Genome Browser: GBrowse is a combination of a database and interactive web pages for manipulating and displaying annotations on genomes.
AJAX GBrowse: A branch of the GBrowse software currently under developement that is being implemented with the enhanced features of modern Web 2.0 applications to provide a richer, smoother and more responsive user interface.
SO Term Finder: An application for browsing SO terms provided by the Broad Institute.
Ontology Lookup Service: An Ontology browser which includes the Sequence Ontology and is provided by EMBL-EBI.
OBO-Edit: A tool for viewing and editing OBO ontologies.