The Sequence Ontology - SO Compliant Software

September 2012 Karen Eilbeck presented a paper titled Using GVF for Clinical Annotation of Personal Genomes at the AIMM workshop part of ECCB12, in Basel Switzerland.
July 2012 Mike Bada presented a paper titled 'Efforts toward a More Consistent and Interoperable Sequence Ontology' at the International Conference on Biomedical Ontology in Graz, Austria.
September 2011 Mike Bada, University of Colorado, joins to SO team, to work on interoperability with the BFO
September 2011 The NHGRI have funded SO's renewal R01
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.

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.

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 July SO presented at the International Conference of Biomedical Ontology.

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.