SO software grant awarded.

A research proposal titled "Software to facilitate the adoption of the Sequence Ontology for genome management" was awarded by the NIH (RO1HG004341-01).
Author: Karen Eilbeck
Date: August 28th 2007

Pending SO Release.

We plan to provide a stable release of SO every 2-3 months. Each release will contain coherent blocks of changes, and come with a set of extensive notes about what happened.

This will provide two channels of access for SO users. The 'bleeding edgers' can use the CVS incremental updates, and those who need more stability in their lives can use CVS to see what is coming between releases.

The releases will also be stored on the SO website: www.sequenceontology.org/releases/2.1/so.obo

and the website www.sequenceontology.org/releases/latest will point to the latest release.

As we have had a couple of SO mile stones recently; the adoption of the biosapiens protein terms and the immunology workshop additions, it is time to make a new release. This will be version 2.2

By the end of the month (2 weeks from now), there will be a SO release.

Author: Karen Eilbeck
Date: August 8th 2007

Sequence Ontology Integrates Biosapiens protein feature terms

The SO has been collaborating with the Biosapiens project to develop terms necessary to describe polypeptide features. The biosapiens protein feature ontology was developed as a means to organize the protein sequence and structure annotations which are provided via DAS servers. Gabrielle Reeves from the EBI is responsible for these polypeptide terms and is on board as a SO developer. Protein based queries to the Term Tracker will be directed to Gabby.
The developers should note that the original Biosapiens ID remains as an alt_ID for each term. A new category: biosapiens, has been added to SO to label these terms and provide a quick way to make a protein feature slim ontology.

Author: Karen Eilbeck
Date: August 8th 2007

Changes to Sequence Variation terms

There have been some major changes to the sequence_variation terms in SO. The child terms are now kinds of sequence_alteration, which is a kind of sequence_feature. A new term, 'sequence_variation is the parent of the terms allele, genotpe etc.
Author: Karen Eilbeck
Date: August 7th 2007