Greetings GO ontology watchers,

The following weekly ontology reports are now available:

Ontology changes, full details: web page | text

Ontology changes, less detailed: web page | text

The GO Consortium is currently looking at improving the terms and annotations associated with the apoptosis process. If you would like to contribute to this effort please have a look here http://wiki.geneontology.org/index.php/Apoptosis, or contact us (http://www.geneontology.org/GO.contacts.shtml).

On the 1st of June 2010, the format of GO annotation files available from the GO Consortium web and ftp site will change, with files being supplied in a 17-column GAF format (GAF2.0) instead of the current 15 columns.

The format of the new annotation file is described on the GO website.

In essence, this format change means that two columns will be added to the end of the current tab-delimited file format:

We are pleased to announce that we are about to introduce cross-product definitions, in the form of intersection_of tags, into the "extended" version of GO (ontology/obo_format_1_2/gene_ontology_ext.obo). The target date for this addition is January 18, 2010.

The GO Consortium are pleased to announce that we have now introduced a new relationship type, has_part, into the "extended" version of GO (ontology/obo_format_1_2/gene_ontology_ext.obo).

The has_part relation is documented at:

http://geneontology.org/GO.ontology-ext.relations.shtml

Note that has_part links will not be included in the "standard" gene_ontology*.obo files, such
as gene_ontology.1_2.obo and gene_ontology.1_0.obo.

Abstract: The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries.

This talk was presented at ICBO 2009.

• Slides on slideshare

We are pleased to announce that we are about to introduce a new relationship type, has_part, into the "extended" version of GO (ontology/obo_format_1_2/gene_ontology_ext.obo). The target date for this addition is Thursday, July 30, 2009.

This addition may have considerable impact on your tools and analyses because:

1. Loading scripts that use gene_ontology_ext.obo will need to be modified to take the has_part links into account by July 30.

Most of us who work with the Gene Ontology have long forgotten what it felt like to not understand what "GO" meant, or what an ontology was. But that's the place where many of our users are. With that in mind, the Rat Genome Database (RGD) has produced a short tutorial video designed to introduce novice users to what an ontology is, why ontologies are useful and where to find ontology annotations assigned to genes and/or gene products.

A special issue of BMC Microbiology highlights some of the recent achievements of the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium: an international group of scientists working with GO to develop terms to describe the the complex interplay between microbes and the hosts that they colonize.

Having successfully implemented the 'regulates' relationships in the biological process (BP) ontology, we have now added 'regulates' relationships within the molecular function (MF) ontology and between the BP and MF ontologies. These changes are only present in the file:

go/ontology/obo_format_1_2/gene_ontology_ext.obo

Specifically, we have made the implicit regulatory relationships between 'regulation of molecular function' BP terms and the corresponding MF terms explicit. For example: