[Gofriends] Announcement: Introduction of has_part relationship in extended GO on July 30

[Midori Harris]

Dear GO Friends,

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.
  2. GO analysis tools that use gene_ontology_ext.obo will need to be modified 
to take the has_part links into account by July 30.
  3. The meaning of has_part has important implications for the propagation of 
gene product annotations over relationships in the ontology.
  4. There are important display considerations for graphs or denormalized trees 
that include has_part links.
  5. In some cases, the extended GO file will capture more information than the 
"standard" files.

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.

Has_part links will be added first in the Cellular Component (CC) 
ontology, and later into the Biological Process (BP) ontology.

The advantage of using has_part in CC and BP is that it will allow us to 
reduce the number of artificial compositional terms that we have 
previously used to avoid introducing erroneous paths in the ontology. The 
graphs will also become somewhat less entangled.

For example, the U5 snRNP is present in two types of precatalytic 
spliceosome, the "major" U2-dependent type and the "minor" U12-dependent 
type, but is not simultaneously part of both. The extended GO will be able 
to capture this without imposing misleading paths or creating unwieldy 
terms: the ontology will simply contain two has_part links:

   U2-dependent precatalytic spliceosome has_part U5 snRNP
   U12-dependent precatalytic spliceosome has_part U5 snRNP

The has_part relation is documented at:

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

Please let us know if you have questions or comments about this plan.

On behalf of the GO Consortium,
Midori

============================
Midori A. Harris, Ph.D.
GO Editor
EMBL - EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

Tel: +44 (0) 1223 494667
Fax: +44 (0) 1223 494468
Email: midori at ebi.ac.uk