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[Gofriends] Announcement: Introduction of has_part relationship in extended GO on July 30
midori at ebi.ac.uk
Wed Jul 15 08:41:43 PDT 2009
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
Note that has_part links will not be included in the "standard"
gene_ontology*.obo files, such as gene_ontology.1_2.obo and
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:
Please let us know if you have questions or comments about this plan.
On behalf of the GO Consortium,
Midori A. Harris, Ph.D.
EMBL - EBI
Wellcome Trust Genome Campus
Cambridge CB10 1SD UK
Tel: +44 (0) 1223 494667
Fax: +44 (0) 1223 494468
Email: midori at ebi.ac.uk
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