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[Gofriends] Dual-Taxon annotations in GO gene association files

Gwinn Giglio, Michelle mgiglio at som.umaryland.edu
Wed Sep 24 10:59:33 PDT 2008




Dear GO Friends,

Symbiotic interactions include a wide range of relationships between
organisms, some are beneficial (e.g. mutualism) and some are not (e.g.
parasitism).   During symbiotic interactions many gene products are required
to carry out the functions and processes required for initiating and
maintaining the interaction.  It is often the case that one organism may be
able to interact with many different species and that specific gene products
in that organism are required for interactions with one symbiotic partner,
but not others.  In order to fully capture the complexities of the
interactions between species, it is desirable to be able to store not only
the taxon id of the organism the gene product comes from but also the taxon
id of the organism the gene product interacts with.  Therefore, the GO
adopted "Dual-Taxon" annotations for annotating interactions between
organisms.

In a Dual-Taxon annotation, two taxon ids are placed in the taxon column of
the gene association file and separated by a pipe.  The first id represents
the organism encoding the gene product and the second id represents the
organism with which the gene product interacts.

Although the ability to make such annotations has existed in the GO for
several years, it is only in the last 6 months that dual-taxon annotations
have begun to appear in GO gene association files.  There are now 3
association files which contain dual-taxon annotations:  Magnoporthe grisea,
Oomycetes, and Pseudomonas syringae.  These annotations are the result of
efforts by the PAMGO (Plant-Associated Microbe Gene Ontology) Project.

More inforamtion on Dual-Taxon annotations can be found here:
http://www.geneontology.org/GO.annotation.conventions.shtml#interactions

More information on the PAMGO project can be found here:
http://pamgo.vbi.vt.edu

The dual-taxon annotations are not yet visible in the GO database or AmiGO,
but they will be arriving soon.

Please let us know if you have any questions,

Michelle

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