This page describes the syntax used to make annotation extensions. Also see the [http://wiki.geneontology.org/index.php/Annotation_Extension GO Annotation Extension wiki page].

== Compound terms: ==

These are separated by a comma ',' and relate back to the term in conjunction (i.e. both apply simultaneously), e.g.

{{{

gene x
protein kinase activity
has_substrate(gene y),during(GO:processZ)

}}}

should be interpreted as gene x phosphorylates protein Y during process Z

== Independent annotations: ==

These are separated by a pipe '|' and independently relate back to the term. This is done in order to avoid making multiple identical annotations to one gene to incorporate different extensions 

{{{

gene x
protein kinase activity
has_substrate(gene y),happens_during(GO:processZ)|has_substrate(gene a),happens_during(GO:processB)

}}}

should be interpreted as 
 * gene x phosphorylates protein Y during process Z, and
 * gene x phosphorylates protein A during process B

Note that you cannot use "pipes" in combinations of qualifiers in Artemis becasue they cannot be disambiguated. For example,  you can have a single pipe in the residues field, e.g.

{{{
/GO="aspect=F; term=calcium ion binding; GOid=GO:0005509;
 residue=99|108; evidence=IDA; db_xref=PMID:12943532;  date=20040602"
}}}

but, if we have to add 2 annotation extension, each of which only applied to one of the modifications (for example, the residues were phosphorylated by different kinases), to disambiguate we would need to make 2 separate annotations:

{{{
/GO="aspect=F; term=calcium ion binding; GOid=GO:0005509;
residue=99;  annotation_extension=phosphorylated_by(x); evidence=IDA; db_xref=PMID:12943532;
date=20040602"

/GO="aspect=F; term=calcium ion binding; GOid=GO:0005509;
 residue=99; evidence=IDA;  annotation_extension=phophorylated_by(z); db_xref=PMID:12943532;
 date=20040602"
}}}

If you used pipes in both places it would not be possible for a human or computer to disambiguate.


== Nested terms: ==

(Note: we are trying to avoid nested terms as these are not handled by Chado or GO)

For extensions within extensions (i.e. an extension points to an entity which itself is a term+extension)

{{{

e.g. 
gene x
meiotic telomere clustering
dependent_on(GO:0005515^has_substrate(bqt3)) 

}}}

should be interpreted as "gene x is involved in the process 'meiotic telomere clustering' and its involvement is dependent on protein binding to substrate Bqt3"

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