wiki:AnnotationExtensionSyntax

Version 9 (modified by gomidori, 10 years ago) (diff)

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This page describes the syntax used to make annotation extensions
(to go back to the wiki: https://sourceforge.net/apps/trac/pombase/wiki/)

Compound terms:

These are separated by a comma ',' and relate back to the term in conjunction.

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

e.g 
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
gene x phosphorylates protein A during process B

Nested terms:

For extensions attached to an entity which is itself and extension

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

should be interpreted as gene x is involved in process and is dependent on protein binding to substrate bqt3

In development:

Some way to specify residues on the target

e.g
gene x  
protein kinase activity
has_substrate(gene y,residue=S87)

should be interpreted as
gene x phosphorylates protein Y on residue S87
e.g2: reciprocal for PSI-MOD

gene y
phosphorylated residue
modified_by(gene x),residue=S87

should be interpreted as 
gene y is phosphorylated on residue S87 by protein X

I think this would be easy to extend?

gene y
phosphorylated residue
modified_by(gene x),residue=S87,residue=T90

should be interpreted as 
gene y is phosphorylated on residues S87 and T90 by protein X