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layout id title contact status implementations
rule
GORULE:0000005
No ISS or ISS-related annotations to 'protein binding ; GO:0005515'
edimmer@ebi.ac.uk
Approved
code language source
SELECT gene_product.symbol, CONCAT(gpx.xref_dbname, ':', gpx.xref_key) AS gpxref, IF(association.is_not=1,"NOT","") AS 'not', term.acc, term.name, evidence.code, db.name AS assigned_by FROM association INNER JOIN gene_product ON association.gene_product_id = gene_product.id INNER JOIN dbxref AS gpx ON gene_product.dbxref_id = gpx.id INNER JOIN term ON association.term_id = term.id INNER JOIN evidence ON association.id = evidence.association_id INNER JOIN db ON association.source_db_id=db.id WHERE evidence.code IN ('ISS','ISO','ISA','ISM') AND term.acc = 'GO:0005515'
SQL

If we take an example annotation:

gene product: protein A
GO term: protein binding ; GO:0005515
evidence: IPI
reference: PMID:123456
with/from: with protein A

this annotation line can be interpreted as: protein A was found to carry out the 'protein binding' activity in PMID:12345, and that this function was Inferred from the results of a Physicial Interaction (IPI) assay, which involved protein X

However if we would like to transfer this annotation to protein A's ortholog 'protein B', the ISS annotation that would be created would be:

gene product: protein B
GO term: protein binding ; GO:0005515
evidence: ISS
reference: GO_REF:curator_judgement
with/from: with protein A

This is interpreted as 'it is inferred that protein B carries out protein binding activity due to its sequence similarity (curator determined) with protein A, which was experimentally shown to carry out 'protein binding'.

Therefore the ISS annotation will not display the the interacting protein X accession. Such an annotation display can be confusing, as the value in the 'with' column just provides further information on why the ISS/IPI or IGI annotation was created. This means that an ISS projection from protein binding is not particularly useful as you are only really telling the user that you think an homologous protein binds a protein, based on overall sequence similarity.

This rule only applies to GO:0005515, as descendant terms such as mitogen-activated protein kinase p38 binding ; GO:0048273 used as ISS annotations are informative as the GO term name contains far more specific information as to the identity of the interactor.

For more information, see the binding guidelines on the GO wiki.