Difference between revisions of "Talk:2010 GO camp binding documentation issues"

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[[User:Siegele|Siegele]] 21:54, 29 June 2010 (UTC)
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As many terms in the Molecular Function ontology implicitly or explicitly imply the binding of a chemical or protein, it is unnecessary to co-annotate a gene product to a term from the binding node of GO to describe the binding of substrates or products that are already adequately captured in the definition of the Molecular Function term.
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For instance, an enzyme MUST bind all of the substrates and products of the reaction it catalyzes. Similarly, a transporter MUST bind the molecules it transports. Therefore, as binding is implied, curators should avoid making redundant annotations. 
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There will be some cases, however, where it is appropriate to annotate a binding relationship. For example, published experiments may show that a gene product binds a non-hydrolyzable ATP analog, without demonstrating that it has ATPase activity. In such a case, it would be appropriate to annotate to GO:0005524 ATP binding using an IDA evidence code.
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The GO is committed to ‘annotating to the experiment’. Therefore the curator should try to capture the specifics as much as feasible: use the binding term if the experiment shows binding, but not catalysis transport; don’t use the binding term if the experiment shows catalysis or transport.
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The curator may come across Molecular Function terms where the definition doesn't adequately describe the specific substrate/target being bound, and where the request of a more specific Molecular Function would be considered inappropriate.  In such cases, the annotation extension column (column 16) can be used to capture this information using the accession from CheBI (add link) for small molecules or from UniProt (others?) for proteins.  Enter the substrate/target information in column 16 in the form CheBI:xxxx or UniProt:xxxx.  Remember, use annotation extension column (16) only if this information is not already included in the GO term and/or definition.

Revision as of 13:54, 29 June 2010

Siegele 21:54, 29 June 2010 (UTC)

As many terms in the Molecular Function ontology implicitly or explicitly imply the binding of a chemical or protein, it is unnecessary to co-annotate a gene product to a term from the binding node of GO to describe the binding of substrates or products that are already adequately captured in the definition of the Molecular Function term.

For instance, an enzyme MUST bind all of the substrates and products of the reaction it catalyzes. Similarly, a transporter MUST bind the molecules it transports. Therefore, as binding is implied, curators should avoid making redundant annotations.

There will be some cases, however, where it is appropriate to annotate a binding relationship. For example, published experiments may show that a gene product binds a non-hydrolyzable ATP analog, without demonstrating that it has ATPase activity. In such a case, it would be appropriate to annotate to GO:0005524 ATP binding using an IDA evidence code.

The GO is committed to ‘annotating to the experiment’. Therefore the curator should try to capture the specifics as much as feasible: use the binding term if the experiment shows binding, but not catalysis transport; don’t use the binding term if the experiment shows catalysis or transport.

The curator may come across Molecular Function terms where the definition doesn't adequately describe the specific substrate/target being bound, and where the request of a more specific Molecular Function would be considered inappropriate. In such cases, the annotation extension column (column 16) can be used to capture this information using the accession from CheBI (add link) for small molecules or from UniProt (others?) for proteins. Enter the substrate/target information in column 16 in the form CheBI:xxxx or UniProt:xxxx. Remember, use annotation extension column (16) only if this information is not already included in the GO term and/or definition.