Talk:2010 GO camp binding documentation issues
Siegele 21:24, 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.
In cases where the definition of a Molecular Function term doesn't adequately describe the specific substrate/target being bound, and where the request of a more specific Molecular Function would be considered inappropriate, the annotation extension column (column 16) can be used to capture this information.
However, use the ‘with’ column (8) or annotation extension column (16) to add information to the annotation, only if this information is not included in the GO term and/or definition.
The above paragraph indicates that curators will want to include additional information in their annotations where the definition of an associated Molecular Function term is unable to adequately describe the specific substrate/target being bound, and where the request of a more-specific Molecular Function term would be considered inappropriate. The annotation extension column (16) can be used to capture this information. However, use the ‘with’ column (8) or annotation extension column (16) to add information to the annotation, only if this information is not included in the GO term and/or definition.
Future ontology development efforts should be relied upon to improve the searching capability of any user using GO who is specifically interested in gene products carrying out a certain type of substrate/product binding.
The annotation extension (column 16) should only be used for direct (target of catalytic activity (using relationship ontology).
Curators should use their judgment to decide whether the interaction is physiologically relevant and capture information relevant to the in vivo situation, not artificial substrates.
Annotations to the protein binding terms should be maximally informative. Where possible the precise identity of the interacting protein should be captured in the 'with' field of an annotation. Similarly, usage of child terms that describe a particular class of protein binding (e.g. receptor tyrosine kinase binding) should be applied in preference to the parent term 'protein binding'; GO:0005515.
Ongoing relevant ontology development Has_part relationships provide links to implied substrate binding (Chris and Jane are developing has_part relationships to implying substrate binding) existing GO to follow this new format eg Transcription factor activity has_part DNA binding. Request new 'has_part' relationships (and terms) if these do not exist.