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Binding Survey May 2010

1. Binding group survey May 2010

This survey needs to be completed before the forthcoming Binding group conference call on Wednesday 26th May. The results will be used to inform the conference call discussion

Question Title

* 1. Currently column 8 (with) is used for a wide range of identifiers. The creation of column 16 will lead to protein identifiers being located in both both column 16 and column 8.

Which of the following statements do you agree with?

All proteins identifiers present in column 8 should be represented in column 16

Duplication of identifiers in column 16 (as well as column 8) is not necessary

I don't understand the question

There is no need to choose between these options

Question Title

* 2. See http://wiki.geneontology.org/index.php/Binding_discussion_emails#Use_of_column_16_to_capture_in_vivo_participant.

Proposal: where groups can use column 16, then a valid use would be to identify 'in vivo' targets of an interaction.

While in many cases, the participant identifiers of a binding annotation supported by the IPI evidence code will the same in both column 8 (with) and 16, this will not be the case for cross-species experiments. The intent of these experiments is that the use of proteins from different species indicates the in vivo binding interaction (ie. a demonstration of mouse protein A binding human protein B would infer that in the in vivo situation of mouse protein A is expected to bind mouse protein B, human protein A binds human protein B).

A concern with this proposal is that in cross species experiments the 'in vivo' target annotation is inferred by the curator or author based on orthology and does not have direct experimental support.

Which of the following statements do you agree with?

In vivo participants should be added to column 16

In vivo participants should NOT be added to column 16

I don't understand the question

Question Title

* 3. Column 16 can be used to capture information that a protein kinase phosphorylates a specific target.

For instance, in PMID:17182001 GSK3beta phosphorylates Sufu to regulate Hedgehog signalling, as Sufu is a substrate of the GSK3beta kinase, going along with the guidelines we previously agreed we would prefer if curators did not to annotate directly to both the catalytic activity term AND also describe the binding to its substrate:

GSK3beta GO:0005515 protein binding IPI with=Sufu
GSK3beta GO:0004672 protein kinase activity IDA

It would seem more informative if the curator could specify in the molecular function annotation for protein kinase activity, that the substrate of this interaction is Sufu:

GSK3beta GO:0004672 protein kinase activity IDA col16=has_input[Sufu]

Which of the following statements do you agree with?

The target of an enzyme activity (when not specifically implied by the GO term) should be included in column 16

Column 16 should not be used to list targets of an enzyme activity

I don't understand the question

Question Title

* 4. Current annotations such as
GSK3beta GO:0004672 protein kinase activity IPI with='Sufu'

...are less informative, as the annotation is only able to state that the activity of GSK3beta has been inferred by the fact that it binds to Sufu - with this annotation format the curator can not explicitly state the identity of Sufu as the substrate of the interaction.

Of the 30,000 manual annotations to the GO term (or child terms) GO:0003824 catalytic activity, only 162 annotations use the IPI evidence code.

Which of the following statements do you agree with?

catalytic activity annotations should NOT be made using the IPI evidence code

Continue to allow annotations to a catalytic activity term using the IPI evidence code and including a protein identifier in the 'with' column (8)

I don't understand the question

Question Title

* 5. The term GO:0005515 (protein binding) has numerous children.
Some for specific proteins, e.g. p53 (GO:0002039), others for classes of proteins, e.g. IgM (GO:0001791) or GO:0019900 (kinase binding).

Which of the following statements do you agree with? (can tick more than one box)

The GO term GO:0002039 p53 binding (and similar terms) should be obsoleted because there is usually only one p53/genome, instead column 16 or the 'with' column (8) should be completed with 'protein binding' (56 annotations associated with this term)

The GO term GO:0002039 p53 binding (and similar terms) ARE useful and should not be obsoleted

GO terms such as GO:0003779 actin binding are appropriate because often it is not possible to identify which actin isoform is bound

I don't understand the question

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* 6. Any comments about binding issues you would like to raise?