Annotation Conf. Call 2016-07-11

Agenda

Annotation Consistency Exercise for 2016-07-26

• PomBase is next up on the rota

Revised Protein Binding Doucmentation

• On the 2016-06-28 call, we discussed how each group currently annotates protein binding experiments as it was pointed out that the current documentation does not likely reflect universal practice, specifically wrt the issue of the direct or indirect nature of the interactions captured using 'protein binding' (GO:0005515) or its children.

 The 'with' column (8) and the annotation extension column (16) should be used only for direct interactions and only when the binding 
 relationship is not already included in the GO term and/or definition. See "column 16 documentation for relationship types to use when 
 adding IDs in the annotation extension column (16). 

• We surveyed curators on the call and found that there are differences in how groups use interaction experiments for GO annotation.
• We also discussed whether we are comfortable with having differences or should try to adhere to a common practice; generally, people felt it was okay to have some differences here, but we need to reflect that in the documentation.
• Here is a draft of an update to the binding section of our curation documentation. Let's discuss if this accurately reflects what we do and why, and then make changes, if needed, and update the documentation.

 The Molecular Function (MF) ontology can be used to capture macromolecular interactions, such as protein-protein, protein-nucleic acid, protein-lipid interactions, etc.  While GO annotations are not considered to be a repository of all protein-protein interactions, many gene products are annotated to 'protein binding' (GO:0005515) or one of its child terms.  In making these annotations, contributing groups may follow slightly different practices with respect to the types of experimental evidence used to support these inferences, e.g. some groups may use co-immunoprecipitation as supporting evidence for a protein binding annotation between two gene products, others not.  However, all groups generally adhere to the principle that, when annotated, protein binding interactions inform what is believed to be the normal biological role of a gene product, i.e. the protein-protein interactions support an author's hypothesis about how the gene product is thought to execute its molecular function in the context of a normal biological process.  Protein-protein interactions for which there is not yet sufficient biological context are discouraged as sources of GO MF annotations.