Annotation Conf. Call 2016-07-26

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Bluejeans URL:


Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Please indicate on the Meeting Logistics Page if you plan to come.
  • We are also gauging interest in a one- or half-day Noctua/LEGO workshop at USC (either before or after the main consortium meeting) so have added another column to the table to see if people can also attend that.
  • Please add your information as soon as possible so we can make arrangements.

Annotation Consistency Exercise for the Remainder of 2016

  • Thanks to everyone who agreed to select and present a paper for the remainder of this year:
  • August 23 - SGD
  • September 27 - dictyBase
  • October 25 - RGD
  • November 22 - Zfin
  • If you have thoughts about the exercises, please send them along to David and Kimberly. At the end of the year, we will evaluate how this is working and if we need to make any changes to the format to keep these exercises useful for people.

Revised Protein Binding Documentation

  • 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.
 Current Documentation: 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.
 Proposed New Guideline: 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 
  • We also discussed, on the last conference call, the criteria by which protein binding annotations from IntAct are exported to GO. A response from Sandra Orchard is on the 2016-06-28 minutes.
  • A summary:
 * Only experimental data is used for making the decision to export the protein pair to UniProtKB/GOA as a true binary interacting pair
 * The export decision is always based on at least two pieces of experimental data. A single evidence cannot score highly enough to 
 trigger an export
 * An export cannot be triggered if the protein pair only ever co-occurs in larger complexes, there must be at least one evidence that 
 the proteins are probably in physical contact.

LEGO Model for FlyBase Annotation Consistency Exercise Paper