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.

 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 Guidline: 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.   

Questions about Subcellular Localization Experiments and Cellular Component Annotations

• The UCL group would like clarification and guidelines on how curators should annotate the various membrane and child terms that describe the extent to which a gene product is contained within a membrane.
• Here is a representative branch of the CC ontology wrt these types of terms:
  • membrane part
    • [isa]intrinsic component of membrane
      • [isa]integral component of membrane
      • [isa]anchored component of membrane
    • [isa]extrinsic component of membrane
• Examples from the literature:

 EXAMPLE 1: PMID:18502731
 What annotations for VGAT and VGLUT2?
 Summary of methods in the paper:

 Electron microscopy shows synaptic vesicle localisation (Figure 4)
 Immunolocalization supports the localisation of VGAT and VGLUT2 to synaptic vesicles

 The curator knows that these proteins have transmembrane domains
 Would you annotate to 
 integral component of synaptic vesicle membrane ; GO:0030285 | IDA
 Or
 synaptic vesicle ; GO:0008021 | IDA
 integral component of synaptic vesicle membrane ; GO:0030285 | IC from GO:0008021
 (NB: The IC doesn’t show the full-picture because the membrane domains/anchors are author knowledge so often curated as a NAS/TAS 
 which can’t be included in the with statement for an IC annotation).

 Example 2: PMID:17110340
 integral component of synaptic vesicle membrane ; GO:0030285
 or
 anchored component of synaptic vesicle membrane ; GO:0098993

 Summary of methods in the paper:
 The protein composition of purified synaptic vesicles (SVs) was analysed by Mass spectrometry (MS) and 1D SDS-PAGE, and 410 proteins 
 were unambiguously identified
 Proteins are classified as: 
   Copurifying with SVs
   Ubiquitously distributed on subcellular membranes (i.e present on SVs but not enriched relative to other fractions).
 Western blots were used to quantitate the levels of SV proteins.
 Three different electron microscopy (EM) procedures imaged surface proteins, and show the surface of SVs to be covered with proteins, 
 but doesn’t identify individual proteins
 They model the SV (Figure 4) to show transmembrane domains of proteins and anchored proteins- some of these are known to me membrane 
 proteins by their previous structure (e.g. they are known ion channels)

 From this paper, would you annotate to:
 integral component of synaptic vesicle membrane ; GO:0030285 | IDA
 anchored component of synaptic vesicle membrane ; GO:0098993 | IDA
 (e.g. incorporating author say-so/previous knowledge of the protein domains into the IDA evidence code)
 Or 
 synaptic vesicle membrane ; GO:0030672 | IDA
 integral component of synaptic vesicle membrane ; GO:0030285 | IC from GO:0030672
 anchored component of synaptic vesicle membrane ; GO:0098993 | IC from GO:0030672
 (NB: The IC doesn’t show the full-picture because the membrane domains/anchors are author knowledge so often curated as a NAS/TAS 
 which can’t be included in the with statement for an IC annotation).