Annotation Conf. Call 2016-07-11: Difference between revisions
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=Bluejeans URL: = | =Bluejeans URL: = | ||
=Agenda= | =Agenda= | ||
==Next GOC Meeting - USC, Los Angeles, CA== | ==Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016== | ||
[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Logistics Meeting Logistics Page] | [http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Logistics Meeting Logistics Page] | ||
==Annotation Consistency Exercise for 2016-07-26== | ==Annotation Consistency Exercise for 2016-07-26== | ||
*PomBase is next up on the rota | *PomBase is next up on the rota |
Revision as of 14:54, 11 July 2016
Bluejeans URL:
Agenda
Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016
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 Membrane 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
- membrane part
Definition: The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. Source: GOC:mah Comment: Note that proteins intrinsic to membranes cannot be removed without disrupting the membrane, e.g. by detergent.
- [isa]integral component of membrane
Definition: The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. Source: GOC:go_curators, GOC:dos
- [isa]anchored component of membrane
Definition: The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping. Source: GOC:dos, GOC:mah
- [isa]extrinsic component of membrane
Definition: The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region. Source: GOC:dos, GOC:mah, GOC:jl Comment: Note that proteins extrinsic to membranes can be removed by treatments that do not disrupt the membrane, such as salt solutions.
- 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).