4 November 2014 PAINT Conference Call

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PAINT call Agenda and Minutes Nov. 4, 2014

Participants: Donghui, Suzi, Paul T., Moni, Karen, Chris, Rama, Mark, Pascale, Li, Huaiyu

Agenda

  • How to annotate or propagate a transmembrane protein? Many receptors are annotated to GO:0009897 external side of plasma membrane. Its definition is "The leaflet the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface." Does it exclude transmembrane protein? Many receptors are also annotated to GO:0016021 integral component of membrane, but based on the definition, "This component includes gene products that are buried in the bilayer with no exposure outside the bilayer." This problem was encountered when I (HM) curate the IL receptor families, such as PTHR10573.
  • Comment from Paola: GO:0009897 'external side of plasma membrane' includes transmembrane proteins, as shown under 'Ontology structure' in this documentation page:

http://geneontology.org/page/membrane-proteins

(BTW, I just corrected the typo in the def. of GO:0009897)

As for GO:0016021 'integral component of membrane', its complete definition reads: "The component of a membrane consisting of gene products and protein complexes that have some part that penetrates at least one leaflet of the membrane bilayer. This component *includes* gene products that are buried in the bilayer with no exposure outside the bilayer.". Therefore, annotating receptors to this term is correct, as shown in the figure at the top of that documentation page (the term names in that figure have been slightly changed, but the names in the text above the figure are the current ones).

Please open a ticket on the ontology request SF tracker if any of this is still unclear. Thanks!

Minutes

  • Huaiyu: There are two issues here. 1. The ontology issue to annotate a transmembrane protein. 2. Annotation should be to biology with prior information or to observations.
  • Marc & Pascale: comment on the membrane/transmembrane issue: agree with Huaiyu, you should take into account what is known about a protein. If the protein has TM domains, it's totally OK to annotate GO:0016021 'integral component of membrane'. One needs to take all the biological knowledge into account. Annotating "GO:0009897 external side of plasma membrane" is the CC equivalent of annotating "apoptotic DNA fragmentation" for testing apoptosis; it's a read out. The annotator needs to do the inference to decide which is the best term to use for the annotation.
  • Paul & Karen: There are definitely some improvements to the ontology that should be made. Paul suggested that a term that includes the "fully spanning plasma membrane" information that Huaiyu wants to have annotated more accurately could have parentage under "external side of plasma membrane" to show more clearly in the ontology that "external side of plasma membrane" includes a wide variety of things, from peripheral membrane proteins to fully spanning plasma membrane. It might also be appropriate to add to the definition of the term "external side of plasma membrane" to make it explicit that proteins anchored in the membrane can include proteins that fully span the membrane.
    - Note from after the meeting: David Osumi-Sutherland is already working on a reorganization of membrane terms.
  • Karen & Li: Annotation of experimental results:
    - The type of FACS analysis we discussed here is a read out for whether some part of the protein is accessible to antibodies from the external side of the cell. It says nothing whatsoever about whether that protein is peripheral, partially embedded in the membrane, or fully spanning the membrane. We think the FACS experiment should be annotated only for what it shows. It is inappropriate to roll information based on sequence analysis, e.g. presence of membrane spanning domains, into an annotation from this experiment with an experimental evidence code and say that it was experimentally demonstrated that the the protein is a transmembrane protein because it is a false representation of the source of the information.
    - When we know information from other sources, we should annotate that information based on its actual source. If the source of the information that a protein is "fully spanning plasma membrane" is based on its sequence analysis, then we should indicate that. Then we can make an annotation to to the desired specific term using the GO IDs for the multiple GO terms used to synthesis this information into the most specific annotation.