4 November 2014 PAINT Conference Call

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.