Protein complexes
- NOTE: This is a work in progress. Also, we need to add examples - what works and what doesn't.
- How do we view protein complexes in GO. The complex should be stable. If not stable, it's just protein binding. I'm sure we had something written down for this - Birgit? Do GO and IntAct guidelines agree on this.
- GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, still make the def generic, and add 'For example, in human this complex contains...' as a def gloss or def comment. Species-specific complexes don't belong in GO, but rather in IntAct and/or PRO (or just IntAct?).
- Ideally, add capable_of functions link. If not possible, see if capable_of_part_of process links can be made. If none is applicable, we do host complexes based on their subunits only.
- Indicate cellular location as specifically as possible, unless parent already has one
- How to request protein complexes in GO based on the above (TG template, TG freeform)
- Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011: http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects
- What IntAct is doing:
We didn't draw up an official set of rules but in summary this is what we do (and it pretty much matches what Paola says below and the wiki she cites): A complex should be taxon agnostic but may be restricted to certain taxonomic groups, such as pro- vs eukaryotes. ... should contain subunits in the def ... should have a 'as precise as possible' part_of relationship to the CC (may have to create new terms here as well of course!) which can be a complex (in cases of subcomplexes) or a location ... have, if possible, capable_of and capable_of_part_of annotation extensions. ... should have is_a relationship to an appropriate child term of 'protein complex'. This could be a term based on it's composition or function but NOT based on the PB. If no appropriate term exists, we create one based on either of the two classes. There is now a TG template for creating complex-by-MF which make curators' life much easier :) If there is no appropriate CC or complex-by-MF parent the new complex will be a direct child of 'protein complex'.