Ontology meeting 2013-08-29
Attendees:
Minutes:
TG template for 'protein localization to'
Where are we with this?
E.g. see https://sourceforge.net/p/geneontology/ontology-requests/10302/
protein-DNA-complexes (bumped from last week)
HAROLD: Can we come up with guidelines for when a complex is a protein-DNA complex? Does the complex have to be assembled on DNA and ONLY exist when bound to DNA?
Is a complex that preforms and then binds DNA considered a protein-DNA complex?
It relates to many of Birgits new complex terms. E.g. DNA bending complex ; GO:1990104
Questions/points that arose in last week's discussion:
- Do PRO define the complex based on activity, or do they defer to the generic GO complex?
- If we're defining complexes as being CAPABLE_OF an activity, then they don't need to be DNA-bound (if they're acting on DNA)
- Do we really want protein-DNA complexes where the DNA is a SUBSTRATE (E.g. DNA helicase complex)? We think not.
- In experiments, can you accurately tell if the proteins are DNA-bound, or is it just an in-vivo assay used to detect the complex?
- 'protein-DNA complex' isn't a child of 'protein complex'.
- One option is to obsolete 'protein-DNA-complex' and broaden the definition of protein complex so it can be a grouping parent.
- The most genuine protein-DNA complex we can think of is the NUCLEOSOME.
Equivalent classes for Acid/Base transport and transport activity
During the merge of the x-transport the following inferred equivalent classes came up:
GO:0008519 'ammonium transmembrane transporter activity' GO:0051739 'ammonia transmembrane transporter activity'
GO:0015708 'silicate transport' GO:0051207 'silicic acid transport'
Both pairs are correctly defined with the appropriate ChEBI classes. Due to our bio-chebi adapter, we infer them to equivalent. Tanya mentioned that some transporters might be specific to certain forms so it might not be possible to merge them