Ontology meeting 2013-08-29

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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.

locations of complexes

From InTact. See: [1]

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