Ontology meeting 2013-08-29: Difference between revisions

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From InTact. See: [https://sourceforge.net/p/geneontology/ontology-requests/10283/]
From InTact. See: [https://sourceforge.net/p/geneontology/ontology-requests/10283/]
===happens_during===
We talked about using this relation between phases and regular processes, but it seems it's already being used in c16 between pairs of regular processes. Are phases types of processes? Can with finalise the definition of happens_during?


===Equivalent classes for Acid/Base transport and transport activity===
===Equivalent classes for Acid/Base transport and transport activity===

Revision as of 15:39, 27 August 2013

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]

happens_during

We talked about using this relation between phases and regular processes, but it seems it's already being used in c16 between pairs of regular processes. Are phases types of processes? Can with finalise the definition of happens_during?

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