Ontology meeting 2013-08-29

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Attendees:

Minutes:

Documentation/outreach

  • drupal update (Chris)
  • need to redirect people wanting pseudo rdf/xml to new owl
- Drupal transition imminent. Seth, Chris and Moni will be working on in. Documentation needs updating as part of the transition. 
- Action: everyone look at the webpages. Organise meeting to develop plan and divide up work.
- Rachael and Rama's spreadsheet: [1] need to add a column for whose responsibility

TG template for 'protein localization to'

Where are we with this?

E.g. see https://sourceforge.net/p/geneontology/ontology-requests/10302/

  • need to set up a JIRA item to track the various sub-tasks
Looks like the xps are already pretty complete, let's go ahead and make the template
AI:Heiko to make template

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.
AI: get rid of this grouping. This sort of query can be done in other ways.

How do annotations to proteins that are part of a complex propagate?

For example, a protein complex may be located in the membrane but not all it's members actually contact the membrane. Is it right to make that complex part_of membrane in the ontology? Stemming from this ticket: https://sourceforge.net/p/geneontology/ontology-requests/10283/

We'll use has_part e.g maltose transport complex has_part integral to membrane. This sounds a bit odd but logically it works. Eventually we'll move to using GPAD relations between protein and GO term but this solution will work for now.

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?

  • punt til DavidOS starts?

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'

"In this review we use the term ‘ammonia’ to refer to the combination of NH3 and NH4+. 
When referring to a specific molecular form, we will specifically identify either ‘NH3’ or 
‘NH4+’.(snip) Ammonia exists in two molecular forms, NH3 and NH4+. Renal ammonia transport 
has been thought classically to involve passive NH3 diffusion and NH4+ ‘trapping’. However, 
both NH3 and NH4+ have limited permeability across plasma membranes and are transported by specific mechanisms."

Weiner & Verlander

GO:0015708 'silicate transport' GO:0051207 'silicic acid transport'

"The term ‘‘silicon’’ not only refers to the element, but is used as a generic term when the 
specific form of a silicon compound is unknown [17]. The predominant form of silicon in aqueous 
solution at low concentrations is silicic acid, Si(OH)4. This is a weak acid with a pKa of 9.8 
for the formation of SiO(OH)3-."

Hildebrand.

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

  • and we have to rethink our entire strategy for conjugate bases....


Assert-Report

Did anyone check the assert report this week?

http://build.berkeleybop.org/view/GO/job/build-go-assert-inferences/43/artifact/assert-report.txt

There are 203 added axioms and 84 removed axioms.