Ontology meeting 2013-06-27

From GO Wiki
Jump to navigation Jump to search

Attendees:

Minutes:

EXISTS, TAGGED-INFERRED, NOT-ENTAILED

We need a strategy to deal with the growing list of these in the weekly assert report.

Suggestions so far: have the report tag new ones and old ones? It might be easier for us to go through and assert the ones we're sure we want to keep, and the ones we're still considering (recording the fact that we've done that somewhere) and ask Heiko to delete everything else?


BUMPED FROM LAST MEETING: Missing EC numbers in GO

It seems we don't have the resources to implement a pipeline for these. Shall we wait and see if the new GO Editor can take this on? Shall we discuss this at the next GOC meeting to see how much of a priority it should be?

In the meantime, we can add single terms when requested by curators, cross-referencing to Rhea or asking Rhea to add the reaction if missing.

But can we close the following SF tickets?

https://sourceforge.net/p/geneontology/ontology-requests/9319/ (Becky's - nearly done anyway)

https://sourceforge.net/p/geneontology/ontology-requests/9320/ (Jane's)

https://sourceforge.net/p/geneontology/ontology-requests/9321/ (Paola's)


We never really got to the bottom of handling multi-step reactions. If we create separate GO terms for the subreactions with HAS_PART relationships to the parents, it's tricky to name the sub-reactions. There's no place at the moment where we can take these names. So, do we want to continue just to add one GO term for the overall reaction, stating in the definition that the reaction is multi-step?


BUMPED FROM LAST MEETING: Follow-up: template for assembly/disassembly of CC terms

Chris/Heiko, where are we with this?


BUMPED FROM LAST MEETING: Organelle vs. macromolecular complex

Stemming from some observations on inferred links in the assembly node, e.g.:

(Added inferred link) GO:0000921 'septin ring assembly' GO:0070925 'organelle assembly'

GO:0000921 'septin ring assembly' also has the is_a parent 'cellular protein complex assembly'. This was added back in 2008 (http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0000921#term=history). However, 'septin ring' only has 'organelle' as ancestor, not 'protein complex'. Should we make 'macromolecular complex' and 'organelle' disjoint?

The proposal would be to have

organelle DisjointWith mm complex


BUMPED FROM LAST MEETING: 'Encoded' vs. 'non-encoded' molecules in GO

Stemming from this SF request from Peter: https://sourceforge.net/p/geneontology/ontology-requests/10200/

At the time of writing, I'm waiting for Peter to suggest defs. and placement.


BUMPED FROM LAST MEETING: Muscle Fiber vs Muscle cell

[1]

Also see email thread from Chris (subject:muscle fibers in a tangle)

Muscle Issues

  • We need to go through each fiber term and check whether we mean the contractile fiber (CC) or the muscle cell (CL).
  • Should we use the CL naming as default?
  • GO isn't consistent in CC and BP about naming.


BUMPED FROM LAST MEETING: Project Management in JIRA

As we likely won't have time to go through this, and we won't have an Editors call next week due to EBI GO Editors interviews, may I suggest that we all look at our tickets and schedule progress on them if necessary.


MEMBRANE SIDES VS LEAFLETS

SF item from Alan Bridge: https://sourceforge.net/p/geneontology/ontology-requests/10223/

Is a membrane side equivalent to a membrane leaflet (one of the lipid layers)? If so, can all 'internal/external side of membrane' terms be changed to 'internal/external leaflet of membrane'?

See:

  • leaflet of membrane bilayer ; GO:0097478
  • external side of plasma membrane ; GO:0009897
  • internal side of plasma membrane ; GO:0009898
  • GO:0031232 extrinsic to external side of plasma membrane
  • GO:0031233 intrinsic to external side of plasma membrane
  • GO:0031234 extrinsic to internal side of plasma membrane
  • GO:0031235 intrinsic to internal side of plasma membrane
  • GO:0031237 intrinsic to external side of plasma membrane, in periplasmic space
  • GO:0031362 anchored to external side of plasma membrane
  • GO:0071575 integral to external side of plasma membrane


TG template for 'cell differentiation'

Are we ready for this?

See e.g. http://sourceforge.net/p/geneontology/ontology-requests/9698/


TG template for 'anatomical structure development'

See e.g. http://sourceforge.net/p/geneontology/ontology-requests/9697/

We're probably not ready for this yet, but we may want to schedule necessary work - or push to a later date?


STRUCTURAL MOLECULE ACTIVITY

Is there a long-term plan for where we can't use annotation extension? E.g. for mappings. Looking for a term to map to KW: viral matrix protein, which is a structural constituent of virion.