Ontology meeting 2013-03-7

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MINUTES: David

ATTENDEES: David, Jane, HJD, Tanya, Heiko, Chris

ChEBI paper?

Submitted 3/1/13.

Monthly update: Project Management in JIRA

Not today. But should we request a bug fix in OBO-EDIT for merged cross-products?

Cell cycle arrest

obsolete or merge? Here are the terms w/ 'cell cycle arrest' in name or synonym: I suspect that they will be merged but we are going to check with the experts. We need to check the OBO-EDIT behavior for merges before we do this. 

GO:0007050	cell cycle arrest
GO:0072694	cell cycle arrest in response to caffeine
GO:0036226	cell cycle arrest in response to glucose starvation
GO:0030996	cell cycle arrest in response to nitrogen starvation
GO:0000751	cell cycle arrest in response to pheromone
GO:0021883	cell cycle arrest of committed forebrain neuronal progenitor cell
GO:0000077	DNA damage checkpoint
GO:0006977	DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
GO:0071849	G1 cell cycle arrest in response to nitrogen starvation
GO:0071850	mitotic cell cycle arrest
GO:0071851	mitotic G1 cell cycle arrest in response to nitrogen starvation
GO:0036227	mitotic G2 cell cycle arrest in response to glucose starvation
GO:0071157	negative regulation of cell cycle arrest
GO:0010503	negative regulation of cell cycle arrest in response to nitrogen starvation
GO:2000002	negative regulation of DNA damage checkpoint
GO:0071158	positive regulation of cell cycle arrest
GO:0010505	positive regulation of cell cycle arrest in response to nitrogen starvation
GO:2000003	positive regulation of DNA damage checkpoint
GO:0071156	regulation of cell cycle arrest
GO:0010504	regulation of cell cycle arrest in response to nitrogen starvation
GO:2000001	regulation of DNA damage checkpoint
GO:0039592	suppression by virus of G2/M transition of host mitotic cell cycle
GO:0046792	suppression by virus of host cell cycle arrest

Automatic inferences

These will now go live because the inference errors should have been fixed.

Definition of 'cellular' in GO terms

'Cellular' as we use it in GO is supposed to be an indication of granularity; 'cellular' terms are meant to represent processes occurring at the level of a cell, as opposed to a tissue or whole organism. But the ontology is not always consistent in this regard (see this SF item: https://sourceforge.net/tracker/?func=detail&aid=3459403&group_id=36855&atid=440764). We need to come up with a definition for cellular - and use it consistently.

This is an interesting issue. We have talked about this before and it is difficult. We want something like cell-cell signaling to be a cellular process. The underlying problem is the ontology is inconsistent. Could we add a has_quality statement to these. The counterpart to all of these would be multicellular. Many of the cellular terms are under 'cellular response'. What we would really like is to have all the xps in one file. Then we could see missing logical definitions easily. Maybe we need to look at Mereoting the logical definitions in.


Interactions with CL

See http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Interactions_with_CL

We really haven't done much with this. We do not need to attend every meeting, but we should be aware of what is going on.

Follow-up: Protein complexes

See AI here: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Protein_complexes

(18/02/2013) Chris writes:

We have 1469 descendants of protein complex

We have a capable_of definition for 315 of these in x-complex.obo (ready to be moved into gene_ontology_xp_write, then soon the main GO)

The remaining 1154 don't have obvious capable_of definitions from text parsing using MF and BP. Scanning the list it seems to be that many of these have to be defined compositionally. So much for our purism...

HJD will peruse the list.

Follow-up: Protein/glycoprotein/lipoprotein terms in ChEBI

Harold and Judy to report (see background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-02-7#Protein.2Fglycoprotein.2Flipoprotein_terms_in_ChEBI)

All protein terms will live in PRO. Should we change our logical defs to use PRO protein?

SF upgrade

What do we think?

Advantages:

  • mark-up for threads, figures can be embedded etc.
  • Actively maintained (SF not fixing bugs in current tracker)
  • Better handling of attachments

Disadvantages:

  • Email configuration options annoying
  • Long threads go over multiple pages
  • Searching remains rubbish

Jane will continue to investigate. Had a look at the Pombe site. Chris will set up a sacrificial tracker.

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