Ontology meeting 2013-03-7
ATTENDEES: David, Jane, HJD, Tanya, Heiko, Chris
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
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
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
(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?
What do we think?
- mark-up for threads, figures can be embedded etc.
- Actively maintained (SF not fixing bugs in current tracker)
- Better handling of attachments
- 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.