Ontology meeting 2015-07-16
Attendees: Paola, Chris, Harold, Heiko, Tanya, Melanie, Paul T
Minutes: Paola
Future calls
Please note that Paola will be on leave for the next two weeks. Could someone else please make a note to send round agendas, meeting details and reminders for the calls of July 23 and 30? (There are already a couple of items in next week's agenda.) Thanks!
AI: David OS was volunteered. Paola emailed him and added note to internal calendar.
How to handle regulation of processes where we have decided not to represent the primary process
This stems from several pending TG requests that would like to have terms for secretion of specific proteins. The ultimate goal of these requests is to be able to represent the regulation of these secretory processes. At the Barcelona meeting we decided that we should remove the primary processes from GO, but then how will we handle the regulatory processes?
https://sourceforge.net/p/geneontology/ontology-requests/10600/
No real solution. Do we want to have a regulation of levels or are these just phenotypes?
Paul T thinks that secretion and regulation of secretion would not be the right annotations. He argues that there’s a phenotype of observing something outside of a cell, this is not a mechanism. He noted in a previous email: “I looked at one of Stan’s examples (http://www.ncbi.nlm.nih.gov/pubmed/?term=8679543), and I think regulation of secretion would be wrong. They don’t measure the secretion process, or indeed anything downstream of receptor activation. I’d suggest that they are using the word “secretion” in figure 2 colloquially to mean the amount of extracellular protein, but not to mean the biological process of secretion. The last sentence in the paper summarizes their findings very nicely: we have shown for the first time that a rat model NK cell, RNK-16, coexpresses the EP3 and EP4 subtypes of PGE2 Rs and that PGE2 activates MMP-1 and MMP-3 of RNK-16 cells through an EP4 R-dependent mechanism, which also mediates the chemokinetic effect of PGE2 on transmigration of RNK-16 cells through a model vascular basement membrane. In this case, rather than regulation of secretion, I’d consider an annotation to “regulation of protease activity” with specific reference to MMP1, MMP3. Or a LEGO model! :-)”
Is the use of ‘secretion’ ever legitimate then? Don’t know. Great example to bring to annotation group. Let’s discuss there. Ask: will there be legitimate examples? Or is ‘secretion’ always used as a colloquialism to represent something else? What should we do with these terms? Any terms we could suggest instead?
[Harold] There is also the issue that even if the annotation would be ok, the specificity should be represented in column 16, not a protein-specific term.
AI: Paola will email David H and suggest to present at next annotation call. Done. In the meantime, no approval of new terms with X secretion or regulation of X secretion terms via TermGenie or SF.
Melanie: are there ways to know about previous discussions in similar cases? Black lists, procedures? Chris: there is some annotation guidance on QuickGO. It percolates to Protein2GO. It should live in version control so it can be propagated to the ontology files.
AI: resume discussion with Tony. Chris emailed him + us.
AI: Tanya will coordinate with Heiko to show the same type of information on TG.
Jira tickets - postponed
Time for our periodic review of Jira tickets, especially unassigned ones. Please go through JIRA issues in advance of meeting. We will aim to devote about 20' of the call to discuss Jira tickets.
Follow-up: no more merges
Where are we with the action items from this: http://wiki.geneontology.org/index.php/Ontology_meeting_2015-07-02
AI: Heiko will check on the AmiGO side. We will come back to this in two weeks.
Implement MF patterns using directly regulation relations? - postponed
Chris has added relations such as 'direcly activates' and 'directly inhibits' to RO. These have lots of potentially useful applications, for example in definining enzyme activators and inhibitors
https://sourceforge.net/p/geneontology/ontology-requests/11733/
Background and details of relations: An OWL Model of Biological Regulation
Are these ready to use for design patterns for MF, e.g.
ubiquitin ligase activator activity EquivalentTo: 'enzyme activator activity' that 'directly activates' some 'ubiquitin protein ligase activity'
(Note - Does sound a little odd. From its name, 'activates' feels like it should have a continuant as its range...)
Is the def tight enough?: 'directly activates': "p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q."
David H has been pushing for direct regulation to be reg of an MF or of some MF that is part of a process. This sounds like it could be broader, although maybe that hinges on what 'immediately upstream of' means. Also, in the activator/inhibitor branch, we have:
- enzyme activator activity: "Binds to and increases the activity of an enzyme."
- enzyme inhibitor activity: "Binds to and stops, prevents or reduces the activity of an enzyme."
etc
Rename GO:0031386 'protein tag'
This is a function term, but the label refers to a gene product/aminoacid sequence. See email thread 'Fwd: MF overhaul'.
This was discussed about 10 years ago (see https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1186763&group_id=36855). No solutions were proposed at the time. We’ll live with it. It’s a role rather than an activity.