Ontology meeting 2016-10-27

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Attendees: Paola, Harold, Tanya, Moni, Melanie, Jim, Chris

Minutes: Paola

Regrets: David H

GoToMeeting invite: https://global.gotomeeting.com/join/859015101

Skip next week's call?

Some of us will be traveling to the GOC meeting or on leave.

All agree to cancel.

Items for discussion at GOC LA meeting

A reminder to add any items we'd like to discuss (or be discussed if we're not present in person) here: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda

Melanie notes: "Looking at the agenda right now, it seems a bit annotation heavy, with not many topics about editing. Do you know if this will come up in the 'Overview/Plan for upcoming 5 years' or under 'Informatics and Infrastructure 5 year plan'?

Specifically, it would be useful to:

- summarize GO development over the last year in terms of GH tickets, projects, papers...

- discuss how the decrease in the numbers of GO editors will be handled, both for every day editing activities and community projects"

AI: add to the agenda for the GOC meeting (link is above).
AI: ask David H if he'd be willing to present.
AI: Melanie will prepare stats for GitHub work.
AI: Harold will prepare a slide about his plant enzyme terms, and one about ec2go mappings.
AI: Tanya will get numbers on how many helpdesk tickets the editors took care of and similar. Timespan: last 12 months. Moni will send Tanya the URL for slideshare. (Done.  Slides provided back to Paola/DavidH)
AI: all editors involved in specific projects should prepare 1 slide per project, intended as short updates.

FYI: proposal on modified protein terms

Paola did some edits to the Google doc draft and passed it on to David H, who will look at it next week and prepare some slides for the GOC meeting. So, no work needed now. Link to the doc: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit

For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#Follow-up:_Modified_proteins

Consult on new term request (in TG)

From Aleks:

 [Term]
 id: GO:1905603
 name: regulation of maintenance of blood-brain barrier
 namespace: biological_process
 def: "Any process that modulates the frequency, rate or extent of maintenance of blood-brain barrier." 
 [GO_REF:0000058,    GOC:als, GOC:TermGenie, PMID:22524708]
 synonym: "regulation of maintenance of BBB" EXACT [GOC:TermGenie]
 intersection_of: GO:0065007 ! biological regulation
 intersection_of: regulates GO:0035633 ! maintenance of blood-brain barrier
 created_by: als
 creation_date: 2016-10-26T13:18:16Z

Also pos and neg version.

Tanya finds the new term weird based on the def of the core term 
(“Preserving the permeability barrier between the blood and the brain in a stable functional or structural state. The cells in the brain are packed tightly together preventing the passage of most molecules from the blood into the brain. Only lipid soluble molecules or those that are actively transported can pass through the blood-brain barrier.”).
Chris: Go with standard def. But what is the biology behind it? Where’s the boundary between maintenance of the BBB and its regulation? 
The former sounds like a regulation of permeability term, and we wouldn’t want reg of reg. The biology should be broken down better if that’s possible based on available knowledge. 
AI: tanya will open a ticket and ask Alice to comment. Done. [1]

ec2go mappings

(If not resolved yet) Stemming from Doug's comment on the recent change: "So it sounds like this is a planned and good loss of annotation. Is an ~80% loss of ec2go-derived annotations similar to what MGI sees? I would think this might be similar for any group using the ec2go file? I guess if the ec dbxrefs were to higher level terms then including annotation to all the children could account for the vast majority of derived annotations. On a related note, I still did see three "-" containing EC numbers in ec2go: EC:4.2.1.-xref: > GO:scalarane-17alpha-19-diol synthase activity GO:0102643. Is that something that needs cleaning?"

Harold replied "We had 17,000 and now we are down to 900-ish but it was a loss of nonsense: One protein would annotations, for example, to all children of an oxido-reductase"

AI: Harold will email the go-friends list with an announcement and a note that the change is deliberate. He’ll also reply to Doug on the stray three "-" containing EC numbers.

Follow-up: Github Ontology Tracker Update - incomplete

See https://github.com/geneontology/go-site/issues/240. Chris says "Looks like a GitHub issue" - anything we can do about it?

Chris is not convinced that it’s a GH issue. 
AI: Melanie will test it: do a change in GH, then run the script.

FYI: contacts for UniProt annotations

Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_contacts_for_UniProt_annotations

We realised that we could do with a single GH user - one for sending emails to help@uniprot.org, since they can triage UniProt annotations regardless of their provenance (SIB vs GOA). Melanie contacted Sylvain with this proposal. Sylvain will discuss with Chris and David H at the GOC meeting.

persona.org

I presume that this is already being looked into, (in fact, I have a vague memory that this was mentioned in passing some time ago) but I couldn't find a ticket for it, so just checking:

"Persona is no longer actively developed by Mozilla. Mozilla has committed to operational and security support of the persona.org services until November 30th, 2016. On November 30th, 2016, Mozilla will shut down the persona.org services. Persona.org and related domains will be taken offline. If you run a website that relies on Persona, you need to implement an alternative login solution for your users before this date. For more information, see this guide to migrating your site away from Persona: https://wiki.mozilla.org/Identity/Persona_Shutdown_Guidelines_for_Reliers"

Chris: you’ll see this reflected first in Noctua; will be able to log in via GH or Google; that’ll happen before the GOC mtg. For TG, we’ll probably use the same mechanism we use for Noctua. TG may have to be down for a week or so during that change.

GitHub projects

See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects

Plan is to look at https://github.com/geneontology/go-ontology/projects/1 and see how this works for us. Feel free to add there.

AI: From the next call onwards, let's try to use GH projects features, and have as many cards/tickets as we'd have for agenda items. If this doesn’t work for us, we’ll revert back to plain wiki. We can create a ticket for an agenda item that needs discussion captured, and create just a plain card (no linked ticket) for non-discussion items.