Ontology meeting 2016-10-27: Difference between revisions

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


===Follow-up: contacts for UniProt annotations===
===FYI: contacts for UniProt annotations===


Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_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 our proposal, and we're waiting to hear from him.
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 OS at the GOC meeting.


===persona.org===
===persona.org===

Revision as of 11:14, 27 October 2016

Attendees:

Minutes: David OS?

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.

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"

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.


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"

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?

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 OS 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"

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.