Manager Call 2017-12-06: Difference between revisions
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**Highest priorities: | **Highest priorities: | ||
***Public-facing web pages | ***Public-facing web pages | ||
***Noctua and GO-CAM | ***Noctua and GO-CAM (need to consolidate and remove links to older documentation) | ||
****Relations | ****Relations | ||
****User guide | ****User guide | ||
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****Annotation files | ****Annotation files | ||
****Ontology files | ****Ontology files | ||
**New documentation review by expert, new users | |||
= Minutes = | = Minutes = |
Latest revision as of 11:14, 13 December 2017
Agenda
GO helpdesk
The current solution is really not appropriate for most of our users. The bar is too high to submit any request. Can we re-evaluate the decision to have a simple form/email mechanism ? See discussion in https://github.com/geneontology/go-annotation/issues/1670
GH tickets reminder
https://github.com/geneontology/helpdesk/issues/78 From geneontology/go-annotation#1388
We all need a way to be reminded which tickets are assigned to us!
Can this be done in some sort of "git hub" management mode (i.e select all tickets and send a message saying "you are the assignee of this ticket, please check if it can be closed").... A monthly alert......I will never look otherwise.... I think this would get a lot of GitHub tickets "unstuck"
At least for the go-ontology and go-annotation repos that would be really nice.
Thanks, Pascale
One way to do this is to filter on the assigned by field in GH.
GH athon?
Should we have a workshop with the current ontology editors to specifically focus on cleaning up outstanding GH issues? Are there funds for this? If so, where and when would it be? I suspect we would need four days.
Guidelines for Annotation Display
- GO annotation fields required for correct display
- Rachael brought these guidelines to our attention
- Can these be tidied up and put on the website?
Obsolete terms in slims: need a SOP
See https://github.com/geneontology/go-ontology/issues/14677
GO at ISB, April 2018
- What presence will we have? Is anyone submitting an abstract?
- https://www.biocuration.org/biocuration-2018-call-for-abstracts/
Documentathon
- Best practices:
- Have a date last reviewed on every page
- Review web pages under Documentation, FAQ
- Agenda items:
- Annotation guidelines
- Axes of classification for annotation guidelines
- Term usage
- Experiments
- Evidence codes
- Annotation relations
- Need to be clear about the differences between relations used for GP-GO annotation, GO-CAM annotation, and the ontology
- https://github.com/geneontology/go-annotation/issues/1690
- https://github.com/geneontology/go-annotation/issues/1687
- GAF/GPAD
- GO-CAM
- Annotation extensions
- Annotation file pipelines
- https://github.com/geneontology/go-annotation/issues/1683
- https://github.com/geneontology/go-annotation/issues/1682
- https://github.com/geneontology/go-annotation/issues/1674
- Submission SOP
- Error checks and Jenkins jobs/reports
- Dealing with redundant annotations
- Axes of classification for annotation guidelines
- Noctua
- User guide
- Readthedocs
- Can we make better use of this?
- Nice example of formatting: http://firefox-puppeteer.readthedocs.io/en/master/index.html
- Using GO - extract whatever we can from the GO handbook
- File formats available
- Annotation basics
- Reference proteomes vs complete proteomes
- Annotation guidelines
- Goals/Deliverables
- Highest priorities:
- Public-facing web pages
- Noctua and GO-CAM (need to consolidate and remove links to older documentation)
- Relations
- User guide
- Evidence codes
- File pipelines
- Annotation files
- Ontology files
- New documentation review by expert, new users
- Highest priorities:
Minutes
- On call: Chris, David H., Kimberly, Paul T., Suzi
GO Helpdesk
- The move to github was based on resources
- If we want a better system, then we need more resources
- Tickets have been of a more technical nature, perhaps not surprisingly
AI: Chris, Kimberly, Seth can follow-up to see if a WB-like approach of combining an easy email and github would be feasible for GO
GH tickets reminder
- Easy to check tickets assigned to you
- AI:David will review how to do this on the next editors call
GH athon?
- Core ontology editors would get together and work through the backlog of tickets
- There are funds for this but it would be best to do this before the end of this grant year, i.e. by February 2018
- AI: Decide on dates and place
Guidelines for Annotation Display
- GO annotation fields required for correct display
- AI: Will review and discuss on an annotation call
Obsolete terms in slims: need a SOP
- Original guidelines were that obsolete terms would not be removed from slims unless the maintainer of the slim requested it
- AI: Slim metadata should track what version of the ontology the slim was based on
- Ideally, we don't want to keep obsolete terms in a slim
- We need to work with slim maintainers to keep the terms up-to-date
- https://github.com/geneontology/go-ontology/issues/14362 Documentation for metadata about slims (MIAAGS)
GO at ISB, April 2018
- Suzi will be there; talking about OBO
- Paul T. may be able to attend; will send an abstract
- More discussion on the PI call
Documentathon
- In Berkeley
- Start on Monday, 1/22, end on Friday, 1/26