Manager Call 2019-08-21

Agenda

• Agenda: Seth
• Minutes: Pascale

GO users meeting Berkeley 2019

• TODO: Finalize decision on topics/speakers/target audience.

Preliminary agenda is here: https://docs.google.com/document/d/1YBCEeSl1MKPvtRNAMGBGcOZqdZl3wlbwWC1nuDnccqE/edit

• Next: start announcing

GO Meeting general

• Get your people to sign up
• Get your people to pay (used for badges, etc.--the true reg)
• There is only "Yes" and "No", there is no "Maybe"

Review of project process

Thinking about templates and project flow (Chris)

Aims GO meeting

There are 6 weeks left until the GO meeting. We should discuss the status of Priority 1 Tasks that we agreed on:

1. GO-CAM validation software [Jim, Ben, Eric, Laurent-Philippe] (which includes GO-CAM specifications [Kimberly, David, Pascale, Ben, Jim, Huaiyu, Chris, Paul]
2. Integrate line-by-line annotations into Noctua [Kimberly, David, Ben, Dustin] [depends on #1; can we integrate MF? ]
3. Release Noctua Form 2.0 + ART [Tremayne, Kimberly, Seth, David, (Jim), Laurent-Philippe]
4. Retire legacy infrastructure [Chris, Seth]
5. Implement stricter checks on end products for automatic halt of pipeline [Seth, Eric]
6. Quality Control: Create automated reports on pre-releases [Laurent-Philippe]
7. Quality control: Data release pipeline: add a freeze and QC step [Seth, Pascale] - DONE
8. Finalize GPAD/GPI 2.0 Specifications [Kimberly, Seth, Chris]
9. Ontology: Removal of ChEBI roles when they are not strict [Karen]
10. Ontology: Define guidelines for creating new complexes [Ben, David / Judy]

Priority 2 tasks:

1. Stabilize data release pipeline [Seth]
   Looking at more resources here
2. Stabilize release date [Seth] [What is this? What ticket? -Seth]
3. Quality Control: Rules [Pascale, Seth, Eric]
4. Allow GPAD/GPI 2.0 in pipeline [nobody assigned]
5. GPX support [Chris, Seth]
6. Improve Helpdesk [Suzi, Laurent-Phillippe]
7. Tools and APIs [Chris, Laurent-Phillippe]
8. Pathways2GO [David (+Paul), Ben]
9. AmiGO improvements [David, Seth]
10. AmiGO improvements: improve display of 'redundant' annotations [Kimberly ? ]
11. AmiGO: Ribbon display and Alliance slim [Kimberly, Laurent-Phillippe]
12. Ontology: Molecular function refactoring [Paul, Pascale]

Pipeline progress

• release process started

Project for improving mappings?

...[L]et's discuss whether we should initiate a project for improving the mappings: documentation, workflow processes, quality control, staying up to date.

We are of course doing a good job in specific instances, whether it is ones we bring in (interpro/reactom) or ones we maintain (e.g rhea), but this project would be about a broader approach.

Cross references on GO website/AmiGO page

• Follow up on https://github.com/geneontology/amigo/issues/578
• Seth was to create documentation describing how that page is generated; where is that ?

Collaborators Webpage

We need to decide who we put as collaborators and as contributing groups. There is some redundancy. https://github.com/geneontology/geneontology.github.io/issues/130

Annotation files from non-active groups

• GR is not actively maintaining annotations and there are *multiple* issues with their existing file
• GOC should probably take over this file, but there would be some work to do with cleaning it up
• If/when should we do this and where should the set of annotations worth keeping live?

GO stats

Status, remaining work and decision on computing or not the stats for previous releases original issue and recent issue

Notes on zenodo archives and solr 3.6.

GO API & GOlr: availability & comment

On August 17, several down time or freeze of both the GO API and GOlr: status.geneontology.org. Anything particular on that date ?

GO API logs indicate pics of 2000+ packets / mn (usually 100-500 packets / mn). Most queries seems to be slimmer/ribbon related.

Need for a IT/Cloud strategy

While not yet critical / urgent, it is important to have a IT/Cloud strategy for the project to ease the sharing of resources, virtual machines, protocols, loggings etc. LPA created a document for the USC AWS account in April, this could serve as a basis of discussion. Ticket example: https://github.com/geneontology/operations/issues/30

Minutes

GO users meeting Berkeley 2019

Chris - Discuss agenda

Review of project process

We need to have more communication. Product owners need to know what developers are doing. Software team needs to coordinate better - information sometimes comes late, when projects are too advanced, there are wasted efforts. -> To be discussed on tomorrow's software call

Annotation files from non-active groups

Kimberly to contact Pankaj. If they cannot update their file then we'll need to fix it, or ask GOA to maintain it.

GO stats

Status, remaining work and decision on computing or not the stats for previous releases original issue and recent issue -> To be discussed on tomorrow's software call

ACTION ITEMS

• Seth: Set up a wiki page for GO users meeting, and start announcing
• PIs/managers: Start on the GO meeting agenda
• Kimberly: talk to Pankaj to see whether they can clean up their file, and correct annotations

Present

Seth, Chris, David, Kimberly, Huaiyu, Laurent-Phillipe, Pascale, Paul