Manager Call 2016-12-07
Agenda: David Hill
Minutes: Paola Roncaglia
Present: Paola, David, Kimberly, Suzi, Moni, Judy, Paul T, Huaiyu, Chris
Regrets: Melanie, Pascale
ToDo: Send Paul contact info for Pathway Tools to be added to registry at Elixir (Melanie did this? MC: yes, done :)).
- Note that we also do mention other tools on our FAQ page for performing enrichment analyses for species not included in the drop-down list on the website
- Proposal (Paola): general recommendation for endorsing software for use of GOC resources should be that at least one of the members of GOC has used it. - ToDo: Make the FAQ (http://geneontology.org/faq/how-can-i-do-term-enrichment-analysis-species-not-present-list-amigo) match what’s on the Enrichment Analysis Help Page at http://geneontology.org/page/go-enrichment-analysis
Moni will take care of the action item above, but she may need to follow up with the group about some of the details.
(From last week's Ontology meeting)PI discussion of next months' EBI-GO work plan
End of subcontract with EBI of February 2017 - influences work of EBI-GO (DOS, Paola, Melanie) team. Helen has proposed that EBI-GO will step off the GO rotas (GH, TG, Helpdesk) starting December 12th to allow wrap-up of existing tickets concomitantly with other tasks. David Hill (as Ontology Lead ) and GO PIs will discuss further with Helen.
Others funded by GOC are interested in training and joining Ontology Dev team - training being planned.
Note that TAIR's subcontract also ends at the end of Feb. 2017. TAIR/Phoenix plans to scale back involvement in day to day, non-plant related ontology work after March 1, 2017, stepping off the GH/TG rota, and scaling back GO Helpdesk participation to 2x/year.
J: We’re meeting with Helen tomorrow to review the options. Judy, Chris, Suzi, Paul, Helen and Melanie will attend; David can’t. We’ll see about keeping at least some of those people on the rota. See what the best use of the EBI people’s time is. P: D, what is your opinion? D: It would indeed be a huge help if EBIers could address the backlog of tickets in the time remaining before the end of the grant period, so the plan they propose is good for me. P: I’m behind whatever D decides on what the best use of the EBI people’s time is. J: But D can’t join the call tomorrow, so he will join the PIs at their go-tops call today to discuss (6pm UK time).
M: not enough people on the GO helpdesk rota; there are only 6 of us remaining. Think of modifying how the system works? Perhaps have a less involved helpdesk? Make the existing tickets browsable for the general public? Updating the documentation? Just a few ideas. S: how can we make this an action item? J: Find a person among us to devote for two months just to documentation? 50% time? K: have just one skilled person on GO help? that would include working on the documentation. S: if it’s just one person, it becomes un-reviewed documentation. May become too insulated and not fully aware of users’ needs and environment. Share the documentation task among the people we have remaining on the rota? J: maybe we do a rotation of 6 months? and the person would report on the managers call. K: letting more people see what type of things our users need; have a way for GO helpers to become more consistent and see things to completion. J: have one person on outreach/GO help for 6 months once the new cycle starts - or earlier if we can. S: Could the existing team work together to address the documentation issue together? before the grant cycle ends. K: divide doc depending on area of expertise, e.g. K (and maybe D) will work on annotation documentation.
AI: Moni will look into this. It will be a slow process between now and end of January. She will communicate with everyone involved as often as necessary. D and C will look into the ontology documentation.
2016 Year-End Progress Reports
- ToDo: create Google Doc per institution, and also a separate document where all efforts will be combined and summarized. - As we ask institutions to prepare their individual documents, ask them to follow a template. Suzi will prepare the templates and add them to this directory: https://drive.google.com/drive/u/1/folders/0B8kRPmmvPJU3SzNuZ0YzVVJEOWc
Some docs are already being modified on the page. Right now, there is a draft of annotation by Kimberly and DavidH and a single doc that has ontology development in it by Melanie and DavidH. Melanie will be adding the full EBI ontology parts to that doc.
- Recently, it seems like almost every time we make a commit something in one of the pipelines fails. What's going on?
C: there’s no grand relationship between things. I have set up new checks. Will look into this and work with MGI offline to resolve some of the related issues.
Food for thought
- What is the biggest challenge for ontology development?
- What is the biggest challenge for annotation?
- What tool is most urgently needed?
- Annotation-visualization tools and tools for batch requests (DavidH)
- Long term, a new breed of enrichment tools that utilize the OWL representation of annotations.(DavidH)
- How can we be consumers and users of GO ourselves? (eat our own dog food?)
- I have begun trying to cultivate relationships with researchers here to work with them as they use GO. As a result, I have recently been playing around with enrichment tools and other tools on the GO site.(DavidH)
- Suzi: suggestion to set up main and large-scope goals for the year. Addressing the questions in the agenda. Suzi requests that everyone thinks of these questions. -- DavidH and Kimbery have begun collecting things in Github Projects. The ontology group has begun using Github projects to track ontology conference calls. We have also set up a project for the first quarter of 2017 that includes all github tickets that are labeled as mini-projects as proposals for things to complete. - Paul suggests that these goals should be organized on the GOC Projects page at https://github.com/orgs/geneontology/projects
Broad discussion follows. Some thoughts: a proposal to clean up single-step processes; make this a project for new people coming in to ontology development; S: refactoring of molecular function. Maybe DOS should focus on that in his remaining time, but he also has many open GH tickets; use next managers call to go through LEGO curators issues and try to prioritise them; use a managers call to try out/review the GOC projects page.