Manager Call 2016-02-03

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Agenda: Paola

Minutes: Kimberly

Agenda (partly carried over from previous call)

GOC Meetings for 2016

  • There's some confusion among curators about when the next site-wide consortium meeting is and what the aims of the post-ISB Geneva meeting are. Will there be a GOC-wide meeting later in 2016 other than the one in Geneva? If yes, any thoughts on when and where?
  • The schedule for the Geneva GOC meeting says that on Saturday April 16, "Meeting will run from 9am to 1pm." and "Optional break out groups may follow.". To book flights, we'd need to know if we should stay for the Sat afternoon or not please.
  • If you're going, please add your name to the list of attendees here:
  • Geneva agenda includes discussion of protein complex annotation. Any other agenda items yet?

Annotation Files Available for Download

  • Please see GO-Help ticket:
  • Where are annotation files available for download and if/how do these files differ?
  • Preliminary discussion on last managers call resulted in a number of suggestions. We'd like to run these by the PIs to discuss if resources can be allocated and to prioritize. Here's a summary of those suggestions:

1) Add documentation about annotation files available for download, both as a mini-tutorial well visible from the front website page, and as FAQ(s).

(Related: several users commented via the GO survey that the carousel on the front page is too big and not very useful => we could make it smaller at least, then the top articles would be a lot more visible.)

For example, we have an FAQ about finding annotations in QuickGO that can’t be found in AmiGO, but there is no FAQ on using AmiGO.

Note that the ‘Help’ link on AmiGO points to the wiki, we should at least move that documentation to the website… (opened ticket here)

Related: users who access GO information directly via AmiGO have no direct link to documentation or FAQs that are available on the website. That causes a loss of valuable information that we need to address. Huaiyu asks - who’s responsible for AmiGO documentation? (Update: there isn't a designated person, see this ticket)

2) AmiGO allows a maximum download of 10,000 annotations. We may want to speak to Seth to adjust that limit, be able to increase it manually like you can do in QuickGO.

3) On the GO website, under downloads, we need to help users get to AmiGO too.

4) It might be worthwhile to do more naive user testing for AmiGO.

  • Full minutes of last call's discussion are here

Review of Trello board

GO database website access numbers

  • Val notes: "Why are the GO database website access numbers reported so low? PomBase is now averaging 13-15,000 UNIQUE users per month (ex-robots). Unless the EBI are getting the stats wrong. So GO can't possibly be only 35,000 unique per month can it? Does that include AmiGO or is it only the GO website."

GO tools registry

1) remove any MOD-specific tool (i.e. MGI GO Browser, SGD Gene Ontology Slim Mapper, YeastMine)

2) Also remove OBO-Edit from the list, now deprecated for external users

3) Add GOrilla to the list at the bottom of the page here

Any opposition, please speak up now.

Documentation Updates

  • As part of the 'SPOT Documentation Week at EBI' Melanie added a number GitHub issues for updating documentation on the GO site. We will be working on addressing those.

The list of issues resulting from their doc week can be seen here.


  • On call: Chris, Judy, Kimberly, Moni, Paola, Pascale, Paul T., Suzi
  • Judy
    • April 2015 Goals - Progress has been good so far
    • PIs will discuss priorities for 2016 on today's PI call; finishing out this current grant cycle
    • Grant submitted last week
      • Used Skype chat window for continuous communication during writing
      • Will be reviewed in June, council will meet in October
  • Paul T.
    • Huaiyu will send around PDF version of grant science sections

GO Meeting April 2016

  • Planning will come together in the coming weeks
  • See who's coming and adjust schedule accordingly
  • Need ideas for Saturday afternoon break-out groups, e.g. Noctua training
  • Will use JAX's system for registration, but still need to settle on cost - roughly $100
  • Costs include room rental fees, one dinner, Saturday lunch
  • Would be good to know if there will also be a wider GOC meeting later in 2016

Annotation Files Available for Download

  • Users get confused about GO annotations files vs GOA annotation files and what to download where
  • Need more documentation on using AmiGO for downloading annotations
  • Need to increase the number of annotations that can be downloaded
  • May also need some additional UI testing for AmiGO
  • AmiGO does need some additional resources
  • Need documentation about the different types of files and what is in them
  • Need to check with Melanie about the status of the GCRP files discussed previously
  • See Trello ticket on this issue - Reference proteomes should be the default in AmiGO

GO Database Website Access Question

  • Val's question - how are the access stats for GO obtained?
  • Do the numbers include the website AND AmiGO?
  • Chris, Mike, Seth will get back to her

GO Tools Registry

  • Elixir Tools Registry
  • Have a short list ready, link from the GO web site?
  • List includes tools for visualization, search, analysis so it is a mix
  • How inclusive should this list be?
    • Include MOD tools like the MINES?
    • Tag certain tools as GO-approved?
  • One approach - first list would not list MOD-specific tools, but could update the list to include currently maintained tools at the MODs and add them all at once
  • Another approach - given that we're only recommending a small set of tools, have more narrative text for specific GO-approved tools that also links out to the Elixir list for a broader survey
  • Need to synchronize this with what Paola's doing so that anyway coming in to Elixir will have good information about the GO-approved tools and also possibly link from Elixir to GO?