Manager Call 2016-09-21

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USC Meeting

NAR paper

Review Trello board


Present: Moni, Kimberly, Paola, Melanie, Suzi, ChrisM, Huaiyu, Pascale, Judy, PaulT.

Minutes by MMT.


1) Trello Board and Github Projects:

  • Chris would like to move away from using Trello. Waffle was a good candidate - as an overlay to integrate GitHub. Now GitHub has issued GitHub-Projects. Will end up being more versatile. However it does not integrate multiple repos at the moment and GOC has a lot of them. Eventually they will, we assume.
    • Multiple ways to set up. Will prepare a demo for later. We could create a tracker for GO managers, as a GitHub projects, then add GO repos. Would like to test. No timeline yet.
  • Suzi: yes, definitely need to move from Trello towards GH. Too early to waffle will likely force us to transition later. Too late is not ideal. Is there a guess as to when GH is available?


  • it is available now. We tend to underuse GitHub labels, to favor tags. We also underuse Milestones. Currently Waffle provides what GH provides just with the ability to run all of the GH issues from different repos. Looks like Trello, but the cards are already tickets in the repository. This reduces the overwhelming feeling. Nice about waffle is that integrates data from across trackers. GH Projects will have that feature soon.
  • Each project can have its own distinct board in GH Projects. It may give us more specificity but it is spread out.
  • Should we experiment? Each ontology its own project?

Suzi: difficulty would be going across projects.


  • at the end of the day, the links are GH tickets, which can belong to any project.
  • GH makes it easy to keep track of different issues very easily.s
  • We could have a GO-managers tracker and each comment to an issue generates bi-directional links. (Kimberly +1).
  • PaulT: would we want to put a team to work on this?
    • Team: ChrisM, Kimberly, Moni. Will report with ideas next call / or two calls from now.

Judy: are we planning to merge together the annotation and ontology trackers?

Chris: GH builds bi-directional links between two tickets.

  • Let's ask Stanford to please create standing call for managers. For consistency, keep BlueJeans.


2) USC Meeting.


  • Need to send email out to ask people to please double-check table of attendees.
  • Book your hotel before 13-October.
  • PaulT will send a reminder.


  • ChrisM: Jim Balhof cannot come the whole time so would like to have a better idea regarding topics.
  • PaulT: for now, let’s send a call also for agenda items. Separate page for agenda:
  • Let’s create a table to include:
    • Topic,
    • preferred time (due to travel needs) in Notes Column,
    • estimated amount of time,
    • names of possible presenters.
  • Monday all day Noctua training.
  • Suzi arriving early - 2 Nov.
  • ChrisM: also let’s take another look at proposal, move things along to strategize the plan for the meeting.
  • Suzi: some time should also be set aside to go through what we promised as a proposal
  • Kimberly: when will we know about funding?
    • AGR received positive announcement on the topic.
    • GO is waiting on news. Judy: let’s kindly ask for an update on council report.


3) NAR Paper

  • Paul will be working on it this week, 22-Sep
    • Extensive outline has been put together.
    • Paul will start calling on people for content.
    • Would like for us to please prioritize sections, as well as to assign names to sections.
    • Planning to submit by 1-Oct.
  • Managers, please sign up for sections, add draft text with what you think is the highest priority. Please do so by Monday 26-Sept at the latest.
  • Also, here is an idea about a provocative thing to do with a publication: given that we rely on people publishing papers, everyone who writes a paper that ends up on the GO is in effect an author of the GO product. Think whether we could ‘cite’ all of them somehow. Make a big acknowledgements page with this paper - something provocative so we may direct the attention regarding where the GO comes from.
    • Suzi: nice idea.
    • moni: we could always enter all the acknowledgements into a web page and write a note about it on the NAR paper. Directing users towards a list of ‘who make the GO’.
    • Kimberly: how about “this people’s research have contributed knowledge to GO annotation”.
    • Melanie: how about the ‘contributors’ in OWL to let people include this information as well.
    • Chris: we could also do this with PMIDs. A list of authors who have contributed annotations.
    • Judy: and authors, # of journals, how many articles per journal.
    • Suzi: personal acknowledgement to some groups as well.
    • Paul: The idea is not to make them authors, but would be great to include in the citations, it could be in the acknowledgements list “all the authors” who contributed information in the GO resource, or the web page. Not sure the final way to do it, but would be good to viscerally communicate to users where the information ultimately comes from, and acknowledge the people who writes papers we find useful.
    • Kimberly: do we have any data on highly cited papers that have contributed data to GO?
    • Chris: how about “drive by” annotations of high-profile papers.
    • Paul: we also thought having link from link-out pages from PubMed to annotations done using that PubMed.
    • Chris: We have already done this and it is in AmiGO. Please see an example at
    • Paul: perhaps this could be coupled with a call for authors to review what resulted from annotating with the contents of their papers.