Managers 13Sept06

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Present: Michael Ashburner, Judy Blake, Mike Cherry, Rex Chisholm, Jennifer Clark, Midori Harris, David Hill, Eurie Hong, Suzi Lewis, Chris Mungall

Minutes: Eurie

Scientific Advisory Board Meeting Debriefing

We discussed our impressions of take home messages from the SAB meeting. If any of the managers would like a copy of the pink sheets, they can get a hard copy.

Metrics

One of the major messages conveyed by the SAB was the need for metrics. We have developed metrics covering the breadth and depth of the Reference Genome effort and the SAB encouraged defining metrics for ontology development as well as define progress and activities in terms of dollar amounts. Judy mentioned that Peter Good has indiciated that NIH and NHGRI are moving towards measurable contracts. Although some types of financially based metrics may be too extreme, Suzi pointed out that we do need to consider the money aspect.

For ontologies

David mentioned that he has been thinking about how to define metrics for the ontologies. It can be difficult and sometimes not appropriate to define the quality of the ontology using numbers but there are some things you can measure in the ontologies:

  • number of terms
  • number of relationships
  • average relationship per term
  • avaerage depth of each tree

Chris already runs a script nightly that measures these statistics on OBO files! Right after the call, he sent out these two URLs: Main GO/OBO stats page and Page of statistics

High numbers don't necessarily mean anything. You could clean up a graph and reduce the numbers but it's still an improvement to the ontologies. These numbers can be used to describe a major change.

There Also need to document the process of decision making.

ACTION ITEM: David and Midori will have a proposal for documentation process and identifying metrics for the January meeting

Other areas

Other suggestions for metrics were keeping track of the number of publications that use GO and keep track of number of public databases that integrate GO terms. All this information could be displayed on a web page on our site. We may need to develop a structure for monthly reports in order to track such information consistently.

Also, we'll need to look into software for tracking bug fixes and feature adding.

ACTION ITEM: Suzi will propose across the board metrics for the group.

Expansion of AmiGO

The advisors did like the idea of expanding AmiGO to be a hub. Chris, Jane, and Eurie have created a smaller group of people consisting of members of the AmiGO working group, the software group, and the production group to shepherd these changes.

Judy mentioned that AgBase has a nice simple entry and basic search. Users can pick any subset of organisms or all organisms to do their query. And suggested the idea of just merging the AmiGO search page with the main GO home page. This is an idea that Jane had proposed as well.

Another considerations for AmimGO is to highlight the work done by the Reference Genome group and displaying the orthology clusters.

Biological Process is_a complete subgroup

David presented an update of the work done by the is_a complete subgroup. Jane, Jen, Tanya, and David stepped through the ontology from the top down. Tanya documented decisions along the way for documentation and future consistency. The following major

  • physiological process was merged into biological process
  • distinctions were made between multicellular organism processes and cellular processes in order to make clear distinctions between unicellular and multicellular organisms
  • there are branched for development and developmental processes

Work still to do:

  • locomotion and cell motility
  • localization
  • metabolism
  • CNS

Plan for moving forward:

  • CNS is_a complete will be reviewed by those who did the work
  • the rest of the graphs will be divided among the is_a complete subgroup to finish up
  • graphs will be sent out to the GOC for approval
  • David is going to Hinxton in 3 weeks and will finish up work then

Comments from the SAB made it clear that changes shouldn't be held back until they are complete. Changes to sections of the graph will be released as they are completed. This allows specific stages to be released and other stages (such as regulation) to be tackled as a whole at a later time. The graph currently is avaialable on the scratch directory and is called IsaComplete.obo. The changes to the file are listed in two files called isa[date].

It was really useful for everyone to be in one location and work on the project. John Day-Richter had looked into software that facilitates remote meetings it cost $350/year.

ACTION ITEM: Jen will get the software in place.

Project Management Software

Suzi pointed out that Peter Good indicated that it is not good enough to have milestones, we also need to show that progress is being made towards those milestones on a month-to-month basis. Software like Microsoft Project may just be too much for our needs. We will need to find something that is not labor intensive to learn and also a program that can be shared so not one person has responsibility of updating progress.

ACTION ITEM: Suzi will investigate project management software and propose options to the group.

Users Meeting Debriefing

This was briefly discussed. It was really surprising that over half of the attendees were members of the GOC. Advertising for this meeting was done through similar channels as the previous Users meeting in Norway.

We may need to rethink the users meeting concept and start from scratch. There was some discussion about whether users include future potential annotators. But all this was tabled for the January meeting.

ACTION ITEM: User Advocacy group come up with a proposal for users meetings in January.

Budget

Judy mentioned rollover is being approved - waiting for final paperwork.

Action Items Summary

  • David and Midori will have a proposal for documentation process and identifying metrics for the January meeting
  • Suzi will propose across the board metrics for the group.
  • Jen will get the software to facilitate remote meetings in place.
  • Suzi will investigate project management software and propose options to the group.
  • User Advocacy group come up with a proposal for users meetings in January.

Next Call

Wednesday, September 27, 2006 at 8 AM PDT, 10 AM CDT, 11 AM EDT, 4 PM BST Agenda: Eurie Minutes: Chris

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