Manager 18February2015
Agenda
- Future development of Protein2GO
- What are the plans?
Minutes
- On call: Chris, Huaiyu, Paola, Rama, Kimberly, Judy, David, Paul T., Pascale
- Pistoia Alliance
- Judy:
- want to work on ontology equivalencies; holding/held a webinar
- http://www.pistoiaalliance.org/
- Judy:
- CAF/CAT Discussion
- Kimberly, Rama:
- have some questions about how to move forward with development of Protein2GO
- how best to coordinate with UniProt, Tony
- there are both technical issues and annotation issues
- Chris:
- Rachael was our tracker, but she is no longer at UniProt and a GO manager.
- need a tracker that GO managers can all see
- need to develop annotation extension feedback
- also need a high level review of where things stand with Protein2GO migration on the whole
- Chris, Judy:
- in a holding pattern right now wrt Protein2GO migration
- Rama:
- more integrated workflow for some groups makes moving to a GO-specific curation tool more difficult
- David:
- one area for tool development: good idea to have pre-seeded annotation extension options
- e.g. transcription - input gene, output transcript or catalytic activity - input enzyme, output substrate
- Chris:
- would be good to add these use cases to Noctua tracker
- Summary and Action Items:
- holding pattern with Protein2GO migration, but there will be requirements still coming in for current users
- where to put these? what tracker to use?
- consult with Tony - can we use github and put code, requests there?
- CAF/CAT big picture
- review doc from initial requirements gathering
- get in touch with other groups about requirements to assess where things currently stand wrt workflow and migrating to a CAF/CAT
- Kimberly, Rama:
- Moving AmiGO to the cloud
- Rama, Chris:
- priority to move AmiGO to the cloud for better accessibility
- set up a meeting with Stuart and Berkeley
- Rama, Chris:
- Files - behind-the-scenes organization
- Rama, Chris:
- xrefs_abbs file
- old, stanza-type file still supported
- new source file lives in github; yaml format; handles more detailed metadata
- source file no longer in SVN repository (SVN holds derived production version)
- if people need to add a new namespace - can ask Seth and Chris for now
- in long run, github is actually easier for management (can edit via web interface)
- David:
- can we have a directory/table to tell users where editable files are located
- Chris:
- in the xrefs_abb header, there is information about where to edit the file
- David:
- which files, how they’re used, where they live - big picture diagram is helpful
- Chris:
- could give periodic updates on behind-the-scenes organization
- Rama:
- would be good to explain how things work - GAFs, Jenkins scripts, Mike’s scripts, GO slims
- have a consortium-wide call in March to talk about these things
- Rama, Chris:
- Priorities for Remainder of Grant Cycle
- Judy:
- PI meeting in Hinxton
- met with Alex and Claire, also Helen
- discussed format of next grant proposal
- Paul T:
- what do we feel we have to accomplish before next grant submission
- what does that mean for priorities and allocation of resources
- still need to work out specifics
- Judy:
- need to continue to put a lot of effort into the common annotation environment
- need to work on user experience, interface
- will probably have additional meetings to address these issues
- rearrange Trello boards accordingly
- Judy:
- PAINT curation
- Pascale:
- still problems using PAINT, accessing database
- can we have more frequent checks for potential connection errors
- Pascale: