AmiGO Hub: Group Meetings: Difference between revisions

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=next meeting=
=Next Hub Meeting: July 15th, 2008=
*Date: July 3, 2007
*Chair: Eurie


See [[AWG_meeting_chairs|meeting chair rota]] for next chair
[[AHWG-20080715|Agenda and Action Items]]


=Previous Meetings=
=Previous Meetings=


==June 26, 2007==
===[[AHWG-20080701|July 1, 2008]]===
Chair: Rama<br>
Present: Seth, Eurie, Amelia, Jane, Chris, Ben<br>
meeting mode: Phone call<br>


===[[AHWG-20080617|June 17, 2008]]===


*About meeting Chairs- No body in the group (other than Ben and Rama) was aware of the reverse order of Chairs for Hub and WG meetings. We decided we will keep it simple and the next person in the list will chair the next meeting (we won't differentiate Hub and WG meetings). We will put a Star next to the name who is going to chair the next meeting.
===[[AHWG-20080603|June 3, 2008]]===


Action Item for Ben- He will update the Wiki to reflect this.
===[[AHWG-20080520|May 20, 2008]]===


*Main agenda- We went through the 'big features' that Chris sent around last week.
===[[AHWG-20080506|May 06, 2008]]===


===[[AHWG-20080415|April 15, 2008]]===


On Jun 21, 2007, at 6:26 PM, Chris Mungall wrote:
===[[AHWG-20080401|April 01, 2008]]===


Here are some non-trivial new features I'd like to see added to AmiGO over the next year. These are kind of orthogonal to features like shopping carts, which are needed to. They often involve new types of data, or radically new displays
===[[AHWG-20080318|March 18, 2008]]===


*bi-axial grid type exploration of annotations (eg BP/CC, or BP/Taxon). See the emails I sent a month or so ago.
===[[AHWG-20080304|March 04, 2008]]===


===[[AHWG-20080115|January 15, 2008]]===


We will make this an optional view, not default. For people doing advanced queries. How easy would it be to implement? Chris thinks it shouldn't be hard. This view can be used to generate a slim.
==[[AHWG-2007|2007 Meeting minutes]]==
No time frame yet. Will be useful to have a demo for the WG.


We will make sure we take care of items from the last list before the next Consortium meeting (references, structured comments, reference genomes).
For references genomes, we need the orthologs in the DB. Then Seth/Amelia can take over. That is going to be discussed in the next software meeting.


*option to split a tangled DAG into separate is_a and part_of views (and other relations, like regulates). As in oboedit
[[Category:AmiGO Hub]]
(requires improvements to graph_path building)
 
 
Will be discussed over email.
 
*combined function-process views; pathway style?
(relies on links being established)
 
The biaxial grid will help to figure out these. We need some mapping to proceed on this.
 
*cross-product displays
(can test with current GO-CL cross products. May require API changes)
*advanced inter-ontology queries
(example: what kinds of processes potentially gives rise to nurse cells? this can be answered if we know that cystoblast division results_in_division_of cystoblast, and nurse cell develops_from cystoblast)
(depends on xps)
 
Will require loading the cell ontology into the DB. Has to be discussed in the larger meeting with some mockups. We don't want to answer user questions about other ontologies. So, we won't show/allow to browse the other ontologies, but we can integrate it.
 
*orthology and protein family based views
 
In addition to ref.genomes. chris will look at the grant proposal to see what we proposed for ortholog displays.
 
*Facebook style API to allow people to develop their own applications that plug into amigo, can be shared with friends... particularly for doing specific kinds of analyses. In addition, I'd like to use AmiGO for other kinds of OBO annotation - this isn't something GO is funded to support. But it would be nice to reuse code as much as possible.
 
Amigo infrastructure will allow that.
 
Put these on the tracker? Chris will do with more descriptions.
 
Eurie- these are very sophisticated ideas. We should prep the WG by just going through these ideas. Many of them are not aware of the changes going on with the ontology file and they don't know how everything comes together. If it is easy to do a mock up then we should do it, not wait for the mock ups to discuss.
 
Jane- wait for the current release and then bring it up with WG.
 
 
*Amelia's item-
 
It's basically that I think we need more users in the AmiGO working group, and that we confine the AWG chats to talking about issues that directly affect the users and focus on issues rather than on admin issues.
Comments from Plant community? We want to develop AmiGO for GO, not for Plant. We can still get other input.
Keep these meetings very focussed is important. Also we need to keep the discussions connected.
 
Action Item- Eurie/Jane will bring up the issue of inviting non consortium members to the WG discussion in the next Managers meeting.
 
==June 12, 2007==
Chair: Seth, Absent: Eurie
===Agenda===
*Progress towards June release
*Integration of new functionality
*What formats should be added
*Test protocols for WG
*Amelia's prototypes
===Minutes===
*Progress ok, should have something testable this week
*Decided that since the flat file was deprecated, it should be replaced with OBO format
*Discussed how the WG should test for this release
*Discussed what the new front page should look like
*Discussed naming the new functionality
*Varsha from the HGNC to join the AWG
===Action Items===
*Inform other groups of our conference call time
*Replace flat file with OBO file
*Get prototypes to WG
*Solicit names for "termfinder" and "map2slim" from WG
*Front page mockups, ask how WG likes them
*Start automated testing
 
==May 29, 2007==
===Agenda===
Chair: Jane
 
===Minutes===
 
Aim of the meeting was to look into AmiGO 1.0 release status in regard to the new features voted for by the AWG:
 
===List as voted on by the AWG===
'''1.  download options'''
*basic option is in there (tab-delimited)
*long term needs more interface needs work to display extra download options
 
Discussion about the AWG exercise, to get people talking about features they do and don't like about different commonly used web interfaces. Eurie voiced concerns that the AWG doesn't know why it's performing these exercises, hence they lose interest.
'''2.  sorted search results'''
*implemented (has a bug)
'''3.  searching with mis-spelled terms'''
*no progress on this item (what do AWG think?)
'''4.  improved gene product search'''
*implemented
'''5.  a tie between:'''
'''5a. organize and allow filtering species by kingdom'''
*out of time - need data in database
'''5b. advanced Search radio button'''
*implemented (near as)
 
====Long-standing wish list items====
'''1.  Term Finder'''
*Had to redesign to fit into AmiGO 1.0, almost there
 
Discussion on session data. Will look at further.
 
'''2.  Term Mapper'''
*As Term Finder
 
'''3.  IEA'''
*Wait until AmiGO 2.0
 
 
Ben to send log files to Amelia.
 
====Additional functionalities====
1.  New short URL
*already there, and ready. Need to give people more warning
**COMMENT: more warning for what, testing?  not users - they should never care about URL syntax as long as they are backwards compatible.
 
 
Timescale: testing during June, July release?
'''Soft deadline for first beta - last week of June.'''
 
==May 1, 2007==
===Agenda===
Chair: Ben
 
*Can we discuss the role of the meeting_chair tomorrow?  Most of us assume that people remember these meetings and call/logon etc without  reminders (Rama)
 
===Minutes===
 
* we will set up an email reminder (Friday morning Pacific US time).  This will go to the HUB group with a reminder to send agenda items.  There will be a link to this wiki page so that we can determine who the chairperson is.  This is better than the chart (AWG meeting chairs) because we often skip a meeting.  Ben will set up the cron job that sends the email.
* meeting chair should add minutes on this page, and update next meeting chair.
* If there are no agenda items, we can assume that there is no meeting
* similar policy will be adopted for full AWG.  You might get stuck with back-to-back chairing due to missed meetings.  Suck it up.
* we would like to set up webx "working group" meetings to review other sites' methods and interfaces for the types of queries we will run.  We should use Jane's flowcharts: [[AmiGO_workflows]]
 
==Feb 20th, 2007==
===Agenda===
None Specified
===Minutes===
* Ben - new servers on schedule, Stuart confirms we will switch over wed. afternoon (PDT)
* Rotating meeting chairs debate: We will just rotate chairs week-by-week.
 
See: [[AWG_meeting_chairs|Revised Rota for chairing AWG meetings]]
 
* Seth is tweaking autocomplete.
* Jane does not like Princeton GO slim mapper - doesn't show division of GPs into slim catgories.
* Seth not sure if Chris' API handles shows the genes mappings or just numbers.
* dividing lines between amigo1/amigo2. - should slim mapper be integrated into 1.0 vs. 2.0.
* Ben - if we release seperately, we should freeze dev. on amigo 1.  Would people care if we stopped developing amigo 1.0?  Similar question with autocomplete - we shouldn't back add this to amigo 1.0.
* How complete is map2slim?  Jane will look at it once Seth repairs it.
* Comments on term finder - separate ontologies, other comments?
* Demo of term finder - should we have filters by individual evidence codes?  Should we keep them there for educational purposes?    How to handle different types of identifiers?  Even synoymns of valid go gene products?    Expected outputs?  Coming soon, connecting term finder and map2slim?
*Wiki page organization screwed up by Category:Amigo working group.  Jane will make a new Amigo working group page (w/out category)

Latest revision as of 08:54, 3 July 2008