AmiGO Hub: Group Meetings: Difference between revisions

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=next meeting=
=Next Hub Meeting=
*Date: Aug 21, 2007
*Date: Oct 2, 2007
*Chair: Seth


See [[AWG_meeting_chairs|meeting chair rota]] for next chair
=Previous Meetings=
 
==September 18, 2007==
 
===Present===
Rama, Eurie, Mary, Amelia, Seth, Chris
 
===Action items===
 
*In order to prevent any future confusion/problems with the rota and schedule, Seth will be permanent chair for hub and WG; all items should go to him and an agenda will go out on Friday (Seth)
 
*The web presence group and the AmiGO working group will be merged for the purpose of reporting during the meeting (Chris/Eurie)
 
*Chris proposed that the WG should get together as a group and discuss/use AmiGO sometime during the upcoming meeting (Seth will send email to WG)
 
===Discussion===
 
*Timeline: the next release will be finished during the period that Amelia is in Berkeley and work on the new release will start.
 
*Future directions: The next planned release will concentrate on integrating the reference genome and having it be more interactive than AmiGO has been to date


=Previous Meetings=
*Mary, Amelia and others offered suggestions for reference genome displays
 
*Briefly discussed time when Mary could work directly with Berkeley group


==August 9, 2007==
==August 9, 2007==

Revision as of 12:49, 18 September 2007

Next Hub Meeting

  • Date: Oct 2, 2007

Previous Meetings

September 18, 2007

Present

Rama, Eurie, Mary, Amelia, Seth, Chris

Action items

  • In order to prevent any future confusion/problems with the rota and schedule, Seth will be permanent chair for hub and WG; all items should go to him and an agenda will go out on Friday (Seth)
  • The web presence group and the AmiGO working group will be merged for the purpose of reporting during the meeting (Chris/Eurie)
  • Chris proposed that the WG should get together as a group and discuss/use AmiGO sometime during the upcoming meeting (Seth will send email to WG)

Discussion

  • Timeline: the next release will be finished during the period that Amelia is in Berkeley and work on the new release will start.
  • Future directions: The next planned release will concentrate on integrating the reference genome and having it be more interactive than AmiGO has been to date
  • Mary, Amelia and others offered suggestions for reference genome displays
  • Briefly discussed time when Mary could work directly with Berkeley group

August 9, 2007

Chair: Jane

(meeting postponed from Tuesday 7 because of clash with reference genomes meeting)

Progress on current release:

  • map2slim interface needs finalising - Seth has simplified to hide more complex options unless selected
  • Amelia writing session code to allow transfer of data from slim mapper to term enrichment tool
  • intermediate page giving a summary of the gene/protein ids e.g. ambiguous ids, genes from different species etc.
    • list invalid genes
    • list ambiguous gene names/symbols

AmiGO future releases

  • future hub chats - use webex - Seth to demo new AmiGO architecture, highlight problems in development
  • Action item: software group to put together a summary of options/issues for presenting IEAs in AmiGO

July 24, 2007

Chair: Chris

Review previous Action Items from previous meeting

(no minutes from July 11, so going with:) http://gocwiki.geneontology.org/index.php/Hub_group_meetings#June_26.2C_2007

  1. Action: Ben will update the Wiki about Chair rotations
 DONE: chairs must move the star
  1. Action: Chris to put big ideas on the tracker
 TODO
  1. Action: Eurie/Jane will bring up the issue of inviting non consortium members to the WG discussion in the next Managers meeting.
 DONE

carried over from June 12:

  1. Inform other groups of our conference call time
 DONE!
  1. Replace flat file with OBO file
 Done. beta can export obo
  1. Get prototypes to WG
 Done
  1. Solicit names for "termfinder" and "map2slim" from WG
 ONGOING

current candidates:

  • term enrichment
  • map2slim; goslimmapper
  1. Front page mockups, ask how WG likes them
 Done
  1. Start automated testing
 TODO: Seth

Amelia suggested using log files.

Topics

What is the AmiGO Hub?

Information about the hub is hard to find on the gocwiki. Are we a mysterious shadowy cabal pulling strings and levers at the heart of GO? Or are we just confused?

In this meeting we will delve into the heart of this issue and try and resolve exactly how the Hub related to the following nodes in the GO organisational DAG.

Some background:

Releases and release cycle

Some questions, sorry if we have been over some already but I think it'd be good to get some of this down :

  1. when is the next release?

Coding:

 Seth still needs code from Amelia
 TODO: Integrating termfinder and map2slim.

Note: Ben is gone in 2 weeks for a week

 Search relevance is done.
 TODO: Seth will coordinate with John on OE ranking

alpha version ready this week

  1. what features will be in the next release?
  2. what is the test process & can we improve it?
  3. what is the release cycle?

2/year; used to be 4/year

Ben suggested auto check versions of perl modules to help speed up testing of stanford deployment

  1. what are the obstacles to a faster release cycle?
  2. how are features and bugs prioritised?
 TODO: top5. to go in tracker; currently just languishes in email
List as voted on by the AWG
=================
1.  download options
2.  sorted search results
3.  searching with mis-spelled terms
4.  improved gene product search
5.  a tie between organize and allow filtering species by kingdom and advanced Search radio button
Long-standing wish list items
=======================
1.  Term Finder
2.  Term Mapper
3.  IEA
Additional functionalities
====================
1.  New short URL
2.  Term tracker


  1. what is our plan for the GOC meeting?

We only have a short time between next release and meeting; not enough time for a full release

focus on refGenomes; get a prototype to show of refg graph views, integrated with database

AOB

Jane will be on Maternity leave from Aug18

Open up AWG meeting to consortium in 3 weeks

 TODO: discuss a1 & a2 in 2 weeks


June 26, 2007

Chair: Rama
Present: Seth, Eurie, Amelia, Jane, Chris, Ben
meeting mode: Phone call


  • 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.
Action Item_ Ben will update the Wiki about Chair rotations
  • Main agenda- We went through the 'big features' that Chris sent around last week.


On Jun 21, 2007, at 6:26 PM, Chris Mungall wrote:

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

  • bi-axial grid type exploration of annotations (eg BP/CC, or BP/Taxon). See the emails I sent a month or so ago.


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. 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

(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.

Chris will put these ideas on the tracker with more detail/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: 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)