Web Presence Working Group: Meetings (Archived)

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Next meeting

June 5, 2007
Chair: Jane (I think still - if not, she needs to edit this page)

See meeting chair rota for next chair

Previous Meetings

May 8th, 2007


  • Go over the workflows that will lead to a user downloading a file. Workflows can be found here:
  • Discussion and suggestions of various download options
    • NCBI-Entrez Nucleotide
    • BioMart
    • others
  • Members of the working group volunteer to come up with an assessment of the options listed in 2 for the next AWG chat.

Web chat transcript

Action Items

  • The following people will evaluate the web interfaces for the next AmiGO working group
    • Pascale: Dictybase BioMart
    • Ben: EBI BioMart
    • Rama: EBI SRS
    • Donghui: NCBI Entrez Nucleotide

April 17th, 2007

  • Ben and Chris talked about couple of tables in the database that don't have unique keys (evidence and association tables).
  • Seth requested all of us to test the boolean search and send him comments
  • Ben mentioned that the new go-dev servers can be used to test GO-Full. Toy is old and slow.

April 10th, 2007


  1. Testing of IEA instantiation of AmiGO 1.0 at: http://toy.lbl.gov:9002/cgi-bin/amigo/go.cgi
  2. Testing boolean search feature at: http://toy.lbl.gov:9002/cgi-bin/amigo2/obo-search-client.cgi


  • Group felt that AmiGO a bit sluggish with IEAs
  • Large numbers of results also difficult to interpret
  • Discussed possibility of adding 'views' to improve speed and organise web pages
  • Download options for AmiGO discussed
  • Web chat transcript

Action items

  1. Seth to write scripts to measure AmiGO response speed
  2. Software group to discuss possibility of creating 'views' for the database
  3. Seth to add wildcards to boolean searches and email AWG

March 13th, 2007


  • Revealing the 5 top vote getters for features to be added to AmiGO in the next release

Web chat transcript

Action Items

The following feature requests will be implemented for the next release

  1. Download options
  2. Sorted search results
  3. Searching with mis-spelled terms
  4. Improved gene product search
  5. a tie in 5th place between Organize and allow filtering species by kingdom and Advanced Search radio button

Feb 13th, 2007


  1. Hardware upgrade update - delay (Ben)
  2. GO loading refactor outline on wiki page (Ben)
  3. Requests for the June release of AmiGO (see the SourceForge feature request tracker) and bug fixes (Amelia)
  4. Demos of new AmiGO additions (Seth)


  • Hardware upgrade: there are still a few issues remaining to be fixed, but the new servers should be up and running in the near future
  • AmiGO June release: there seem to be three main areas of focus for the June release of AmiGO:
    1. Providing data downloads in various formats
    2. Sorting search results
    3. Improvements to the BLAST search facility
    Additionally, there are the features that Seth is working on: the GO term finder implementation, map2slim functionality and search autocompletion.
    Working groupers are encouraged to brainstorm for any possible new features and add them to the tracker for the next chat
  • Seth demonstrated a couple of new features he has been working on; the search autocompletion, http://toy.lbl.gov:9002/cgi-bin/amigo2/autocomplete-client.cgi, and an AmiGO data manager, http://toy.lbl.gov:9002/cgi-bin/amigo2/data-manager-client.cgi. He will send out the URL of the GO term finder implementation later in the week for the working group to test and comment on.
  • Web chat transcript

Action Items

  1. everyone to collate AmiGO feature requests before the next session, and add them to SourceForge. We'll prioritize what should be done at the next meeting
  2. Seth to send out URL of new widgets and functions, and AWG to comment before the next meeting

Tuesday August 1, 2006


  1. Outstanding issues for the August release
  2. Some Standard Operating Procedures (SOP) for the working group-
    1. We should talk/chat on a regular basis. How does 1st and 3rd Tuesday of every month sound?
    2. Should we do IRC chat or call regularly. I like the Chat for two reasons- We can all see the transcript after each meeting and we don't have issues of poor phone connection etc. We haven't tried the IRC chat even once. We could also flip between the two modes depending on the needs.
    3. How do we want to use the AmiGO WG Wiki?
    4. Testing- After we test and make comments, unless it is a bug, all text/display suggestions should be looked at few others before they are implemented.
    5. Emails- please respond even if you agree with what is going on. We cannot assume silence implies agreement.
  3. November release
    We would like to Display IEAs. What needs to be done? I see 3 distinct big issues.
    1. Interface should be able to handle IEAs (i.e) we cannot have 50K annotations displayed over 100 pages. We should make sure we are displaying the IEA data in a meaningful way. Accurate counts and a download button become very essential for this.
    2. Efficiency of retrieval, performance. We don't want to see server errors or the browser timing out.
    3. As Mike pointed out in one of the earlier emails, the IEAs are loaded only once a month and it takes a week to load.
      Some questions I have on this-
      • Can we live with IEA data loaded once a month?
      • How does this schedule affect loading non-IEAs on a regular fashion?

Web chat transcript

May 30, 2006

Summary (from Rama)

ASAP: replace all Contact links to gohelp. Shu offered to do this.

In the November release

  • we will not have a new window open when you click on a term. This will take care of not having the search box/link back to home on every term page.
  • IEAs will be displayed in November release.
  • We would like a summary of counts- IEAs and non-IEAs/species on the term details page so that users get an idea and they can click on what they want. This way, we don't retrieve all the annotations for display and slow the server down.
  • Download option will be implemented.
  • We should write a specs document on what we want the Download button to do before it can be implemented.

After the November release:

We all agreed that AmiGO should be more than for browsing ontologies and annotations. We would like this to be a hub where some of the GOC approved software is available. Towards this end, we will offer a web interface for map2slim tool as part of AmiGO. Since resources are limited, we will evaluate and prioritize.

GOst batch query-

  • Shu offered to take a look at the GMOD Blast interface
  • We decided to have a 100 sequence cut-off
  • Provide more BLAST parameters

On the results page, will provide an option to view one sequence at a time or an option to download.