AmiGO Release schedule

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Documentation of past and future AmiGO releases.

Upcoming releases

August 2006

  • Multiple sequence search
  • Add filter toggle, number of best hits option, and more option values for expect threshold
  • Autofresh page after submitting sequence
  • Reset button to reset filters. This should go on all pages.
  • Save filter settings (cookies)
  • Annotation counts (several users have pointed this out). get rid of counts when we can't provide the accurate #
  • Display assigned_by information (column #15 from the gene association file)
  • Display term definition source dbxref

Test version is available: http://toy.lbl.gov:8091/cgi-bin/amigo2/go.cgi (AmiGO) and http://toy.lbl.gov:8091/cgi-bin/gost2/gost.cgi (GOst)

November 2006

  • Displaying IEAs will be explored. Interface needs to be modified to handle IEAs.
  • A new window should not 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.
  • We would like a summary table of counts- IEAs and non-IEAs per 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: We should write a specs document on what we want the Download button to do before it can be implemented.
  • GOst batch query- [this will be in August release]

Shu has offered to take a look at the GMOD Blast interface. We decided to have a 100 sequence cut-off. On the results page, we will provide an option to view one sequence at a time or an option to download.


Offering more parameters for BLAST queries will be explored for future.

NOTE about IEAs- The database that includes IEAs (called GO FULL) is currently only updated once a month. It currently takes 7-8 days to create the GO FULL database so at best AmiGO could only be updated every 1.5 weeks. It is now updated every 2 or 3 days. So with the current database loading software displaying IEAs would mean updating AmiGO much less often.

This is suboptimal. But currently AmiGO cannot handle IEAs in a meaningful way. Should this be handled in two steps?

  1. phase1 - Prepare the interface, make changes to the application to deal with IEAs
  2. phase2 - Consider options to load the database more often.

Future

  • Interface makeover
  • Links to user comment form
  • Updating AmiGO user help documentation
  • Do we want to make AmiGO as a hub for all GOC software? Should we try to offer map2slim via AmiGO as the first project?

Past releases

March 2006

New Features

  • New Ontology Filter added. This allows you to restrict your search to a particular ontology (Function, Process, Component). You can search for terms within an ontology or search to see annotations in one ontology for gene products (Gene Symbol/Name)
  • While on the Term Details page:
    you can now filter the gene_associations. You have three options in this pull-down: No associations, Direct associations and All associations
    you have options to view Term Ancestors or Term siblings with capabity of expanding and collapsing a term node

Enhancements

  • Term search result is sorted based on term name and Comments are displayed right under the definition (where applicable)
  • Obsolete terms appear last in the term search results page
  • Matching query strings in the Synonym field are highlighted.
  • Data source is sorted alphabetically
  • Help link (a hyperlinked question mark '?') has been added to the Data source and Evidence Code filtering options on the front page
  • In the Advanced search page, in the 'Fields' pull down, the option 'External references' is now called 'Accession ID/DB_object_ID' to correspond with the column names of the gene_association files. Accession ID/DB_object_ID refers to DatabaseIDs. Examples are: S000000001 for SGD, SPAC9.03c for Pombe GeneDB, FBgn0015331for FlyBase.
  • A new graph constructing API is now default
  • AmiGO docucumentation is updated