Difference between revisions of "AmiGO Release schedule"

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=== March 2006 ===
=== March 2006 ===
) 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)
New Features<br>
*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)
<br>
<br>
2) While on the Term Details page-
*While on the Term Details page-
2.1) you can now filter the gene_associations. You have three options in this pull-down: No associations, Direct associations and All associations
2.1) you can now filter the gene_associations. You have three options in this pull-down: No associations, Direct associations and All associations<br>
2.2) you have options to view Term Ancestors or Term siblings with capabity of expanding and collapsing a term node
2.2) you have options to view Term Ancestors or Term siblings with capabity of expanding and collapsing a term node<br>


Enhancements-
Enhancements<br>


3) Term search result is sorted based on term name and Comments are displayed right under the definition (where applicable)
*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


4) Obsolete terms appear last in the term search results page
*Matching query strings in the Synonym field are highlighted.


5) Matching query strings in the Synonym field are highlighted.
*Data source is sorted alphabetically


6) 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


7) 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.


8) 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


9) A new graph constructing API is now default
*AmiGO docucumentation is updated
 
10) AmiGO docucumentation is updated




[[Category:AmiGO working group]]
[[Category:AmiGO working group]]

Revision as of 00:57, 9 July 2006

Documentation of past and future AmiGO releases.

Upcoming releases

August 2006

  • Reset button to reset filters. This should go on all pages.
  • Save filter settings (cookies)
  • Annotation counts (several users have pointed this out). Can we get rid of counts if we can't provide the accurate #?
  • Display assigned_by information (column #15 from the gene association file)

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-

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.

Unknown

  • Interface makeover
  • web-based map2slim

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-

2.1) you can now filter the gene_associations. You have three options in this pull-down: No associations, Direct associations and All associations
2.2) 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