Reference Genome February 2010 (Archived)

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PAINT updates

PAINT beta 21

  1. NOT propagation should work as we've discussed thus far and it figures out per node whether it should have a NOT (which should behave correctly in the case of annotating an ancestral node that has descedants with and without NOT qualifiers to the term). Note that the propagation is still automatic, while maintaining logical consistency.
  2. Added ability to search for terms along with genes in the "Find" dialog. You can choose whether the search string should be searched against genes or terms from the radio buttons on the top of the "Find" dialog.

PAINT beta 20

Feb 10, 2010

  1. Fixed annotation matrix display of NOT terms given the discussion with Paul. To summarize, an annotation appears as NOT only if all descendant terms also have a NOT qualifier.
  2. When annotating with a term that has a NOT qualifier, the NOT is propaated to the annotated nodes.
  3. When dragging a term over the nodes in the tree, a tooltip with the node's ID will popup.
  4. Fixed the issue with tooltips not popping up when hovering over nodes in the tree after creating an annotation.

PAINT beta 19

Feb 4, 2010. Here are some key changes to this release:

  1. Drastically sped up deleting an association from an ancestral node (we're talking orders of magnitude here, folks).
  2. Sped up (somewhat) the creation of new associations. Keep in mind that the GO database is hit during this step, so your connection speed to the database will affect the speed of this step. Still, should be somewhat faster than before.
  3. Added support for partial matches to "Find". Also changed the look of the dialog a bit (it looked kinda ugly IMO) and added support for pressing <Enter> to start the search, rather than having to click on the "Ok" button.
  4. All panels should now retain the menu when undocked.

PAINT beta 18

Feb 3, 2010. It has the following changes:

  1. Improved annotating rules.
  2. Undocking the Annotation Matrix will keep the menu.
  3. Synchronized horizontal scrolling in the Annotation Matrix. Scrolling sideways will cause both the matrix and headers (terms) to scroll together.

PAINT demo

Ed Lee gave a demo of the PAINT tool to the reference genome group.

Electronic jamboree


Monthly conference call

We discussed the format of the GO annotation camp, the prioritization of the lung branching morphogenesis targets, and PAINT. Minutes are available here: 9_FEB_2010_RefGen_Phone_Conference

Suggestions for annotation projects

We have added a page where curators can suggest annotation projects to the reference genome group: Suggestions_for_RefG_annotation_targets

Annotation camp: Geneva 2010

More details are available:

  • Objective: This annotation camp will be focused on updating and refining skills of existing GO biocurators including new GO biocurators in existing annotation groups and including the Swiss-Prot curation team. We hope members of each MOD will be represented.
  • Deliverables: (1) final annotation documentation for each of the three annotation topics.
    • There will be a special emphasis on the reference genome project. Deliverable: (2) annotation propagation rules for the reference genome project.
  • Agenda

Structure: There will be three (3) ‘focused annotation sessions’ where specific annotation issues will be discussed. Suggestion for discussion topics should be added to the GO camp agenda: 2010_GO_camp_Meeting_Logistics#Suggestions_for_annotation_issues_to_be_discussed

    • Curators are being asked to vote for the topics they would like to discuss at the camp by March 1st so we have sufficient time to prepare discussions.

Suggestions for annotation issues to be discussed

1. Binding and complexes

1.a. Binding documentation

1.b. Annotation of complexes

2. Biological processes

2.a. Use of regulation

2.b. Response to terms, how will these relate to signaling terms and to final cellular effect

2.c. How is a downstream effect defined (i.e when not to capture phenotypes )

3. Use of column 16

Plan for annotation status reporting tool

Kara and her group have started to work on a tool that would display the annotation status of the Panther families. There will be a regularly updated web page that will show the following information:

  1. Panther family ID
  2. Date selected for concurrent annotation
  3. Date Panther family last annotated (tree annotations)
  4. Number of members
  5. Number of RefG members
  6. Number of members with EXP
  7. Date more recent member last annotated
  8. We could add 'date comprehensively annotated' for groups that can provide this information

Current status:

Sven Heinicke (developer at Princeton) is working through ID mapping issues:

of the 339448 proteins in the seq2pthr.gz file:

61123 exist in the gene_product table 5126 have entries in the dbxref table but not the gene_product table 273199 new rows in the dbxref table (and gene_product) will have to be created

the script to load them into the go database should start being tested in Princeton's go developement database starting March 1.

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