Reference Genome March 2010 (Archived)

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PAINT updates

PAINT beta24

  1. This release fixes issues with GAF I/O (both generating and reading GAFs work correctly). The GAFs produced are still invalid as we had to introduce new ECOs for NOT annotations.
  2. We've also added a fix to handle the database name discrepancies for E.coli between the Panther data and the GO data.

PAINT beta23

  1. Adding a NOT attribute changes the WITHs identifiers to the annotated node and children as follows:
    • rapid_divergence - sets the parent of the annotated node in the WITHs
    • missing_residue(s) - clears out the WITHs
    • descendant_sequence(s) - adds the leaves with NOT experimental evidence to given term in the WITHs
  2. Removing a NOT attribute will revert the WITHs to the positive annotation for the annotated node and children

PAINT beta22

  1. stop any automatic inference of NOT annotations in PAINT
  2. use the same basic infrastructure for NOTs as we already have. You would first annotate the positive annotation to an ancestral node (e.g. dragging from the matrix). You would then click on a descendant node where you believe the NOT first evolved, and click on the qualifier box of the annotation you want to negate. If the node has descendant sequences with a "NOT x" annotation, then there will be a new menu item that can be selected from the dropdown called something like "descendant sequences" (in addition to the currently available items "PUBMED:", "rapid divergence", "missing residue(s)"). Note that you cannot create an annotation for an ancestral node that only has NOT descendants. You'll need to first create a positive annotation on a more ancient ancestor, as Paul mentioned.
  3. Refactored GO fetching so that it handles searching for updated GO ids (the current GO OBO file had been updated, making some GO ids in certain families no longer the primary id).

Monthly conference call

9_MAR_2010_RefGen_Phone_Conference

  • Lung branching morphogenesis primary annotations are almost complete
  • GO annotation camp: working groups topics have been defined

Suggestions for annotation projects

Ref.Genome in AmiGO

http://amigo.berkeleybop.org/cgi-bin/amigo/amigo_exp?mode=live_search Seth has implemented some enhancements. Check it out.

  • Example query: top and homolset:yes

Annotation status reporting tool progress

Kara's group: 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 these missing rows into the go database has been run.


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