Reference Genome March 2010 (Archived)

PAINT updates

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

1. 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.

1. 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).

Suggestions for annotation projects

• Next project : heart development (Varsha and Ruth)
• We have added a page where curators can suggest annotation projects to the reference genome group: Suggestions_for_RefG_annotation_targets

Annotation status reporting tool progress

Kara's group

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