Reference Genome March 2010 (Archived): Difference between revisions

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===PAINT beta22===
===PAINT beta22===
# stop any automatic inference of NOT annotations in PAINT
# stop any automatic inference of NOT annotations in PAINT
# use the same basic infrastructure for NOTs as we already have.  You would
# 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.
first annotate the positive annotation to an ancestral node (e.g. dragging
# 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).
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.
# 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==
==Monthly conference call==

Revision as of 15:41, 9 March 2010

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
  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

Suggestions for annotation projects


Annotation status reporting tool progress

Kara's group

Back to Reference_Genome_Annotation_Project page

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