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geneontology / paint

This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
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issues with propagations & with info for NOT annotations #19

Closed krchristie closed 8 years ago

krchristie commented 8 years ago

Hi,

I initially saw this for Paint2.0-beta14. I noticed that Pascale recently reported someting using 2.0-b15, so I just downloaded it and see the same issue in Paint2.0-beta15.

In the family PTHR13405, FB:FBgn0039004 has a NOT annotation to the BP term SMAD protein import into nucleus (GO:0007184). There are two problems related to this NOT annotation.

  1. NOT annotation to specific term blocking propagation of a more general term There is an annotation for YEAST NUP133 to "protein import into nucleus" (GO:0006606) that I propagated to the root node. However this term is not propagated to the Drosophila gene FB:FBgn0039004, even though the experimental annotation to the Drosophila gene is more specific than the term that is being propagated, and thus shouldn't block it.
  2. gene with NOT annotation being used to support propagation of positive annotation In all the annotation lines for the GO term "protein import into nucleus" (GO:0006606), the FB gene ID is included as well as the SGD ID, even though the annotation to the FB gene is a NOT annotation. Here is a sample line from a gaf (saved by 2.o-b15)
MGI     MGI:2442620     Nup133          GO:0006606      PAINT_REF:13405 IBA     PANTHER:PTN000334066|SGD:S000001790|FB:FBgn0039004      P       nucleoporin 133 UniProtKB:Q8R0G9|PTN000334084|4832420O05Rik|mermaid     protein taxon:10090     20160427        GO_Central

-Karen

Note: I committed this family to SVN in November 2015 from Paint1.14. I have NOT updated SVN with new files saved from 2.0-b14.

selewis commented 8 years ago

Fixed in PAINT 2.17, please test

krchristie commented 8 years ago

Looks great. Thanks Suzi