Difference between revisions of "Annotation Call September 9, 2014"

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m ("Binding" term (GO:0005488))
(Agenda)
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=Agenda=
 
=Agenda=
  
=== Ub/Ub-like functions (David H)===
+
===Upcoming GOC meeting===
 +
http://wiki.geneontology.org/index.php/2014_Barcelona_GOC_Meeting_Agenda
 +
We are collecting agenda items for the next meeting. Please send us any items that you would like discussed.
 +
 
 +
===Jenkins Reports===
 +
http://build.berkeleybop.org/view/GAF/
  
1) We need annotator feedback on the fate of 'ubiquitin thiolesterase
+
Please check the reports for your GAF file and make efforts to fix them.
activity' (GO:0004221). This term can either be obsoleted or merged into
 
'ubiquitinyl hydrolase activity' (GO:0036459). There has been an
 
observation that many of the annotations to (GO:0004221) could actually be
 
transferred to 'ubiquitin-specific protease activity' (GO:0004843).
 
Annotators will need to reexamine the annotations to GO:0004221 and
 
reannotate to either GO:0036459 or GO:0004843. See SF items:#11094 and
 
#10519
 
  
2) Moving along with the E1,E2, E3 terms, GO:0019787 small conjugating
 
protein ligase activity suffers from the same issues as the original
 
ubiquitin ligase terms. We need to revamp the MF ontology for the other
 
small proteins in the same way that we did for the ubiquitin activating,
 
ligase and conjugating enzymes. Looking at annotations to GO:0019787, it
 
appears that all three types of enzyme activity have been annotated using
 
this term. We need to go back and reexamine those annotations once this
 
part of the ontology has been cleaned up. See SF item #11026
 
  
 
==="Binding" term (GO:0005488)===
 
==="Binding" term (GO:0005488)===
Line 80: Line 70:
  
 
RGD: 1
 
RGD: 1
 +
 +
=Next Call=
 +
=== Ub/Ub-like functions (David H)===
 +
 +
1) We need annotator feedback on the fate of 'ubiquitin thiolesterase
 +
activity' (GO:0004221). This term can either be obsoleted or merged into
 +
'ubiquitinyl hydrolase activity' (GO:0036459). There has been an
 +
observation that many of the annotations to (GO:0004221) could actually be
 +
transferred to 'ubiquitin-specific protease activity' (GO:0004843).
 +
Annotators will need to reexamine the annotations to GO:0004221 and
 +
reannotate to either GO:0036459 or GO:0004843. See SF items:#11094 and
 +
#10519
 +
 +
2) Moving along with the E1,E2, E3 terms, GO:0019787 small conjugating
 +
protein ligase activity suffers from the same issues as the original
 +
ubiquitin ligase terms. We need to revamp the MF ontology for the other
 +
small proteins in the same way that we did for the ubiquitin activating,
 +
ligase and conjugating enzymes. Looking at annotations to GO:0019787, it
 +
appears that all three types of enzyme activity have been annotated using
 +
this term. We need to go back and reexamine those annotations once this
 +
part of the ontology has been cleaned up. See SF item #11026
 
   
 
   
  
 
[[Category: Meetings]]
 
[[Category: Meetings]]

Revision as of 13:47, 8 September 2014

Agenda

Upcoming GOC meeting

http://wiki.geneontology.org/index.php/2014_Barcelona_GOC_Meeting_Agenda We are collecting agenda items for the next meeting. Please send us any items that you would like discussed.

Jenkins Reports

http://build.berkeleybop.org/view/GAF/

Please check the reports for your GAF file and make efforts to fix them.


"Binding" term (GO:0005488)

The term "binding" GO:0005488 has been put on the do_not_manually_annotate list, therefore all annotations to this term should be reviewed.

There are 27 annotations direct to this term and all of them have ChEBI IDs in the with field, therefore in most cases a more granular term should be used or created.

Some of the CHEBI IDs are not found and some seem unsuitable for GO (e.g. strychnine).

These are the unique ChEBI IDs used and in the right hand column are potential GO terms that could be used for some of them;

CHEBI ID name Possible GO term
CHEBI:15367 all-trans-retinoic acid GO:retinoic acid binding
CHEBI:17642 pentachlorophenol ?
CHEBI:230446 not found
CHEBI:28973 strychnine unsuitable?
CHEBI:33217 3,3',5,5'-tetrabromobisphenol A GO:organic cyclic compound binding
CHEBI:41922 diethylstilbestrol GO:drug binding
CHEBI:49809 2,2',5,5'-tetrachloro-4,4'-bis(methylsulfonyl)biphenyl GO:organic cyclic compound binding
CHEBI:553541 not found
CHEBI:8925 ryanodine GO:organic cyclic compound binding?

The distribution of annotations is;

MGI: 15

AgBase: 11

RGD: 1

Next Call

Ub/Ub-like functions (David H)

1) We need annotator feedback on the fate of 'ubiquitin thiolesterase activity' (GO:0004221). This term can either be obsoleted or merged into 'ubiquitinyl hydrolase activity' (GO:0036459). There has been an observation that many of the annotations to (GO:0004221) could actually be transferred to 'ubiquitin-specific protease activity' (GO:0004843). Annotators will need to reexamine the annotations to GO:0004221 and reannotate to either GO:0036459 or GO:0004843. See SF items:#11094 and

  1. 10519

2) Moving along with the E1,E2, E3 terms, GO:0019787 small conjugating protein ligase activity suffers from the same issues as the original ubiquitin ligase terms. We need to revamp the MF ontology for the other small proteins in the same way that we did for the ubiquitin activating, ligase and conjugating enzymes. Looking at annotations to GO:0019787, it appears that all three types of enzyme activity have been annotated using this term. We need to go back and reexamine those annotations once this part of the ontology has been cleaned up. See SF item #11026