Difference between revisions of "Annotation Conf. Call 2015-09-22"

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(Created page with "Category:Annotation Working Group =Agenda= ==Annotation consistency exercise== Pombe paper <br> http://www.ncbi.nlm.nih.gov/pubmed/22959349")
 
(add annotation summary)
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Pombe paper <br>
 
Pombe paper <br>
 
http://www.ncbi.nlm.nih.gov/pubmed/22959349
 
http://www.ncbi.nlm.nih.gov/pubmed/22959349
 +
 +
===Annotation Summary===
 +
{| {{Prettytable}}
 +
|-
 +
! Gene
 +
! Qualifier
 +
! Term
 +
! ID
 +
! # of Annotations
 +
! Evidence Code Summary
 +
! 'With' field Summary
 +
! Extension Summary
 +
! Comments
 +
|-
 +
! Molecular Function Annotations
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
|-
 +
| rap1
 +
|
 +
| protein binding
 +
| GO:0005515
 +
| 2/3
 +
| IPI
 +
| bqt4
 +
|
 +
|
 +
|-
 +
| bqt4
 +
|
 +
| protein binding
 +
| GO:0005515
 +
| 2/3
 +
| IPI
 +
| rap1
 +
|
 +
|
 +
|-
 +
| bqt1
 +
|
 +
| protein binding
 +
| GO:0005515
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| 1/3
 +
| IPI
 +
| bqt2, rap1
 +
|
 +
| Not sure if this is the correct representation, or if this should be a protein complex annotation.  This is the Y3H data.
 +
|-
 +
| bqt2
 +
|
 +
| protein binding
 +
| GO:0005515
 +
| 1/3
 +
| IPI
 +
| bqt1, rap1
 +
|
 +
| Not sure if this is the correct representation, or if this should be a protein complex annotation.  This is the Y3H data.
 +
|-
 +
| poz1
 +
|
 +
| protein binding
 +
| GO:0005515
 +
| 1/3
 +
| IPI
 +
| rap1
 +
|
 +
|
 +
|-
 +
| rap1
 +
|
 +
| protein binding
 +
| GO:0005515
 +
|
 +
| IPI
 +
| taz1
 +
|
 +
|
 +
|-
 +
| rap1
 +
|
 +
| protein binding
 +
| GO:0005515
 +
| 1/3
 +
| IPI
 +
| bqt1, bqt2
 +
|
 +
| Not sure if this is the correct representation, or if this should be a protein complex annotation.  This is the Y3H data.
 +
|-
 +
| rap1
 +
|
 +
| protein binding
 +
| GO:0005515
 +
| 1/3
 +
| IPI
 +
| poz1
 +
|
 +
|
 +
| taz1
 +
|
 +
| protein binding
 +
| GO:0005515
 +
| 1/3
 +
| IPI
 +
| rap1
 +
|
 +
|
 +
|-
 +
|-
 +
! Biological Process Annotations
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
|-
 +
| taz1
 +
|
 +
| mitotic telomere tethering at nuclear periphery
 +
| GO:0044820
 +
| 2/3
 +
| IGI-1, IMP-1
 +
| bqt4
 +
| during mitotic G2 phase (GO:0000085)
 +
|
 +
|-
 +
| bqt4
 +
|
 +
| mitotic telomere tethering at nuclear periphery
 +
| GO:0044820
 +
| 3/3
 +
| IGI-1, IMP-2
 +
| taz1
 +
| during mitotic G2 phase (GO:0000085) (2/3 included)
 +
|
 +
|-
 +
| rap1
 +
|
 +
| mitotic telomere tethering at nuclear periphery
 +
| GO:0044820
 +
| 2/3
 +
| IPI-1, IMP-2
 +
| bqt4
 +
| during mitotic G2 phase (GO:0000085) (2/3 included)
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| one curator did both IMP and IGI
 +
|-
 +
| cdc2
 +
|
 +
| negative regulation of mitotic telomere tethering at nuclear periphery
 +
| GO:1904537
 +
| 1/3
 +
| IGI
 +
| rap1
 +
| during mitotic M phase (GO:0000087)
 +
|
 +
|-
 +
| cdc2
 +
|
 +
| negative regulation of protein binding
 +
| GO:0032091
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| 1/3
 +
| IMP
 +
|
 +
| during mitotic M phase (GO:0000087)|has_input-rap1|has_input-bqt4
 +
|
 +
|-
 +
| cdc2
 +
|
 +
| protein serine/threonine kinase activity
 +
| GO:0004674
 +
| 2/3
 +
| IDA
 +
|
 +
| has_input-rap1
 +
| There is no direct evidence to show that phosphorylation of rap1 by cdc2 is what causes dissociation of the tethering. But the authors are suggesting that.
 +
|-
 +
| nda3
 +
|
 +
| ??
 +
| ??
 +
| 1/3
 +
| ??
 +
|
 +
|
 +
| I wasn't sure if there was any GO annotation here wrt regulation of phosphorylation, or if the nda3 mutation was just being used to block the cell cycle at a particular point.
 +
|-
 +
| cdc2
 +
|
 +
| peptidyl-serine phosphorylation
 +
| GO:0018105
 +
| 2/3
 +
| IGI-1, IMP-1
 +
| rap1
 +
| during mitotic M phase (GO:0000087)
 +
| would love to be able to specify the residues; I'm not always certain if this type of evidence also supports an annotation to the corresponding MF term.  Also, I don't know if/what the appropriate way to capture an annotation extension would be for this, has_input(Rap1p)?
 +
|-
 +
| cdc2
 +
|
 +
| peptidyl-threonine phosphorylation
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| GO:0018107
 +
| 2/3
 +
| IGI-1, IMP-1
 +
| rap1
 +
| during mitotic M phase (GO:0000087)
 +
| would love to be able to specify the residues; I'm not always certain if this type of evidence also supports an annotation to the corresponding MF term.  Also, I don't know if/what the appropriate way to capture an annotation extension would be for this, has_input(Rap1p)?
 +
|-
 +
| cdc2
 +
|
 +
| mitotic sister chromatid segregation
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| GO:0000070
 +
| 1/3
 +
| IC
 +
| GO:1904537????????
 +
|
 +
|
 +
|-
 +
| taz1
 +
|
 +
| protection from non-homologous end joining at telomere
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| GO:0031848
 +
| 1/3
 +
| IMP
 +
|
 +
|
 +
|
 +
|-
 +
| taz1
 +
|
 +
| ??
 +
| ??
 +
| 1/3
 +
| ??
 +
|
 +
|
 +
| Not sure if the overexpression constructs are suficient evidence to annotate taz1 to GO:0044820, mitotic telomere tethering at nuclear periphery
 +
|-
 +
| taz1
 +
|
 +
| ??
 +
| ??
 +
| 1/3
 +
| ??
 +
|
 +
|
 +
| Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation.
 +
|-
 +
! Cellular Component Annotations
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
!
 +
|-
 +
| taz1
 +
|
 +
| nuclear chromosome, telomeric region
 +
| GO:0000784
 +
| 2/3
 +
| IDA
 +
|
 +
|
 +
|
 +
|-
 +
| ish1
 +
|
 +
| nuclear envelope
 +
| GO:0005635
 +
| 2/3
 +
| IDA
 +
|
 +
|
 +
|
 +
|-
 +
| atb2
 +
|
 +
| microtubule
 +
| GO:0005874
 +
| 2/3
 +
| IDA
 +
|
 +
|
 +
|
 +
|-
 +
| bqt4
 +
|
 +
| nuclear envelope
 +
| GO:0005635
 +
| 1/3
 +
| IDA
 +
|
 +
|
 +
|
 +
|-|}

Revision as of 05:03, 22 September 2015


Agenda

Annotation consistency exercise

Pombe paper
http://www.ncbi.nlm.nih.gov/pubmed/22959349

Annotation Summary

Gene Qualifier Term ID # of Annotations Evidence Code Summary 'With' field Summary Extension Summary Comments
Molecular Function Annotations
rap1 protein binding GO:0005515 2/3 IPI bqt4
bqt4 protein binding GO:0005515 2/3 IPI rap1
bqt1 protein binding GO:0005515 1/3 IPI bqt2, rap1 Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data.
bqt2 protein binding GO:0005515 1/3 IPI bqt1, rap1 Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data.
poz1 protein binding GO:0005515 1/3 IPI rap1
rap1 protein binding GO:0005515 IPI taz1
rap1 protein binding GO:0005515 1/3 IPI bqt1, bqt2 Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data.
rap1 protein binding GO:0005515 1/3 IPI poz1 taz1 protein binding GO:0005515 1/3 IPI rap1
Biological Process Annotations
taz1 mitotic telomere tethering at nuclear periphery GO:0044820 2/3 IGI-1, IMP-1 bqt4 during mitotic G2 phase (GO:0000085)
bqt4 mitotic telomere tethering at nuclear periphery GO:0044820 3/3 IGI-1, IMP-2 taz1 during mitotic G2 phase (GO:0000085) (2/3 included)
rap1 mitotic telomere tethering at nuclear periphery GO:0044820 2/3 IPI-1, IMP-2 bqt4 during mitotic G2 phase (GO:0000085) (2/3 included) one curator did both IMP and IGI
cdc2 negative regulation of mitotic telomere tethering at nuclear periphery GO:1904537 1/3 IGI rap1 during mitotic M phase (GO:0000087)
cdc2 negative regulation of protein binding GO:0032091 1/3 IMP has_input-rap1|has_input-bqt4
cdc2 protein serine/threonine kinase activity GO:0004674 2/3 IDA has_input-rap1 There is no direct evidence to show that phosphorylation of rap1 by cdc2 is what causes dissociation of the tethering. But the authors are suggesting that.
nda3  ??  ?? 1/3  ?? I wasn't sure if there was any GO annotation here wrt regulation of phosphorylation, or if the nda3 mutation was just being used to block the cell cycle at a particular point.
cdc2 peptidyl-serine phosphorylation GO:0018105 2/3 IGI-1, IMP-1 rap1 during mitotic M phase (GO:0000087) would love to be able to specify the residues; I'm not always certain if this type of evidence also supports an annotation to the corresponding MF term. Also, I don't know if/what the appropriate way to capture an annotation extension would be for this, has_input(Rap1p)?
cdc2 peptidyl-threonine phosphorylation GO:0018107 2/3 IGI-1, IMP-1 rap1 during mitotic M phase (GO:0000087) would love to be able to specify the residues; I'm not always certain if this type of evidence also supports an annotation to the corresponding MF term. Also, I don't know if/what the appropriate way to capture an annotation extension would be for this, has_input(Rap1p)?
cdc2 mitotic sister chromatid segregation GO:0000070 1/3 IC GO:1904537????????
taz1 protection from non-homologous end joining at telomere GO:0031848 1/3 IMP
taz1  ??  ?? 1/3  ?? Not sure if the overexpression constructs are suficient evidence to annotate taz1 to GO:0044820, mitotic telomere tethering at nuclear periphery
taz1  ??  ?? 1/3  ?? Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation.
Cellular Component Annotations
taz1 nuclear chromosome, telomeric region GO:0000784 2/3 IDA
ish1 nuclear envelope GO:0005635 2/3 IDA
atb2 microtubule GO:0005874 2/3 IDA
bqt4 nuclear envelope GO:0005635 1/3 IDA
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