Annotation Conf. Call 2015-09-22

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Agenda

Relations used in Col-16

Status on some questionable relations:

  • dependent_on
  • in_absence_of
  • in_presence_of
  • Already deprecated but annotations still exists;
    • independent_of
    • localization_dependent_on
    • requires_sequence_feature
    • requires_substance
    • not_exists_during
    • not_happens_during
    • During

Discussion

  • For groups that don't use protein2GO please make sure to not use these relations in col-16 annotations.
  • Suzi- do you have documentation/suggestions on what other relations can be used to replace these?
    • Rachael- Yes, we are working on that list
    • Heiko is going to implement the checks in Jenkins. Rama will get a list of these checks from Tony and pass them along.

Annotation consistency exercise

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

Discussion

  • MF annotations: we discussed the protein kinase annotation for cdc2 extensively because the evidence was not direct. They used a mutatant cdc2 to show lack of phosphorylation (IMP) and in another experiment they used the p13Suc1-associated kinase complex which contains the cdc2 kinase to show phosphorylation (IDA). Both these pieces are weak evidence for kinase activity. One could look for another paper to make this annotation (i.e. cdc2 kinases rap1). But making this annotation from this paper is not wrong.
  • CC annotations: most of the localization results in the paper are well established in other papers and in this paper these proteins are used as markers. They are showing that their assay/construct is working. Localization is not the main point of the paper. So doesn't make sense to capture these CC annotations.
  • Bqt4 and Rap1 should be annotated to GO:44820 (mitotic telomere tethering at nuclear periphery), not Taz1
  • Evidence for annotating Cdc2 to 'negative regulation of mitotic telomere tethering at nuclear periphery' is indirect but that can be inferred from this paper.
  • The term mame for GO:70197 should be clarified (Midori will make a github ticket and assign to David).
  • there was lot of discussion on whether the term 'negative regulation of mitotic telomere tethering at nuclear periphery' should be related to chromosome segreggation in the ontology.

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 3/4 IPI bqt4
bqt4 protein binding GO:0005515 3/4 IPI rap1
bqt1 protein binding GO:0005515 1/4 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.
bqt1 protein binding GO:0005515 1/4 IPI rap1
bqt2 protein binding GO:0005515 1/4 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.
bqt2 protein binding GO:0005515 1/4 IPI rap1
poz1 protein binding GO:0005515 1/4 IPI rap1
rap1 protein binding GO:0005515 2/4 IPI taz1
rap1 protein binding GO:0005515 1/4 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 1/4 IPI poz1
rap1 protein binding GO:0005515 1/4 IPI bqt1
rap1 protein binding GO:0005515 1/4 IPI bqt2
taz1 protein binding GO:0005515 2/4 IPI rap1
cdc2 protein serine/threonine kinase activity GO:0004674 2/4 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.
taz1 telomeric DNA binding GO:0042162 1/4 TAS happens_during mitotic G2 phase (GO:0000085)
Biological Process Annotations
taz1 mitotic telomere tethering at nuclear periphery GO:0044820 3/4 IGI-2, IMP-2 (one set of annotations notes both) bqt4 during mitotic G2 phase (GO:0000085)
bqt4 mitotic telomere tethering at nuclear periphery GO:0044820 4/4 IGI-1, IMP-3 taz1 during mitotic G2 phase (GO:0000085) (2/4 included)
rap1 mitotic telomere tethering at nuclear periphery GO:0044820 3/4 IPI-1, IMP-3 bqt4 during mitotic G2 phase (GO:0000085) (2/4 included) one curator did both IMP and IGI
rap1 positive regulation of mitotic telomere tethering at nuclear periphery GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 positive regulation of mitotic telomere tethering at nuclear periphery GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 positive regulation of attachment of telomere to nuclear envelope GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 negative regulation of mitotic telomere tethering at nuclear periphery GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 negative regulation of attachment of telomere to nuclear envelope GO:new 1/4 IMP happens_during mitotic G2 phase (GO:0000085)
rap1 positive regulation of chromosome segregation GO:0051984 1/4 IC 1. negative regulation of mitotic telomere tethering at nuclear periphery 2. negative regulation of attachment of telomere to nuclear envelope happens_during mitotic M phase (GO:0000087)
cdc2 negative regulation of mitotic telomere tethering at nuclear periphery GO:1904537 1/4 IGI rap1 during mitotic M phase (GO:0000087)
cdc2 negative regulation of protein binding GO:0032091 1/4 IMP has_input-rap1|has_input-bqt4
nda3  ??  ?? 1/4  ?? 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 2/4 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 2/4 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 postive regulation of peptidyl-serine phosphorylation GO:0033138 1/4 IMP has_regulation_target rap1:Q96TL7; part_of negative regulation of mitotic telomere tethering at nuclear periphery; happens_during GO:0000087 mitotic M phase
cdc2 mitotic sister chromatid segregation GO:0000070 1/4 IC GO:1904537????????
taz1 protection from non-homologous end joining at telomere GO:0031848 1/4 IMP
taz1  ??  ?? 1/4  ?? Not sure if the overexpression constructs are suficient evidence to annotate taz1 to GO:0044820, mitotic telomere tethering at nuclear periphery
taz1  ??  ?? 1/4  ?? Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation.
taz1 attachment of telomere to nuclear envelope GO:0070197 1/4 IMP (or IGI) bqt4 (for IGI) during mitotic G2 phase (GO:0000085)
bqt4 attachment of telomere to nuclear envelope GO:0070197 1/4 IMP during mitotic G2 phase (GO:0000085)
rap1 attachment of telomere to nuclear envelope GO:0070197 1/4 IMP during mitotic G2 phase (GO:0000085)
taz1 chromosome segregation GO:0007059 1/4 IMP during mitotic M phase (GO:0000087)
bqt4 chromosome segregation GO:0007059 1/4 IMP during mitotic M phase (GO:0000087)
Cellular Component Annotations
taz1 nuclear chromosome, telomeric region GO:0000784 2/4 IDA exists_during mitotic G2 phase (GO:0000085) (1 included) 1 included colocalizes_with
ish1 nuclear envelope GO:0005635 2/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with
atb2 microtubule GO:0005874 2/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with (and used synonym tub1)
bqt4 nuclear envelope GO:0005635 2/4 IDA exists_during mitotic M phase (GO:0000087) 1 included) 1 included colocalizes_with
bqt4 nuclear envelope GO:0005635 1/4 IMP colocalizes_with; author states: 'Strong punctate signals of Taz1-GFP-Bqt4DN were observed at the NE throughout the cell cycle'
taz1 nuclear envelope GO:0005635 1/4 IDA colocalizes_with