Annotation Conf. Call 2015-09-22

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