Annotation Conf. Call 2015-09-22: Difference between revisions
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** not_happens_during | ** not_happens_during | ||
** During | ** During | ||
<font color = "red">Discussion</font><br> | |||
* 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== | ==Annotation consistency exercise== | ||
Pombe paper <br> | Pombe paper <br> | ||
http://www.ncbi.nlm.nih.gov/pubmed/22959349 | http://www.ncbi.nlm.nih.gov/pubmed/22959349 | ||
<font color = "red">Discussion</font><br> | |||
* 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=== | ===Annotation Summary=== | ||
{| {{Prettytable}} | {| {{Prettytable}} | ||
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| colocalizes_with | | colocalizes_with | ||
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Latest revision as of 14:41, 22 September 2015
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 |