Annotation Conf. Call 2015-09-22: Difference between revisions
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m (→Annotation Summary: fix table) |
(→Annotation consistency exercise: added one more set) |
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Line 34: | Line 34: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| | | 3/4 | ||
| IPI | | IPI | ||
| bqt4 | | bqt4 | ||
Line 44: | Line 44: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| | | 3/4 | ||
| IPI | | IPI | ||
| rap1 | | rap1 | ||
Line 54: | Line 54: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| 1/ | | 1/4 | ||
| IPI | | IPI | ||
| bqt2, rap1 | | bqt2, rap1 | ||
| | | | ||
| Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data. | | 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 | | bqt2 | ||
Line 64: | Line 74: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| 1/ | | 1/4 | ||
| IPI | | IPI | ||
| bqt1, rap1 | | bqt1, rap1 | ||
| | | | ||
| Not sure if this is the correct representation, or if this should be a protein complex annotation. This is the Y3H data. | | 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 | | poz1 | ||
Line 74: | Line 94: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| 1/ | | 1/4 | ||
| IPI | | IPI | ||
| rap1 | | rap1 | ||
Line 84: | Line 104: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| | | 2/4 | ||
| IPI | | IPI | ||
| taz1 | | taz1 | ||
Line 94: | Line 114: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| 1/ | | 1/4 | ||
| IPI | | IPI | ||
| bqt1, bqt2 | | bqt1, bqt2 | ||
Line 104: | Line 124: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| 1/ | | 1/4 | ||
| IPI | | IPI | ||
| poz1 | | poz1 | ||
| | |||
| | |||
|- | |||
| rap1 | |||
| | |||
| protein binding | |||
| GO:0005515 | |||
| 1/4 | |||
| IPI | |||
| bqt1 | |||
| | |||
| | |||
|- | |||
| rap1 | |||
| | |||
| protein binding | |||
| GO:0005515 | |||
| 1/4 | |||
| IPI | |||
| bqt2 | |||
| | | | ||
| | | | ||
Line 114: | Line 154: | ||
| protein binding | | protein binding | ||
| GO:0005515 | | GO:0005515 | ||
| | | 2/4 | ||
| IPI | | IPI | ||
| rap1 | | rap1 | ||
| | |||
| | |||
|- | |||
| taz1 | |||
| | |||
| telomeric DNA binding | |||
| GO:0042162 | |||
| 1/4 | |||
| TAS | |||
| happens_during mitotic G2 phase (GO:0000085) | |||
| | | | ||
| | | | ||
Line 134: | Line 184: | ||
| mitotic telomere tethering at nuclear periphery | | mitotic telomere tethering at nuclear periphery | ||
| GO:0044820 | | GO:0044820 | ||
| | | 3/4 | ||
| IGI- | | IGI-2, IMP-2 (one set of annotations notes both) | ||
| bqt4 | | bqt4 | ||
| during mitotic G2 phase (GO:0000085) | | during mitotic G2 phase (GO:0000085) | ||
Line 144: | Line 194: | ||
| mitotic telomere tethering at nuclear periphery | | mitotic telomere tethering at nuclear periphery | ||
| GO:0044820 | | GO:0044820 | ||
| | | 4/4 | ||
| IGI-1, IMP- | | IGI-1, IMP-3 | ||
| taz1 | | taz1 | ||
| during mitotic G2 phase (GO:0000085) (2/ | | during mitotic G2 phase (GO:0000085) (2/4 included) | ||
| | | | ||
|- | |- | ||
Line 154: | Line 204: | ||
| mitotic telomere tethering at nuclear periphery | | mitotic telomere tethering at nuclear periphery | ||
| GO:0044820 | | GO:0044820 | ||
| | | 3/4 | ||
| IPI-1, IMP- | | IPI-1, IMP-3 | ||
| bqt4 | | bqt4 | ||
| during mitotic G2 phase (GO:0000085) (2/ | | during mitotic G2 phase (GO:0000085) (2/4 included) | ||
| one curator did both IMP and IGI | | 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 | | cdc2 | ||
Line 164: | Line 274: | ||
| negative regulation of mitotic telomere tethering at nuclear periphery | | negative regulation of mitotic telomere tethering at nuclear periphery | ||
| GO:1904537 | | GO:1904537 | ||
| 1/ | | 1/4 | ||
| IGI | | IGI | ||
| rap1 | | rap1 | ||
Line 174: | Line 284: | ||
| negative regulation of protein binding | | negative regulation of protein binding | ||
| GO:0032091 | | GO:0032091 | ||
| 1/ | | 1/4 | ||
| IMP | | IMP | ||
| | | | ||
Line 184: | Line 294: | ||
| protein serine/threonine kinase activity | | protein serine/threonine kinase activity | ||
| GO:0004674 | | GO:0004674 | ||
| 2/ | | 2/4 | ||
| IDA | | IDA | ||
| | | | ||
Line 194: | Line 304: | ||
| ?? | | ?? | ||
| ?? | | ?? | ||
| 1/ | | 1/4 | ||
| ?? | | ?? | ||
| | | | ||
Line 204: | Line 314: | ||
| peptidyl-serine phosphorylation | | peptidyl-serine phosphorylation | ||
| GO:0018105 | | GO:0018105 | ||
| 2/ | | 2/4 | ||
| IGI-1, IMP-1 | | IGI-1, IMP-1 | ||
| rap1 | | rap1 | ||
Line 214: | Line 324: | ||
| peptidyl-threonine phosphorylation | | peptidyl-threonine phosphorylation | ||
| GO:0018107 | | GO:0018107 | ||
| 2/ | | 2/4 | ||
| IGI-1, IMP-1 | | IGI-1, IMP-1 | ||
| rap1 | | rap1 | ||
| during mitotic M phase (GO:0000087) | | 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)? | | 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 | | cdc2 | ||
Line 224: | Line 344: | ||
| mitotic sister chromatid segregation | | mitotic sister chromatid segregation | ||
| GO:0000070 | | GO:0000070 | ||
| 1/ | | 1/4 | ||
| IC | | IC | ||
| GO:1904537???????? | | GO:1904537???????? | ||
Line 234: | Line 354: | ||
| protection from non-homologous end joining at telomere | | protection from non-homologous end joining at telomere | ||
| GO:0031848 | | GO:0031848 | ||
| 1/ | | 1/4 | ||
| IMP | | IMP | ||
| | | | ||
Line 244: | Line 364: | ||
| ?? | | ?? | ||
| ?? | | ?? | ||
| 1/ | | 1/4 | ||
| ?? | | ?? | ||
| | | | ||
Line 254: | Line 374: | ||
| ?? | | ?? | ||
| ?? | | ?? | ||
| 1/ | | 1/4 | ||
| ?? | | ?? | ||
| | | | ||
| | | | ||
| Not sure if this observation [minichromosome loss] should lead to a 'regulation of mitotic sister chromatid segregation' type of annotation. | | 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 | ! Cellular Component Annotations | ||
Line 274: | Line 444: | ||
| nuclear chromosome, telomeric region | | nuclear chromosome, telomeric region | ||
| GO:0000784 | | GO:0000784 | ||
| | | 3/4 | ||
| IDA | | IDA | ||
| | | | ||
| | | exists_during mitotic G2 phase (GO:0000085) (1 included) | ||
| | | 1 included colocalizes_with | ||
|- | |- | ||
| ish1 | | ish1 | ||
Line 284: | Line 454: | ||
| nuclear envelope | | nuclear envelope | ||
| GO:0005635 | | GO:0005635 | ||
| | | 3/4 | ||
| IDA | | IDA | ||
| | | | ||
| | | exists_during mitotic G2 phase (GO:0000085)|exists_during mitotic M phase (GO:0000087) 1 included) | ||
| | | 1 included colocalizes_with | ||
|- | |- | ||
| atb2 | | atb2 | ||
Line 294: | Line 464: | ||
| microtubule | | microtubule | ||
| GO:0005874 | | GO:0005874 | ||
| | | 3/4 | ||
| IDA | | IDA | ||
| | | | ||
| exists_during mitotic G2 phase (GO:0000085)|exists_during mitotic M phase (GO:0000087) 1 included) | |||
| 1 included colocalizes_with (and used synonym tub1) | |||
|- | |||
| bqt4 | |||
| | | | ||
| nuclear envelope | |||
| GO:0005635 | |||
| 3/4 | |||
| IDA | |||
| | | | ||
| exists_during mitotic G2 phase (GO:0000085)|exists_during mitotic M phase (GO:0000087) 1 included) | |||
| 1 included colocalizes_with | |||
|- | |- | ||
| bqt4 | | bqt4 | ||
Line 304: | Line 484: | ||
| nuclear envelope | | nuclear envelope | ||
| GO:0005635 | | GO:0005635 | ||
| 1/ | | 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 | | IDA | ||
| | | | ||
| | | | ||
| | | colocalizes_with | ||
|-|} | |-|} |
Revision as of 10:19, 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 | 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 | |||
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 | |||
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. | ||
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 | 3/4 | IDA | exists_during mitotic G2 phase (GO:0000085) (1 included) | 1 included colocalizes_with | ||
ish1 | nuclear envelope | GO:0005635 | 3/4 | IDA | exists_during mitotic M phase (GO:0000087) 1 included) | 1 included colocalizes_with | ||
atb2 | microtubule | GO:0005874 | 3/4 | IDA | exists_during mitotic M phase (GO:0000087) 1 included) | 1 included colocalizes_with (and used synonym tub1) | ||
bqt4 | nuclear envelope | GO:0005635 | 3/4 | 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 |