to wee or not to wee - Githubissues

ValWood commented 6 years ago

review of wee

ValWood commented 6 years ago

These will be wee wee1 cpc2 cdr2 sgf73 srk1 pyp1

these will stay at the parent term: spp1 ace2 fkh2 atf1 dml1 loz1 mcs4 mak1 plb1 rad3 rad9 sck2 tor2 tsc2 sak1

ValWood commented 6 years ago

mas5 the annotation to small needs deleting

int6 goes to the new term that will be a sibling of the "wee" term

lkh1 I wrote "reannotate" but did not say to what.

@JackyVH could you glance through the lists above and see if it looks correct?

ValWood commented 4 years ago

this isn't difficult but there are Loads of annotations... I'm wondering if it might be quicker to

automagically move everything to the wee term, and then manually move back the non-wee ones (its a smaller gene set, and I suspect there will be fewer alleles and annotations)

ValWood commented 4 years ago

Hi KIm,

Could you migrate all annotations to

FYPO:0000645 | small vegetative cell and FYPO:0000648 | viable small vegetative cell

to FYPO:0006822 then I will move back the smaller number to the correct parent.

Let me know when you plant to do it so I. can be sure. that I can put a couple of hours aside to do the fixes.

kimrutherford commented 4 years ago

Could you migrate all annotations to

Are these annotation in Canto?

ValWood commented 4 years ago

Hmm, they could be in Artemis. There should not be many in Artemis. I will probably deleted these and prioritise the papers. I will check in a sec.

ValWood commented 3 years ago

some are in phaf_format_phenotypes.tsv I can deal with these.

phaf_format_phenotypes.tsv:SPAC1782.09c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 clp1delta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPAC26F1.10c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 pyp1delta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPAC30C2.06c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 dml1delta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPBC106.10 FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 pka1delta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPBC16H5.07c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 ppa2delta deletion Microscopy PECO:0000005,PECO:0000137 FYPO_EXT:0000001 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPBC1718.07c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 zfs1delta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPBC30B4.04c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 sol1delta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPCC126.04c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 sgf73delta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPCC18.17c FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 SPCC18.17cdelta deletion Microscopy PECO:0000005,PECO:0000137 PMID:23697806 4896 20120101 phaf_format_phenotypes.tsv:SPCC18B5.03 FYPO:0000648 deletion Null 975 h+ SP286 h+ ura4-D18 leu1-32 ade6-M210 wee1delta deletion Microscopy PECO:0000005,PECO:0000137 FYPO_EXT:0000001 PMID:23697806 4896 20120101 grep: phenotype_mapping_old: Is a directory

ValWood commented 3 years ago

also

PMID_15797925_phaf.tsv:SPBC1734.11 FYPO:0000648 deletion null 972 h- deletion microscopy PECO:0000005 PMID:15797925 4896 2017-03-23 PMID_23695302_phaf.tsv:SPAC25B8.19c FYPO:0000648 wild type overexpression 972 h- h- leu1-32 wild type microscopy PMID:23695302 4896 2015-02-12 PMID_23695302_phaf.tsv:SPAC6G10.12c FYPO:0000648 wild type overexpression 972 h- h- leu1-32 wild type microscopy PMID:23695302 4896 2015-02-12

mah11 commented 3 years ago

my share: update ID in PHAFs for wee1, cpc2, cdr2, sgf73, srk1

mah11 commented 3 years ago

did my bit

kimrutherford commented 3 years ago

I got a bit confused on the call. Is this all still the plan?:

Could you migrate all annotations to FYPO:0000645 | small vegetative cell and FYPO:0000648 | viable small vegetative cell to FYPO:0006822 then I will move back the smaller number to the correct parent.

Are there any exceptions? Should this be applied to all genes and annotations in Canto?

ValWood commented 3 years ago

Hi, sorry for the delay. I got side-tracked. This is still the plan.

It applies to any annotation in Canto or Artemis (there should not be any in Artemis) Midori has done the PHAF files.

v

kimrutherford commented 3 years ago

That's done now. In case it's useful, here's what changed:

fypo_term_log.txt

ValWood commented 3 years ago

OK I moved up the ones I do not think are wee. I'll review tomorrow and ask Jacky

ValWood commented 2 years ago

reviewed with @JackyVH

wee annotations that need to be checked

[ ] mid1
[ ] rax2
[ ] mei4 (possibly ectopically expressed in motosis?)
[ ] ace2
[ ] cbf11
[ ] lkh1 (check, but looks OK
[ ] alp41
[ ] ypt1
[ ] ypt2
[ ] cka1
[ ] ptc3
[ ] int6 (note above says int6 goes to the new term that will be a sibling of the "wee" term)
[ ] prp2

wee annotation to remove

[x] mnn9
[ ] mob2 (this might be OK?)
[x] rho1
[x] cpc2

viable small cell to check

[ ] cyr1 might be wee?
[ ] rad3
[ ] fkh2 and sak1 (Garg)
[ ] loz2
[ ] gls1
[ ] mas5 (not above says annotation to small needs deleting)
[ ] aml1

pombase / curation

to wee or not to wee #2085