​https://sourceforge.net/apps/trac/pombase/wiki/CuratorTrainingPapers

Papers needing ODA conversions
Papers with WT info or no annotations

21727087	Antonia
dmr1 (ppr3)	mitochondrial translation phenotype, less translation of mt proteins	allele=deletion
various	add missing phenotype alleles

21745468	Antonia
lkh1, dsk1	((phenotype)) slow cell growth (cell growth assay)	allele=Δdsk1Δlkh1
lkh1, dsk1	((phenotype)) slow cell growth (cell growth assay)	allele=Δdsk1,lkh1-K391A
lkh1	abnormal protein localization to cytoplasm	allele=K391A, in minimal media

17369611	Antonia
rtt109	Delta rtt109/Histone H3 K56R double-mutant phenotype	asynthetic sensitivity to DNA damage

2900761	Antonia
mat2-P...or mat2-Pc/Pi?	Silenced (waiting for GeneDB to update cassette info so this can be annotated)	IMP mat1-
mat3-M...or mat3-Mc/Mi?	Silenced (waiting for GeneDB to update cassette info so this can be annotated)	IMP mat1-
mat1-Mi	Phenotype: can conjugate but not undergo meiosis/sporulate	allele=Mifs15(del_nt43-129)
mat1-Pi	Phenotype: can conjugate but not undergo meiosis/sporulate	allele=Piop7(del_nt19-357)
mat1-Pc	Phenotype: can't conjugate	allele=Pcop5(del_nt17-480)
mat1-Mc	Phenotype: can't conjugate	allele=Mcop7(del_nt19-546)
mat1-Pc	severe reduction in spore formation	allele=deletion
mat1-Pc	process: required for efficient meiosis	IMP, allele=deletion
mat1-Mc	process: required for efficient meiosis	IMP, allele=deletion

mat1-Pc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Pc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Mc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Mc	expression: constitutively expressed (low levels) (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Pi	expression: not expressed (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Pi	expression: not expressed (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
mat1-Mi	expression: not expressed (rich media)	IMP, allele=SP272(h+/h- meiotically competent diploid)
mat1-Mi	expression: not expressed (rich media)	IMP, allele=SP720(fus1 deletion...capture as WT?)
All 4 are upregulated in response to nitrogen starvation. In diploid; downregulation at 6h compared to 4h, in haploid; no downregulation

2328719	Antonia
map1	transcription phenotype, target is not upregulated in response to nitrogen starvation	allele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-PC,(strain is H90))
mat1-Pc	positive autoregulation of transcription in response to nitrogen starvation	allele=mat1-Pc-161()
map1	transcription phenotype, target is not expressed in response to nitrogen starvation	allele=deletion,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
mat1-Pc	transcription phenotype, target is not expressed in response to nitrogen starvation	allele=mat1-Pc-161(),annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm,(strain is H90))
mat1-Pc	low constitutive expression in rich media	allele=H90(fus1 deletion)
mat1-Pm	no constitutive expression in rich media	allele=H90(fus1 deletion)
mat1-Pm	expression in response to nitrogen starvation is dependent on the presence of CL:0002674	annotation_extension=occurs_in(CL:0002675)
mat1-Pc	upregulation in response to nitrogen starvation is not dependent on the presence of CL:0002674	annotation_extension=occurs_in(CL:0002675)
ran1	process: negative regulation of transcription from RNA polymerase II promoter during mitosis (IMP evidence code)	allele=pat1-114,annotation_extension=has_regulation_target(GeneDB_Spombe:mat1-Pm, mat1-Mc and Mat1-Pc

17452352
sequence feature	annotate AACCCT as a GATA transcription factor binding site, seq 5'-ATCA(C/A)AACCCTAACCCT-3'	do we annotate this on the genome sequence?

18077559|Antonia
ams2 hip1	slow cell growth	allele=dbl mutant

20230746	Antonia
ams2	remove NAS and TAS from artemis
ams2	protein is unstable during G2 and M phase, partially stable during G1 and stable during S
ams2	protein stability: is stable during S phase, level increased
ams2	protein stability: is unstable during G2 phase, level decreased OR possibly only synthesised during S phase?
ams2	protein stability: is unstable during G1/M phase, level increased OR possibly only synthesised during S phase?
ams2	protein stability: is degraded by the SCF ubiquitin ligase pathway
ams2	allele=overexpression(overexpression and allele=deletion(deletion)...correct way of writing this is?

18158900	Antonia
double mutant	sim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed cnp1 = normal phenotype
double mutant	sim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed H4 = normal phenotype
double mutant	sim3 mutants (allele=143(G81E),allele=205(E207K)) + overexpressed H3 = reduced viability (inviable ok)
sim3	go biological process: protein localization to kinetochore	annotation_extension=does not happens_during G1

cnb1,ppb1	dbl deletion mutant same phenotype as each single mutant (branched,elongated multi-septate cells + slow growth in presence of mgcl2	worth annotating? i.e. shows may be linked perhaps? dbl mutant not more severe
cnb1,ppb1,pmp1	dbl del + overexpressed = normal cell growth
cnb1,ppb1	deletion,overexpr. slow growth in presence of mgcl2	i.e. large amounts of catalytic domain is not functional without regulatory subunit. is this interesting to capture?
cnb1,ppb1∆C(L445->STOP	deletion,overexpressed. slow growth in presence of mgcl2	constitutively active mutant is not active without regulatory subunit
cnb1,ppb1∆C(L445->STOP	overexpressed,overexpressed. phenotype growth arrest, round small bent pear-shaped cells. depolarized distr of cortical F-actin patches	normal phenotype in presence of CHEBI:61049
cnb1,ppb1∆C(L445->STOP,prz1	overexpressed,overexpressed, deleted. no growth arrest

20018864	Antonia
deletion(prz1), overexpression(ncs1)	slow growth	cell growth assay
deletion(ncs1), overexpression(prz1)	slow growth	cell growth assay
deletion(prz1), overexpression(ncs1)	inviable in_response_to(CHEBI:29108)	IMP
deletion(ncs1), overexpression(prz1)	inviable in_response_to(CHEBI:29108)	IMP
deletion(ncs1),deletion(yam8)	normal cell growth in_presence_of(CHEBI:33120	cell growth assay
ncs1	promoter region lies in -1-130 region caact esp important
ncs1	promoter for upregulation in response to calcium lies in -101-130 region
ncs1	promoter for basal expression lies in -1-130 region
prz1	binds caact in promoter region of ncs1

19606215	Antonia
cnx1	dbl mutant phenotype: abnormal cell wall morphology	allele=lumenal_cnx1p(aa_del488-560),allele=C-termTM_Cnx1p_cmyc(aa_del1-415)
cnx1	some confusing data regarding apoptosis. Notes in hardcopy paper	allele=lumenal_cnx1p(aa_del488-560)
cnx1	allele specifications may not be 100% correct

18621924	Antonia
cyr1,cgs1 dbl deletion	nuclear export abolished	allele=deletion,annotation_extension=localizes(GeneDBSpombe:SPBC106.10)

12557273	Antonia
pik3-/pik3-	spore germination abolished, abnormal spore morphology	occurs in diploid, allele=homozygous?
pik3-/pik3+	FYPO:0000579 normal spore germination	add this with either CL:0000415 + allele=heterozygous or more specific CL if given
pik3	have requested 2 process terms from GO +ve regulation of protein targeting to vacuolar membrane GO:1900485	termgenie..

9191269	Antonia
plc1	qualifier in genedb for binding:"N-term", not clear if it binds N-term or if it binds via N-term"

map3/mam2

diploid strain (CL:0000415) cannot sporulate if both receptors expressed at the same time

1563351	Antonia
MatPi?	expressed in response to nitrogen starvation and M factor in Pcells	IDA
ste6	MatPi? not expressed during N starvation and in presence of M factor in P cells	allele=deletion
ras1	MatPi? not expressed during N starvation and in presence of M factor in P cells	allele=deletion
ras1	MatPi? expressed during N starvation and in presence of M factor in P cells, not constitutively expressed	allele=ras1val17
pat1/ras1	mat1-Pm transcribed	allele=pat1-114/deletion, at high temp
pat1/ste6	mat1-Pm transcribed	allele=pat1-114/deletion, at high temp

[BR]

8196631	Antonia
mfm1/mfm2	FYPO:0000584 decreased sporulation	allele=deletion (both)
mfm1/mfm3	FYPO:0000584 decreased sporulation	allele=deletion (both)
mfm2/mfm3	FYPO:0000584 decreased sporulation	allele=deletion (both)
mfm1/mfm2/mfm3	FYPO:0000583 sporulation abolished	allele=deletion (all 3)
mfm1/mfm2/mfm3	FYPO:0000583 sporulation abolished	allele=deletion (all 3),annotation_extension=in_presence_of(M-factor - externally added),annotation_extension=occurs_in:CL0002674
mfm1/mfm2/mfm3	FYPO:0000590 normal sporulation	allele=deletion (all 3),annotation_extension=occurs_in:CL0002674

7975894	Antonia
gpa1	phenotype: increased expression of MatPi? during nitrogen starvation; constitutively active. Pheromone doesn't influence transcription	Q244L
ras1	phenotype: increased expression of Matpi during nitrogen starvation in the presence of pheromone	G17V
mat1Pm/pi	promoter element mapped in paper -61- -41 (ccctctttctttgttccttat

8314086	Antonia
sxa2	expressed in presence of p-factor
map2	expressed in H- cells
cyr1/sxa2	phenotype G1 arrest in presence of P-factor in rich media	allele=deletion
cyr1/sxa2	abnormal/increased shmoo formation in presence of P-factor in rich media	allele=deletion

18059475	Antonia
fkh2/fhl1	reduced zygote formation	allele=deletion
fkh2/mei4	reduced zygote formation	allele=deletion
fkh2/fhl1/mei4	reduced zygote formation	allele=deletion
ste11	annotate promoter proximal element FLEX1 and FLEXL1 to ste11, artemis
cig2/fkh2	increased zygote formation	allele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/fhl1	reduced zygote formation	allele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/mei4	reduced zygote formation	allele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)
cig2/fkh2/fhl1/mei4	reduced zygote formation	allele=deletion,happens_during(GO:0006995 - cellular response to nitrogen starvation)

10867006	Antonia
ste11	Unable to bind DNA region outside of the consensus motif	ste91

15580593	Antonia
mam2	negative regulation of pheromone INDEPENDENT signal transduction. TG: neg reg of GO:0038034. If I can't get this term from GO then use negative regulation of signal transduction involved in conjugation with cellular fusion + add the extension "in absence of P-factor" (occurs in M-cells)
Mam2 mutants	phenotype: constitutively active (if term goes in	M cells

15659165	Antonia
mam2	negative regulation of pheromone INDEPENDENT signal transduction. TG: neg reg of GO:0038034. Sequesters G alpha. If I can't get this term from GO then use negative regulation of signal transduction involved in conjugation with cellular fusion + add the extension "in absence of P-factor" (occurs in M-cells)
mam2/gpa1	interaction evidence is wrong, but it's the best fit....should I not curate this? I think the evidence is pretty strong

21118960
srw1	another phenotype: decreased cell cycle arrest in response to pheromone	allele=mutPste9(A->C and G-> T and vice versa throughout 27 bp reb1 binding region -198 - -172
srw1	decreased sporulation	mutPste9
srw1 ectopically expressed | reb1 deletion	normal cell cycle arrest in response to pheromone	phenotype
reb1|wee1	phenotype: slow growth at high temperature	allele=deletion(reb1)/wee1-50
reb1|wee1	phenotype: multiseptate (0000118)	allele=deletion(reb1)/wee1-50
reb1|wee1	phenotype: wee	allele=deletion(reb1)/wee1-50
reb1|wee1	phenotype: spheroid cells	allele=deletion(reb1)/wee1-50
reb1|wee1	phenotype: DNA content increased	allele=deletion(reb1)/wee1-50
reb1|wee1	phenotype: normal cell growth at high temperature	in_presence_of:CHEBI:44423, allele=deletion(reb1)/wee1-50
reb1|cdc10	phenotype: slow growth at high temperature	allele=deletion(reb1)/cdc10-129
reb1|cdc10	phenotype: abnormal? cell cycle arrest	qualifier=at_high_temperature,allele=deletion(reb1)/cdc10-129
reb1	change cell cycle arrest in mitotic G1 phase to "increased rate of"	allele=overexpression

9427748
deletion ppb1|overexpression pmp1	suppresses salt stress sensitivity
deletion pmp1|expression of const. active ppb1deltaC (C-term truncated)	suppresses salt stress sensitivity
deletion pmp1|expression of const. active ppb1deltaC (C-term truncated)	suppresses FK506 sensitivity
deletion pmp1|expression of ppb1 overexpressed	sensitive to salt stress and FK506
deletion pmp1|deletion ppb1|deletion pmk1	normal cell growth
deletion ppb1|deletionpmk1	filamentous and multiseptate	allele=deletion
deletion ppb1|overexpression pmp1	normal morphology

11461899
stm1	early G1 arrest in response to nitrogen starvation	allele=deletion,flow cytometry
stm1|ras1	absence of G1 arrest in response to nitrogen starvation	allele+deletion (both) flow cytometry
stm1|ras1	slow cell growth in minimal media containing ammonia nitrogen source	allele=deletion (both) cell growth assay
stm1|gpa2	normal cell growth in minimal media containing ammonia nitrogen source	annotation_extension=condition(overexpression - stm1)allele=deletion (gpa2) cell growth assay
stm1|gpa2	normal septation	annotation_extension=condition(overexpression - stm1)allele=deletion (gpa2) cell growth assay

21960007
mag1	structure PDB ID 3S61	according to authors, does not appear to match however

1448087
pyp2	552 bp 5' UTR
pyp1|pyp2	inviable germinating spore	allele=deletion (both)
pyp1 cdc25	cell cycle arrest	annotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_normal_temperature)
pyp2 cdc25	cell cycle arrest	annotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_normal_temperature)
pyp1 cdc25	cell cycle arrest	annotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_high_temperature)
pyp2 cdc25	cell cycle arrest	annotation_extension=condition(overexpression, pyp1), allele=cdc25-22, anotation_extension=condition(at_high_temperature)

pyp1 cdc2	normal cell length (cell division/cell cycle)	annotation_extension=condition(overexpression, pyp1), allele=cdc2-1w
pyp2 cdc2	normal cell length (cell division/cell cycle)	annotation_extension=condition(overexpression, pyp1), allele=cdc2-1w
pyp1 wee1	elongated cells	annotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_normal_temperature)
pyp2 wee1	elongated cells	annotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_normal_temperature)
pyp1 wee1	normal cell length (possibly could use normal cell growth or normal cell division/mitotic cell cycle	annotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_high_temperature)
pyp2 wee1	normal cell length (possibly could use normal cell growth or normal cell division/mitotic cell cycle	annotation_extension=condition(overexpression, pyp1), allele=wee1-50, anotation_extension=condition(at_high_temperature)

pyp1 cdc25	normal cell length	allele=deletion, pyp1), allele=cdc25-22, annotation_extension=condition(at_normal_temperature)
pyp2 cdc25	elongated cells	allele=deletion, pyp1), allele=cdc25-22, annotation_extension=condition(at_normal_temperature)
pyp1 cdc25	elongated cells	allele=deletion, pyp1), allele=cdc25-22, annotation_extension=condition(at_high_temperature)

16884933
gnr1	decresed sensitivity to pheromone/increased maximum efficacy of response	annotation_extension=condition(overexpression)
git5	normal sensitivity to pheromone/increased maximum efficacy of response	allele=deletion
git5	decresed sensitivity to pheromone/increased maximum efficacy of response	annotation_extension=condition(overexpression)

11470243
fas2	increased accumulation of see below	allele=H201(I1276T),annotation_extension=condition(at_high_temperature)
fas2	increased accumulation of see below	allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
fas2	increased accumulation of see below	allele=H518(I600N),annotation_extension=condition(at_high_temperature)

fas2	decreased accumulation of see below	allele=H201(I1276T),annotation_extension=condition(at_high_temperature)
fas2	decreased accumulation of see below	allele=H265(Q4Y),annotation_extension=condition(at_high_temperature)
fas2	decreased accumulation of see below	allele=H518(I600N),annotation_extension=condition(at_high_temperature)

For the 3 mutants above:
increased accumulation of at high temp: N-monomethyldioleoyl-PE (N-monomethyl-C18:1-C18:1-PE) N,N-dimethyl-C18:1-C18:1-PE N,N-monomethyl-C18:1-C18:1-PE N,N-dimethyl-C16:1-C18:1-PE 1-melissoyl-oleolyl-sn-glycero-3-phosphoethanolamine (C30:0-C18:1-PE) 1-melissoyl-2-oleolyl-sn-glycero-3-phosphocholine (C30:0-C18:1-PC) CHEBI:16337 CHEBI:36711

decreased accumulation of at high temp: (NOT in mutant 518) 1-oleolyl-2-caproyl-sn-glycero-3-phosphocholine (C18:1-C10:0-PC) C18:0-C10:0-PC C18:0-C8:0-PC CHEBI:18303 CHEBI:17517

15075260
pdf1	annotated inviable germinating spore but should it really be inviable spore?	allele=deletion

pdf1	dbl mutant normal growth in presence of sodium orthovanadate	allele=S106A(S106A),allele=H478A(H478A) (2 plasmids)
pdf1	dbl mutant normal growth in presence of sodium orthovanadate	allele=D226A(D226A),allele=H478A(H478A) (2 plasmids)
pdf1	dbl mutant normal growth in presence of 'near alkaline/high' pH (=condition?)	allele=S106A(S106A),allele=H478A(H478A) (2 plasmids)
pdf1	dbl mutant normal growth in presence of 'near alkaline/high' pH (=condition?)	allele=D226A(D226A),allele=H478A(H478A) (2 plasmids)

9017391
gcs1 + ade6	sensitive to cadmium	allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6	sensitive to cadmium	allele=deletion,allele=ade6-210(unknown))
gcs1 + ade6	normal growth in presence of either ions: Ca|Na|Mg	allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6	normal cell growth	annotation_extension=condition(in_rich_media),allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6	resistant to MNNG (N-methyl-N'-nitro-N-nitrosoguanidine)	allele=deletion,allele=ade6-210(unknown))|

gcs1 + ade6	slow cell growth	annotation_extension=condition(in_minimal_media),allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6	slow cell growth	annotation_extension=condition(in_minimal_media),allele=deletion,allele=ade6-210(unknown)
gsh2 + ade6	slow cell growth	annotation_extension=condition(in_minimal_media),allele=deletion,allele=ade6-210(unknown)
hmt1 + ade6	normal cell growth	annotation_extension=condition(in_minimal_media),allele=deletion,allele=ade6-210(unknown)

gcs1 + ade6	normal cell growth	annotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6	normal cell growth	annotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=deletion,allele=ade6-210(unknown)
gsh2 + ade6	normal cell growth	annotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=deletion,allele=ade6-210(unknown)

gcs1 + ade6	sporulation abolished	allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6	normal sporulation	annotation_extension=in_presence_of(CHEBI:16856),allele=apd1-1(unknown),allele=ade6-210(unknown)

ade6	red pigmentation of colonies	allele=ade6-210(unknown)
hmt1 + ade6	red pigmentation of colonies	allele=deletion,allele=ade6-210(unknown)
gcs1 + ade6	absent/reduced red pigmentation of colonies	allele=apd1-1(unknown),allele=ade6-210(unknown)
gcs1 + ade6	absent/reduced red pigmentation of colonies	allele=deletion,allele=ade6-210(unknown)
gsh2 + ade6	reduced red pigmentation of colonies	allele=deletion,allele=ade6-210(unknown)
gcs1 + ade6	absent/reduced red pigmentation of colonies	annotation_extension=condition(in_minimal_media),annotation_extension=in_presence_of(CHEBI:16856),allele=apd1-1(unknown),allele=ade6-210(unknown)
ade6	reduced red pigmentation of colonies	annotation_extension=in_presence_of(CHEBI:46442),allele=ade6-210(unknown)

1448066
ade2/ade6	dbl mutant sensitive to cadmium	allele=ade6-216(unknown),allele=ade2(deletion), growth assay
ade2/ade7	dbl mutant sensitive to cadmium	allele=ade7-50(unknown),allele=ade2(deletion), growth assay
-	asked for a term to describe HMW complex. Link to it
ade2/ade6	dbl mutant can't accumulate HMW PC-Cd-S2- complex	allele=ade6-216(unknown),allele=ade2(deletion)
ade2/ade7	dbl mutant can't accumulate HMW PC-Cd-S2- complex	allele=ade7-50(unknown),allele=ade2(deletion)
-	asked for a term to describe HMW complex. Link to it - GO:0090424

12905027
SPAC3H1.10	MOD requested: cadmium containing modified residue	residue=C173|

19001374	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/211be4406f38d208
hmt1	is involved in the transport of PC2 but NOT PC3 or PC4 into vacuoles	IMP
hmt1	cadmium ion import into vacuole

9016341
ade2 + ade7	sensitive to cisplatin	allele=deletion (ade2) allele=ade7.50
ade2 + ade6	sensitive to cisplatin	allele=deletion (ade2) allele=ade6.216

16928959
perhaps should use +ve reg of transcr instead of calcium response for the var agents		go over again

19646873
gef1delta + orb6-25	normal morphology at high temp	microscopy
rga4 overexpressed + orb6-25	normal morphology at high temp	microscopy
Gef1 overexpression + orb6-as2	stubby PCO:0000005 at normal temp
orb6-25 + rga4delta	stubby at normal temp PCO:0000005

19285552
rgs1	decreased transcriptional response in response to pheromone	allele=noname(overexpression),​​annotation_extension=occurs_in(CL:0002674)
gpa1	can probably migrate some terms to abnormal decrease in transcription/increase, see what midori says

20396879
dak1/dak2 dbl mut	normal cell growth	allele=dak1-delta(deletion),allele=dak2-delta(deletion),condition=PCO:0000014
dak1/dak2	decreased glycerol dehydrogenase activity	allele=dak1-delta(deletion),allele=dak2-delta(deletion),condition=PCO:0000072
dak1/dak2	increased accumulation of DHA	allele=dak1-delta(deletion),allele=dak2-delta(deletion),condition=PCO:0000072
dak1/dak2	slow aerobic cell growth	allele=dak1-delta(deletion),allele=ak2-delta(deletion),condition=PCO:0000072
dak1/dak2/gld1	abolished glycerol dehydrogenase activity	allele=dak1-delta(deletion),allele=dak2-delta(deletion),allele=gld1-delta(deletion),condition=PCO:0000072
dak1/dak2	slow aerobic cell growth	allele=dak1-delta(deletion),allele=ak2-delta(deletion),condition=PCO:0000073
dak1/dak2	slow aerobic cell growth	allele=dak1-delta(deletion),allele=ak2-delta(deletion),condition=PCO:0000076,condition=PCO:0000014
tup11/tup12	increased glycerol dehydrogenase activity	allele=tup11-delta(deletion),allele=tup12-delta(deletion),condition=PCO:0000014
gld1/dak1/dak2	slow cell growth	allele=noname(overexpression),condition=PCO:0000077

9585505
atf1 + pap1	sensitive to cisplatin	allele=atf1-delta(deletion), allele=pap1-delta(deletion), condition=PCO:0000012, CGA

1448080
crm1 + pap1	normal growth at cold /or/ normal cell growth condition=low temp	allele=crm1-809(unknown),allele=pap1-delta(deletion),PCO:0000012
crm1 + pap1	sensitive to staurosporine	allele=crm1-809(unknown),allele=pap1-delta(deletion),PCO:0000012
crm1 + pap1	normal protein accumulation	allele=crm1-809(unknown),allele=pap1-delta(deletion),annotation_extension=has_regulation_target(PomBase:SPAC3C7.14c)

7642144
rpn11| pmd1	resistant to K-252a	allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1	resistant to staurosporine	allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1	resistant to vanadate	allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1	resistant to cycloheximide	allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1	resistant to actinomycin D	qualifier=NOT, allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012
rpn11| pmd1	resistant to thiabendazole	qualifier=NOT, allele=pmd1-delta(deletion),allele=noname(overexpression),​condition=PCO:0000012

21324894
cia1 | mts2	increased protein level	allele=asf1-30(F24S,​G120S,​D173G), allele=mts2-1(unknown), condition=PCO:0000004,annotation_extension=has_regulation/downstream_target(PomBase:SPCC663.05c), western
cia1 | mts2	slow growth	allele=asf1-30(F24S,​G120S,​D173G), allele=mts2-1(unknown), condition=PCO:0000005, condition=PCO:0000012, CGA
cia1 | mts2	slow growth at high temp	allele=asf1-30(F24S,​G120S,​D173G), allele=mts2-1(unknown), condition=PCO:0000012, CGA
cia1 | ubc4	slow growth	allele=asf1-30(F24S,​G120S,​D173G), allele=ubc4ts(P61S), condition=PCO:0000005, condition=PCO:0000012, CGA
cia1 | ubc4	slow growth at high temp	allele=asf1-30(F24S,​G120S,​D173G), allele=ubc4ts(P61S), condition=PCO:0000012, CGA

cia1 + mts2

FYPO:0000783, cia1 normally found in nucleus, but here found in cytoplasm

allele=asf1-30(F24S,​G120S,​D173G),allele=mts2-1(unknown), condition=PCO:0000004, specify cia in annex? has_target cia1?

cia1 | ubc4	increased protein level	allele=asf1-30(F24S,​G120S,​D173G), allele=ubc4ts(P61S), condition=PCO:0000004,annotation_extension=has_regulation/downstream_target(PomBase:SPCC663.05c), western
cia1 | SPBC2A(.04C	increased protein level	allele=asf1-30(F24S,​G120S,​D173G), allele=san1-delta(deletion), condition=PCO:0000004,annotation_extension=has_regulation/downstream_target(PomBase:SPCC663.05c), western

cia1 | hrd1	slow growth at normal temp	allele=asf1-30(F24S,​G120S,​D173G),allele=hrd1-delta(deletion), condition=PCO:0000012
cia1 | hrd1	slow growth at high temp	allele=asf1-30(F24S,​G120S,​D173G),allele=hrd1-delta(deletion), condition=PCO:0000012
cia1 | doa10	slow growth at normal temp	allele=asf1-30(F24S,​G120S,​D173G),allele=doa10-delta(deletion), condition=PCO:0000012
cia1 | doa10	slow growth at high temp	allele=asf1-30(F24S,​G120S,​D173G),allele=doa10-delta(deletion), condition=PCO:0000012

cia1 | san1	normal cell growth	allele=asf1-30(F24S,​G120S,​D173G),allele=san1-delta(deletion), condition=PCO:0000012, condition=PCO:0000006
cia1 | san1	slow growth at high temp	allele=asf1-30(F24S,​G120S,​D173G),allele=san1-delta(deletion), condition=PCO:0000012
cia1 | ubr1	normal cell growth	allele=asf1-30(F24S,​G120S,​D173G),allele=ubr1-delta(deletion), condition=PCO:0000012, condition=PCO:0000006
cia1 | ubr1	slow growth at high temp	allele=asf1-30(F24S,​G120S,​D173G),allele=ubr1-delta(deletion), condition=PCO:0000012
cia1 | ubr11	normal cell growth	allele=asf1-30(F24S,​G120S,​D173G),allele=ubr11-delta(deletion), condition=PCO:0000012, condition=PCO:0000006
cia1 | ubr11	slow growth at high temp	allele=asf1-30(F24S,​G120S,​D173G),allele=ubr11-delta(deletion), condition=PCO:0000012
SPBC2A9.04c | mis12	normal cell growth at high temp	allele=san1-delta(deletion),allele=mis12-537(unknown), condition=PCO:0000012, condition=PCO:0000012
SPBC2A9.04c | pim1	normal cell growth at high temp	allele=san1-delta(deletion),allele=pim1-46(unknown), condition=PCO:0000012, condition=PCO:0000012
SPBC2A9.04c | cnp1	normal cell growth at high temp	allele=san1-delta(deletion),allele=cnp1-1(unknown), condition=PCO:0000012, condition=PCO:0000012

9191271
mfm1	dbl check annotations, allele descr for phenotype annotation	has_regulation_target(PomBase:SPMTR.02))

19366728
SF ITEM	​https://sourceforge.net/tracker/?func=detail&aid=3521043&group_id=65526&atid=2096431
end4	normal nuclear / medial cortex morphology during nitrogen starvation	allele=end4-507(G73D), condition=PCO:0000098, microscopy
end4	abnormal nuclear / medial cortex morphology during nitrogen starvation	allele=end4-507(G73D), condition=PCO:0000097, microscopy

8321236	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/169dc6a662075c56/gene/1
frp1	abolished ferric iron reductase activity, not req yet	allele=G-100(W314->opal)
waiting reply from val on paper

7565608	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/07cc7abfbaa6d1b0
rds1	cellular response to adenine starvation, term req	IMP - IEP is more appropriate perhaps..
ade genes	for FYPO:0000825 annotation add 'during cellular response to adenine starvation' term req	don't add for cyr1
rds1	/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(cellular response to adenine starvation); qualifier=increased; evidence=ECO:0000106; db_xref=7565608; date=20120504"

9135147	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/67ba83cbaba024a7
pmk1	GO:1900529 Label: regulation of cell shape involved in cellular response to glucose starvation	IMP
pmk1	GO:1900530 Label: regulation of cell shape involved in cellular response to salt stress	IMP
pmk1	GO:1900531 Label: regulation of cell shape involved in cellular response to heat	IMP
pmk1	increased cell wall thickness	allele=pmk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
pmk1	delaminate cell wall	allele=pmk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
pmk1	normal arrest in g1 during nitrogen starvation see ​https://sourceforge.net/tracker/index.php?func=detail&aid=3524737&group_id=65526&atid=2096431	allele=pmk1delta(deletion)
pmk1	normal arrest in g2 during glucose starvation see ​https://sourceforge.net/tracker/index.php?func=detail&aid=3524737&group_id=65526&atid=2096431	allele=pmk1delta(deletion)
pmk1 | spk1	sterile	allele=pmk1delta(deletion), allele=spk1delta(deletion)
pmk1 | spk1	abnormal morphology	allele=pmk1delta(deletion), allele=spk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
pmk1 | spk1	normal response to salt stress	allele=pmk1delta(deletion), allele=spk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
spk1	GO:1900532 Label: negative regulation of cell proliferation involved in cellular hyperosmotic response	IMP
byr1	GO:1900532 Label: negative regulation of cell proliferation involved in cellular hyperosmotic response	IMP
wis1 | pmk1	multiseptate	microscopy, allele=wi1delta(deletion), allele=pmk1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
pck2	increased protein phosphorylation	allele=pck2delta(deletion),​​ annotation_extension=assayed_using(PomBase:SPBC119.08),​​ annotation_extension=happens_during(GO:0072690)

1644306	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1b8ed217ce984ab5
tnr1	increased RNA level, northern evidence, need to find what this gene is...	allele=tnr1-18(unknown), annotation_extension=assayed_using(SPBC26H8.01),​ condition=PCO:0000014,​ annotation_extension=happens_during(GO:0071301)
tnr1	cellular response to vitamin b1 - which gene is this??	IMP
thi2	gene expression: expressed in response to thiamine starvation. repressed in response to thiamine....

/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0036225); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"

/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(GO:0071301); qualifier=absent; evidence=ECO:0000106; db_xref=1644306; date=20120509"

/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:16892); qualifier=increased; evidence=ECO:0000106; db_xref=1644306; date=20120509"

/controlled_curation="term=gene expression, mRNA level; annotation_extension=in_response_to(CHEBI:17957); qualifier=decreased; evidence=ECO:0000106; db_xref=1644306; date=20120509"

7499352	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/5cbe479087353d2f
tnr3	increased thiamine level, chromatography evidence - requested form eco: ​http://code.google.com/p/evidenceontology/issues/detail?can=2&start=0&num=100&q=&colspec=ID%20Type%20Status%20Priority%20Owner%20Summary&groupby=&sort=&id=2	allele=pho1-44delta(deletion), allele=tnr3-10(unknown)
tnr3	increased thiamine level	allele=pho1-44delta(deletion), allele=tnr3-5(unknown)
tnr3	increased thiamine level	allele=pho1-44delta(deletion), allele=tnr3-1(unknown)
pho4	cellular response to thiamine starvation	IMP

8675019	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/4b0970d0e5484486/
tnr1	which gene is this? FYPO:0000825 northern ev	allele=tnr1-18(unknown), condition=PCO:0000014, annotation_extension=assayed_using(SPAC17A2.01)
bsu1	cellular response to thiamine starvation	IMP
thi3 | bsu1	slow aerobic cell growth	allele=bsu1delta(deletion), allele=thi3-1(unknown), condition=PCO:0000014, condition=PCO:0000106
thi3 | bsu1	slow aerobic cell growth	allele=bsu1delta(deletion), allele=thi3-1(unknown), condition=PCO:0000014, condition=PCO:0000107

2249257

​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/40213c281e540075

/controlled_curation="term=gene expression, mRNA level; annotation_extension=during(cellular response to thiamine starvation); qualifier=increased; evidence=ECO:0000106; db_xref=2249257; date=20120510"

2020549

​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/1ff0297254ee616d

9560432	​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/de924eb687e556b7
itr2 | itr1	normal cell growth	allele=IM49(unknown),​​ allele=itr1-noname(overexpression), condition=PCO:0000005,​​ condition=PCO:0000014,​​ condition=PCO:0000102,​ condition=PCO:0000111
itr1	carbohydrate import into cell	IMP
itr1	normal myo-inositol import into cell	allele=itr1delta(deletion)
itr2	decreased myo-inositol import into cell	allele=IM49(unknown), condition=PCO:0000014, condition=PCO:0000005, condition=PCO:0000103

9401022	​http://curation.pombase.org/pombe/curs/bbcbdad5461798f3
bgs1	normal response to papulacandin B	allele=cps1-12, condition=PCO:0000005, condition=PCO:0000012, condition=PCO:0000034 | allele=cps1-12, condition=PCO:0000005, condition=PCO:0000025
bgs1	increased glucan synthase activity	allele=cps1-12(unknown) | allele=cps1-12, condition=PCO:0000115
bgs1	increased alpha-glucan level	allele=cps1-12
bgs1	normal beta-glucan level	allele=cps1-12
bgs1	normal galactomannan level	allele=cps1-12

9710608
fnx1	resistant to heat shock	allele=noname(overexpression), condition=PCO:0000014, condition=PCO:0000103
atf1	normal RNA level during nitrogen starvation	allele=atf1delta(deletion),annotation_extension=assayed_using(PomBase:SPBC12C2.13c), condition=PCO:0000014, condition=PCO:0000103
ste11	normal RNA level during nitrogen starvation	allele=aff1(unknown),annotation_extension=assayed_using(PomBase:SPBC12C2.13c), condition=PCO:0000014, condition=PCO:0000103
cyr1	normal RNA level during nitrogen starvation	allele=cyr1delta(deletion),annotation_extension=assayed_using(PomBase:SPBC12C2.13c), condition=PCO:0000014, condition=PCO:0000103
pde1	normal RNA level during nitrogen starvation	allele=cgs2-2(unknown),annotation_extension=assayed_using(PomBase:SPBC12C2.13c), condition=PCO:0000014, condition=PCO:0000103
fnx1	normal response to heat shock	allele=fnx1delta(deletion), condition=PCO:0000014
fnx1	sensitive to amitrole	allele=fnx1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
fnx1	sensitive to 4-nitroquinoline N-oxide	allele=fnx1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
fnx1	normal cellular response to CCCP	allele=fnx1delta(deletion), condition=PCO:0000014, condition=PCO:0000102
fnx1	normal cellular response to crystal violet	allele=fnx1delta(deletion), condition=PCO:0000014, condition=PCO:0000102

22245228	​http://curation.pombase.org/pombe/curs/7b18cacb1717e352
trx1	increased protein level	allele=trx1delta(deletion), annotation_extension=assayed_using(tpx1-tpx1 disulfide/s) western
trx1	increased protein level during cellular response to hydrogen peroxide Western	allele=trx1delta(deletion), annotation_extension=assayed_using(tpx1-tpx1 disulfide/s)
trx1	decreased protein level during cellular response to hydrogen peroxide western	allele=trx1delta(deletion), annotation_extension=assayed_using(tpx1 hyperoxidised)

trx1	increased protein level	allele=trx1delta(deletion), annotation_extension=assayed_using(oxidised pap1) western
trx1	increased protein level during cellular response to hydrogen peroxide Western	allele=trx1delta(deletion), annotation_extension=assayed_using(oxidised pap1)

tpx1	increased protein level	allele=tpx1delta(deletion), annotation_extension=assayed_using(reduced trx1)
tpx1	increased protein level during cellular response to hydrogen peroxide	allele=tpx1delta(deletion), annotation_extension=assayed_using(reduced trx1)
tpx1	decreased protein level	allele=tpx1delta(deletion), annotation_extension=assayed_using(oxidised trx1)
tpx1	decreased protein level during cellular response to hydrogen peroxide	allele=tpx1delta(deletion), annotation_extension=assayed_using(oxidised trx1)

tpx1	increased protein level during cellular response to hydrogen peroxide	allele=C169S(C169S), annotation_extension=assayed_using(reduced trx1)
tpx1	decreased protein level during cellular response to hydrogen peroxide	allele=C169S(C169S), annotation_extension=assayed_using(oxidised trx1)

trx1	remove annex to homeostasis if I get smth for protein reduction
trx1	protein reduction IMP	annotation_extension=has_regulation_target(PomBase:SPCC576.03c),​ annotation_extension=happens_during(GO:0070301) |​ annotation_extension=has_regulation_target(PomBase:SPCC576.03c),​ annotation_extension=happens_during(GO:0072690) |​ annotation_extension=has_regulation_target(PomBase:SPAC29E6.05c),​ annotation_extension=happens_during(GO:0072690) |​ annotation_extension=has_regulation_target(PomBase:SPAC29E6.05c),​ annotation_extension=happens_during(GO:0070301) |​ annotation_extension=has_regulation_target(PomBase:SPAC1783.07c),​ annotation_extension=happens_during(GO:0070301) |​ annotation_extension=has_regulation_target(PomBase:SPAC1783.07c) annotation_extension=happens_during(GO:0072690)

tpx1	increased protein level during cellular response to hydrogen peroxide	allele=noname(overexpression), annotation_extension=assayed_using(tpx1-tpx1	disulfide/s)
tpx1	increased protein level during cellular response to hydrogen peroxide	allele=1-181(del_1-181), annotation_extension=assayed_using(tpx1-tpx1	disulfide/s)
tpx1	decreased protein level during cellular response to hydrogen peroxide	allele=1-181(del_1-181), annotation_extension=assayed_using(tpx1 reduced)
tpx1	decreased protein level during cellular response to hydrogen peroxide	allele=1-181(del_1-181), annotation_extension=assayed_using(tpx1 hyperoxidised)

tpx1	decreased protein level during cellular response to hydrogen peroxide	allele=1-181(del_1-181), annotation_extension=assayed_using(trx1 reduced)
tpx1	increased protein level during cellular response to hydrogen peroxide	allele=1-181(del_1-181), annotation_extension=assayed_using(mrx1 oxidised)
tpx1	increased protein level during cellular response to hydrogen peroxide	allele=1-181(del_1-181), annotation_extension=assayed_using(trx1 trx1 containing disulfides)

tpx1 | srx1

normal cellular response to hydrogen peroxide

allele=srx1(overexpression), allele=tpx1(deletion)

1828464	​http://curation.pombase.org/pombe/curs/1999a5fbfad09eed/
bgs4	increased cell wall apha-glucan level (child of FYPO:0000990)	allele=cwg1-1(unknown), condition=PCO:0000004
bgs4	decreased cell wall beta-glucan level (child of FYPO:0000990)	allele=cwg1-1(unknown), condition=PCO:0000004
cwg2	decreased cell wall apha-glucan level (child of FYPO:0000990)	allele=cwg2-1(unknown), condition=PCO:0000004
cwg2	decreased cell wall beta-glucan level (child of FYPO:0000990)	allele=cwg2-1(unknown), condition=PCO:0000004
bgs4	decreased glucosyltransferase activity	allele=cwg1-1(unknown), condition=PCO:0000004
cwg2	decreased glucosyltransferase activity	allele=cwg2-1(unknown), condition=PCO:0000004
bgs4	normal glucosyltransferase activity	allele=cwg1-1(unknown), condition=PCO:0000005, condition=PCO:0000115
cwg2	normal glucosyltransferase activity	allele=cwg2-1(unknown), condition=PCO:0000005, condition=PCO:0000115

10380645	​http://curation.pombase.org/pombe/curs/26776deaeb7536ef
ctt1	increased resistance to hydrogen peroxide	CGA allele=noname(overexpression), liquid, 30 degrees
ctt1	abolished catalase activity	enzyme assay allele=deletion

18279662	​http://curation.pombase.org/pombe/curs/9276d468f83256bf
png	misfolded glycoprotein binding	IDA

9287302
pgr1	increased increased glutathione-disulfide reductase activity enzyme assay data	WT overexpression
pgr1	resistant to menadione	CGA, WT overexpression, YES, normal temp, agar plates
pap1	decreased glutathione-disulfide reductase activity	allele=deletion
pap1	decreased glutathione-disulfide reductase activity	allele=overexpression
pap1	need to req term: positive regulation of transcription from RNA polymrase II promoter in response to salt stress	IMP annotation_extension=has_regulation_target(PomBase:SPBC17A3.07)
pap1	need to req term: positive regulation of transcription from RNA polymrase II promoter in response to menadione stress	IMP annotation_extension=has_regulation_target(PomBase:SPBC17A3.07)
pgr1	inviable germinating spore, multiple cell divisions	allele=deletion, yes, agar
pgr1	inviable germinating spore, multiple cell divisions	allele=deletion, yes, agar, GSH added
pgr1	inviable germinating spore, multiple cell divisions	allele=deletion, yes, agar, N-acetyl-L-cysteine added
pgr1	increased level of GSSG in cell, enzyme assay data	allele=knockdown, minimal liquid media
pap1	increased level of GSSG in cell, enzyme assay data	allele=deletion, liquid

missing annotations

​http://oliver0.sysbiol.cam.ac.uk/pombe/curs/219e86a87274fe5f/ro/

HTP gene expression data
15004206	for future ref
19366728	table 3 + gene expression omnibus GEOhashGSE14319	for future ref

misc to add

positive reg of protein targeting to vacuolar membrane