Standardize allele names

[ValWood]

These are the only alleles where we have allowed a "." separator post gene name instead of a -

rad15.P
hus5.62
hus5.17
brr6.ts8
rad26.a14
cdc2.RL-GBP
sad1.1
sad1.2
ade8.106
ade7.50
cut12.s11
xlf1.AA
xlf1.EE(T180E,S192E)
srp7.1
I suggest we standardise these to hyphens and make the . version exact synonym for consistency.
Also needs to apply to associated multi-gene alleles
@kimrutherford perhaps you could automate this?

These are odd too, discus or @PCarme refactor
fep1-p.CCAAT
cgs2-p.CRE-mut
ARG.10-TATA-

[ValWood]

srp7.1 is OK its a transcript (this is the main reason we want to eradicate the use in Protein alleles)

[ValWood]

I picked a paper to test from the only author who uses "." but we don't want to add new alleles with "." separators
The instructions have if an allele isn't already in the allele file, name using current convention and put the "." name in the synonym space.

[kimrutherford]

srp7.1 is OK its a transcript

It's also an allele name.

[ValWood]

Right, we should fix that too and make this a synonym as it will cause confusion down the line (or already!)

[kimrutherford]

As a first step, here are the sessions for each of those alleles. I can't see these allele names in any of the input PHAF files so it's just Canto that needs to be updated.

session	allele_name	type	description	gene
23b994e637b6f0cc	ade7.50	unknown	NONE	SPBC409.10

session	allele_name	type	description	gene
23b994e637b6f0cc	ade8.106	unknown	unknown	SPBC14F5.09c

session	allele_name	type	description	gene
42ad3cde8bd52174	brr6.ts8	amino acid substitution(s)	C194G	SPAC8F11.06
48d935f12b87d5c6	brr6.ts8	amino acid substitution(s)	C194G	SPAC8F11.06
4b79f8edcf2340db	brr6.ts8	amino acid substitution(s)	C194G	SPAC8F11.06

session	allele_name	type	description	gene
c717e2d7ee7b8ded	cdc2.RL-GBP	fusion or chimera	GBP-fused Cdc2-F84G-Y15F	SPBC11B10.09

session	allele_name	type	description	gene
014aa031f039268b	cut12.s11	unknown	NONE	SPBC649.05
21507585ab1a2dfc	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
27524319ad84c25c	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
50345fb1226215ae	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
6356242fe0e335bd	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
97c70bbdfd19df1d	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
abbc849e1c0c5544	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
acd1a2d2ddcf29cc	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
e5a15cdcd4aa21c4	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
e7cc68a1da978b38	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05
f96ee693f519ef9d	cut12.s11	amino acid substitution(s)	G71V	SPBC649.05

session	allele_name	type	description	gene
697b0dd703952f05	hus5.17	nucleotide substitution(s)	G253T	SPAC30D11.13
b20fa4124e6891de	hus5.17	nucleotide substitution(s)	G253T	SPAC30D11.13

session	allele_name	type	description	gene
238d4f23ca2cdcd5	hus5.62	amino acid substitution(s)	A129V	SPAC30D11.13
9d68bc80736f1fb4	hus5.62	amino acid substitution(s)	A129V	SPAC30D11.13
a8245a213e3baa92	hus5.62	amino acid substitution(s)	A129V	SPAC30D11.13
b20fa4124e6891de	hus5.62	amino acid substitution(s)	A129V	SPAC30D11.13

session	allele_name	type	description	gene
0633f4467e41f64b	rad15.P	unknown	unknown	SPAC1D4.12
9d68bc80736f1fb4	rad15.P	unknown	unknown	SPAC1D4.12
ab4820f788afe927	rad15.P	unknown	unknown	SPAC1D4.12

session	allele_name	type	description	gene
062ae65578cd43ea	rad26.a14	amino acid insertion	C510CNPLIVC	SPAC9E9.08

session	allele_name	type	description	gene
420a5c4d2fd025ad	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
48d935f12b87d5c6	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
4b79f8edcf2340db	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
5c30b3bf5c5da95c	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
79d476e92beb688e	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
7bbe318b26434db4	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
9079e758e75e287f	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
b0c3bd95702f2fcc	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
e28e479729269ce9	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01
f895d3b39398c5aa	sad1.1	amino acid substitution(s)	A323V	SPBC12D12.01

session	allele_name	type	description	gene
9079e758e75e287f	sad1.2	amino acid substitution(s)	T3S,S52P	SPBC12D12.01
b1bc10e390be46c7	sad1.2	amino acid substitution(s)	T3S,S52P	SPBC12D12.01
c717e2d7ee7b8ded	sad1.2	amino acid substitution(s)	T3S,S52P	SPBC12D12.01

session	allele_name	type	description	gene
c23b5043b024b0a5	xlf1.AA	amino acid substitution(s)	T180A,S192A	SPCC24B10.14c

session	allele_name	type	description	gene
c23b5043b024b0a5	xlf1.EE(T180E,S192E)	amino acid substitution(s)	T180E,S192E	SPCC24B10.14c

[kimrutherford]

Did you fix "srp7.1" already?:
https://curation.pombase.org/pombe/curs/065a5d3851a4f583/genotype_manage/ro

[ValWood]

no....

[ValWood]

I feel so bad changing these. But they really are mainly from a single author.

in the paper we say this:
Periods (“.”) have been used interchangeably in place of hyphens (“-”) in allele short names (e.g. cut12.s11). Although existing alleles will not be renamed, new allele short names should observe hyphens as separators and periods should be used in certain allele names of genes with multiple transcripts (see previous section), or as described in Table 3. Underscores are not allowed in allele variant short names and will be changed to hyphens in existing names with the original names retained as synonyms.

so maybe we should retain this batch. Except cdc2.RL-GBP which is quite new, and I have used - for in another publication. I'm on the fence here so lets wait to see what @PCarme thinks. I'll explain more on a call.

[kimrutherford]

so maybe we should retain this batch.

These two are the only ones that could possibly be confused with transcript names:

• sad1.1
• sad1.2

[kimrutherford]

Did you fix "srp7.1" already?:
https://curation.pombase.org/pombe/curs/065a5d3851a4f583/genotype_manage/ro

no....

Looks like srp7.1 was fixed to srp7-1 on the 16th.

Where did you get the list at the top of this issue?

[ValWood]

Ah OK, I have been slowly fixing things in the logs where gene names don't have hyphens. I must have done this before I started buiding the agent using a paper which used dots in allele names! I'm sure I got the list from the allele names file here https://www.pombase.org/datasets/ai_and_ml_training_datasets

these 2 things must have happened a day a part from different contexts.

[kimrutherford]

OK, that makes sense. The links on that page go to the most recent release from July 1st. This is last night's allele list:
https://curation.pombase.org/dumps/latest_build/misc/all_alleles.tsv