allele comments vs. genotype comments

ValWood commented 2 years ago

Follow on from https://github.com/pombase/website/issues/1916

The 'allele comment' is a fairly recent thing., Historically we put "allele comments' in the genotype comments field. I suspect 99.9% of single allele genotype comments are actually allele comments (and probably genotype comments is not used much, but I am not sure about that).

Could we get a list of

single allele genotype comments
multi-allele genotype comments to confirm this and then decide if we need to migrate single allele genotype comments to allele comments

kimrutherford commented 2 years ago

These are both tab separated files:

single_locus_genotype_comments.tsv.txt

multi_locus_genotype_comments.tsv.txt

ValWood commented 2 years ago

All of the single locus genotype comment are really single allele comments except for:

I don't understand this comment?

[ ] nda3-TB101-Y50S-amino_acid_mutation-expression-wild_type_product_level drug efflux pathways dismantled (MDR-suppressed)

Unecessary

[ ] tco1Ldelta--1790−-1250::ura4+-nucleotide_mutation-expression-wild_type_product_level nt -1790 to -1250 replaced with ura4+
[ ] dhp1+-expression-knockdown promoter switch-off
[ ] spg1+(wild_type)-expression-knockdown nmt-promoter, thiamine repressible
[ ] rgf3+-expression-knockdown P81nmt promoter
[ ] cnd3+-expression-knockdown conditional depletion
[ ] sad1+-expression-overexpression moderate

Need discussion

[ ] nak1*-orb6-Nterm-GPF-Nak1-K39R-Orb6-Cterm_fusion-other-expression-not_assayed nak1+ and orb6+ wild type product levels
[ ] spg1+(wild_type)-expression-overexpression G2-arrested
[ ] nak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayed nak1+ and orb6+ wild type product levels

Ectopic localisation phenotype

[ ] rga4delta622-760-blt1-fusion-rga4delta622-760-blt1-fusion-other-expression-overexpression cytoplasm localised
[ ] pac1-AA-Anchor-away-other-expression-not_assayed nuclear excluded
[ ] pfh1-m21-M21A-amino_acid_mutation-expression-knockdown nuclear localization reduced

Other Phenotype

[ ] sle1delta Increased cortical tubular ER dynamics

Degron https://github.com/pombase/curation/issues/3319

[ ] cdc20+-expression-knockdown cdc20+ with auxin-inducible degron tag
[ ] cdc23-tstd-fusion_C239Y,AA424::TEV,degron-other-expression-not_assayed DHFR degron

Chimera follow https://github.com/pombase/curation/issues/3321

[ ] myo2-LT-+_myp2-aa1622-2104-amino_acid_insertion-expression-wild_type_product_level chimeric protein

Fix https://github.com/pombase/curation/issues/2930

[ ] atg43delta created for PMID:33138913, NOT bioneer. OK but need to address (create different deletion /remove pioneer)

ValWood commented 2 years ago

So, we will fix the above, and everything for single allele can migrate to be an allele comment" Do we need to maintain allele comments outside of Canto?

ValWood commented 2 years ago

multi locus geneotype comments

Comment seem as though they belong on one of the contributing alleles (although comment could be inherited)

[ ] nse4-L68C-L68C-amino_acid_mutation-expression-not_assayed__smc5-E995Q-E995Q-amino_acid_mutation-expression-not_assayed non-hydrolyzable ATP
[ ] byr4delta__mob1-R4-unknown-unknown-expression-not_assayed byr4::ura4+
[ ] mik1delta__rum1+(wild_type)-expression-overexpression__wee1-50-G850E-amino_acid_mutation-expression-not_assayed rum1 nmt promoter
[ ] cdk9-T120G-T120G-amino_acid_mutation-expression-not_assayed__ssu72-C13S-C13S-amino_acid_mutation-expression-not_assayed analogue sensitive
[ ]cut7+(wild_type)-expression-wild_type_product_level__cut7-ST-1-443-partial_amino_acid_deletion-expression-not_assayed deleted head domain
[ ] poz1delta__rad3-D2249E-D2249E-amino_acid_mutation-expression-not_assayed kinase-dead cdc42+-expression-overexpression__esh2-1-P612S-amino_acid_mutation-expression-not_assayed reported as P611S in PMID:15546915
[ ] esh2-1-P612S-amino_acid_mutation-expression-not_assayed__rho1+-expression-overexpression reported as P611S in PMID:15546915
[ ] rad11-D223Y-D223Y-amino_acid_mutation-expression-wild_type_product_level__rad3-D2249E-D2249E-amino_acid_mutation-expression-not_assayed kinase dead
[ ] pyp1deltapyp2deltasty1-T97A-T97A-amino_acid_mutation-expression-not_assayed__wis1-DD-S469D,T473D-amino_acid_mutation-expression-not_assayed (stress-independent Sty1 activation
[ ] cdc13+(wild_type)-expression-wild_type_product_level__cdc13delta1-67-1-67-partial_amino_acid_deletion-expression-wild_type_product_level nondegradable cyclin B

Phenotype

[ ] sle1deltatts1deltayop1delta Increased cortical tubular ER dynamics
[ ] rtn1delta__sle1delta Increased cortical tubular ER dynamics
[ ] sey1delta__sle1delta Increased cortical tubular ER dynamics
[ ] pho2delta__pho8delta the pho8 deletion has decreased alkaline phosphatase activity in high zinc conditions

Not required

[ ] alg10-183-stop-183-stop-nonsense_mutation-expression-not_assayed__gls1delta alg10 supressor mutation

Comment does not make sense

[ ] ccr1delta__ppb1deltaC-unknown-unknown-expression-not_assayed Constitutively active

Chimera not usually a multi -allele genotype?

[ ] myo2-ST-+myp2-aa1923-2104-amino_acid_insertion-expression-wild_type_product_level__myp2delta chimeric protein
[ ] myo2-LT-+_myp2-aa1622-2104-amino_acid_insertion-expression-wild_type_product_level__myp2delta chimeric protein

TeV fusion not usually a multi -allele genotype?

[ ] cnp3C-TEV-cnp3C-TEV-other-expression-not_assayed__plo1-TEVAA341-tev-site@AA341-other-expression-wild_type_product_level protease inactivated

Look like a single allele genotypes?

[ ] cdc27-R5-nt_930-1102_duplicated__translated_product_has_aa_1-271_plus_24_aa_from_different_reading_frame-other-expression-wild_type_product_level nt 930-1102 duplicated; translated product has aa 1-271 plus 24 aa from different reading frame
[ ] gar2::ura4+-disruption__Gar2_aa_1-163,Ura4_aa_1-39-disruption-expression-not_assayed Gar2 aa 1-163,Ura4 aa 1-39
[ ] cdc27-R22-nt_C_inserted_after_782__translated_product_has_aa_1-164_plus_12_aa_from_different_reading_frame-other-expression-wild_type_product_level nt C inserted after 782; translated product has aa 1-164 plus 12 aa from different reading frame
[ ]. cdc27-R39-nt_807-828_duplicated__translated_product_has_aa_1-179_plus_4_aa_from_different_reading_frame-other-expression-wild_type_product_level nt 807-828 duplicated; translated product has aa 1-179 plus 4 aa from different reading frame

Degron should be represented in single allele description

[ ] pol1+-expression-knockdown__spp2+-expression-knockdown pol1+ with auxin-inducible degron tag,spp2+ with auxin-inducible degron tag
[ ] cdc20-ct1deltaN-1-1217,Y1520N,D1625G,L1726S,S1904P-amino_acid_deletion_and_mutation-expression-not_assayedpol1+-expression-knockdownspp2+-expression-knockdown spp2+ with auxin-inducible degron tag| - [ ] spp2+ with auxin-inducible degron tag

True genotype comment

[ ] alg10delta__gls1delta worse growth than \"healthy\" gls1delta

P81nmt should be in allele name:

[ ] rgf1+-expression-knockdown__rgf2delta P81nmt-rgf1rgf2delta

Discuss nak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayedpmo25-35-T236A-nucleotide_mutation-expression-not_assayed nak1+ and orb6+ wild type product levels mor2-786-A1673G-nucleotide_mutation-expression-not_assayednak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayed nak1+ and orb6+ wild type product levels cdc3-124-E43K-amino_acid_mutation-expression-not_assayednak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayed nak1+ and orb6+ wild type product levels nak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayedorb6-25-unknown-unknown-expression-not_assayed nak1+ wild type product level nak1-167-unknown-unknown-expression-not_assayednak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayed orb6+ wild type product level nak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayedsid2-250-unknown-unknown-expression-not_assayed nak1+ and orb6+ wild type product levels cdc16-116-unknown-unknown-expression-not_assayed__cdc3-124-E43K-amino_acid_mutation-expression-not_assayed__nak1-orb6-Nterm-GPF-Nak1-Orb6-Cterm_fusion-other-expression-not_assayed nak1+ and orb6+ wild type product levels

dcr1delta__med31-ins-F23-LVRIC-amino_acid_insertion-expression-not_assayed hypomorphic Med31 allele from Dicer G0 suppressor screen par1delta__spg1-106-unknown-unknown-expression-not_assayed loss of function

ValWood commented 2 years ago

We can discuss this. Once your part is done (we can decide when we speak) this ticket can transfer to the curation tracker for the tidy up.

kimrutherford commented 2 years ago

So, we will fix the above, and everything for dingle allele can migrate to be an allele comment" Do we need to maintain allele comments outside of Canto?

We could move them to pombe-embl/supporting_files/allele_comments.txt or we could enable adding comments as allele notes in Canto like FlyBase do, then move them inside Canto to be notes.

kimrutherford commented 9 months ago

Put off until we have allele page, then discuss.

Curators will then need to review the comments.

pombase / website

allele comments vs. genotype comments #1919