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Quality control for PomBase alleles
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Update to new nomenclature #79

Closed manulera closed 1 year ago

kimrutherford commented 1 year ago

Hi @manulera

What do I need to do for this issue?

manulera commented 1 year ago

Hi @kimrutherford. Sorry for the empty issue. This is to update descriptions once I have a file migrating from the current nomenclature to the new one, so similar to #76, but with more alleles.

I will write in detail once the file is ready.

manulera commented 1 year ago

Hi @kimrutherford, there is a new set of changes in this file that contain the migration to the new syntax:

https://github.com/pombase/allele_qc/blob/master/manual_fixes_pombase/allele_auto_fix_old2new.tsv

And a few minor manual fixes:

https://github.com/pombase/allele_qc/blob/master/manual_fixes_pombase/unknowns_with_correct_descriptions.tsv

If you can integrate those, we are done with migration to the new syntax.

kimrutherford commented 1 year ago

Hi Manu. I tried applying both file on my desktop copy on the Canto database. It all looks good. I'll apply the fixes to the main pombe Canto tonight (UK/Spanish time).

manulera commented 1 year ago

🥳🥳🥳

kimrutherford commented 1 year ago

I'll apply the fixes to the main pombe Canto tonight (UK/Spanish time).

That's done in time for the nightly load.

manulera commented 1 year ago

Hi Kim,

It seems that the changes did not go through, but actually it's ok because I have realised one type of change was not recorded. I will fix it and let you know.

For example:

systematic_id   allele_description  allele_name allele_type change_description_to
SPAC23C11.16    FN-519-AA   plo1-FN519AA    amino_acid_mutation FN519AA

Did not go through

kimrutherford commented 1 year ago

Ah, sorry. I forgot to apply the fixes to the PHAF files.

manulera commented 1 year ago

@kimrutherford, I have added a few extra rows (below) to this table with missing fixes.

https://github.com/pombase/allele_qc/blob/3a05faa9e437a15b222f197d0ff9d36ef1dbb47f/manual_fixes_pombase/unknowns_with_correct_descriptions.tsv#L7-L12

Basically, the auto-fix was not going in (rightly so) because the alleles had sequence errors. I have added some CTD fixes as well.

kimrutherford commented 1 year ago

For example: systematic_id allele_description allele_name allele_type change_description_to SPAC23C11.16 FN-519-AA plo1-FN519AA amino_acid_mutation FN519AA Did not go through

Hi Manu. I'm a bit confused. Which allele fixes file has the changes that didn't go through?

kimrutherford commented 1 year ago

I'm a bit confused. Which allele fixes file has the changes that didn't go through?

Sorry, ignore me. :-)

I'm not confused anymore and I've applied the allele fixes to the PHAF files.

kimrutherford commented 1 year ago

The load failed because of an unrelated reason (the PubMed API had a temporary error) so we'll need to wait until Thursday to check the alleles in Chado.

manulera commented 1 year ago

Alright, thanks!

kimrutherford commented 1 year ago

we'll need to wait until Thursday to check the alleles in Chado.

The load works and it looks like the alleles are fixed. Let me know if you see any problems.

manulera commented 1 year ago

Hi @kimrutherford, it seems that most of them went through, but there are a few that did not. It seems that they are the ones that either had an empty description, or an empty name. Because they are only in one publication each, I will just go ahead and fix them manually.

systematic_id   allele_description  allele_name         allele_type                         change_description_to   change_name_to  change_type_to                  auto_fix_comment                                                                                                            sequence_error  solution_index  allele_parts    rules_applied                               reference       comment_on_change   add_synonym     add_comment
SPAC140.02                          gar2::ura4+         disruption                          gar2::ura4                                                              syntax_error                                                                                                                                                gar2::ura4+     disruption:usual                            PMID:9211982                                        
SPAC1565.08     G338D                                   amino_acid_mutation                 G332D                                                                   old_coords_fix, revision 8148: join(1306439..1306512,1306569..1308942)                                                      G338                            G338D           amino_acid_mutation:single_aa               PMID:29352077                                       
SPAC57A10.14    Q64->stop                               nonsense_mutation                   Q64*                                    partial_amino_acid_deletion     syntax_and_type_error                                                                                                                                       Q64->stop       nonsense_mutation:stop_codon_text           PMID:29352077                                       
SPBC16D10.04c   K961T                                   amino_acid_mutation                 K960T                                                                   old_coords_fix, revision 20110324: complement(join(3592359..3592685,3592733..3593447,3593496..3596292,3596335..3596692))    K961                            K961T           amino_acid_mutation:single_aa               PMID:22682245                                       
SPBC3H7.13                          csc1::ura4+         disruption                          csc1::ura4                                                              syntax_error                                                                                                                                                csc1::ura4+     disruption:usual                            PMID:23874188                                       
SPCC306.03c     T117I                                   amino_acid_insertion_and_mutation                                           amino_acid_mutation             type_error                                                                                                                                                  T117I           amino_acid_mutation:single_aa               PMID:31072933                                       
SPCC338.08      60-100              ctp1-delta60-100    amino_acid_mutation                                                         partial_amino_acid_deletion     type_error                                                                                                                                                  60-100          partial_amino_acid_deletion:multiple_aa     PMID:25580577                                       
SPCC622.09      G52D                                    amino_acid_mutation                 G53D                                                                    histone_fix                                                                                                                 G52                             G52D            amino_acid_mutation:single_aa               PMID:29352077
manulera commented 1 year ago

Then, this one: ctp1-delta60-100 is from the phaf files. I don't know why it was not fixed. Maybe in the phaf file script you are not taking into account the change_type_to column?

manulera commented 1 year ago

These fixes from change_log/manual_cannot_fix_new_03082023.tsv did not go through either:

systematic_id   allele_name allele_description  allele_type reference   change_description_to   change_name_to  change_type_to  comment_on_change   add_synonym add_comment
SPNCRNA.98  srp7-U88G,delta84-88,omega8nt   U88G,nt84 deletion,8 nucleotides inserted after nt83    nucleotide_insertion_and_mutation   PMID:1315954    T-84-GCTGCAGC,T88G      srp7-U88G,delta84,omega8nt          
SPNCRNA.98  srp7-U88G,omegaUCGA U88G,UCGA inserted after nt84   nucleotide_insertion_and_mutation   PMID:1315954    T88G,T84-TCGA                   
SPBC1A4.03c top2-1-40/SV-delta-Sph  amino acids 1-40 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1200-1485 deleted    amino_acid_mutation PMID:1332977    2-41,M1-PKKKRKV,1200-1485       amino_acid_insertion_and_mutation           
SPBC1A4.03c top2-1-40/SV-delta-Xba  amino acids 1-40 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1221-1485 deleted    amino_acid_mutation PMID:1332977    2-41,M1-PKKKRKV,1221-1485       amino_acid_insertion_and_mutation           
SPBC1A4.03c top2-1-74/SV-delta-Sph  amino acids 1-74 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1200-1485 deleted    amino_acid_mutation PMID:1332977    2-75,M1-PKKKRKV,1200-1485       amino_acid_insertion_and_mutation           
SPBC1A4.03c top2-1-74/SV-delta-Xba  amino acids 1-74 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1221-1485 deleted    amino_acid_mutation PMID:1332977    2-75,M1-PKKKRKV,1221-1485       amino_acid_insertion_and_mutation           
SPBC1A4.03c top2-26-40/SV-delta-Sph amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1200-1485 deleted   amino_acid_mutation PMID:1332977    27-41,T26-PKKKRKV,1200-1485     amino_acid_insertion_and_mutation           
SPBC1A4.03c top2-26-40/SV-delta-Xba amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV,and amino acids 1221-1485 deleted   amino_acid_mutation PMID:1332977    27-41,T26-PKKKRKV,1221-1485     amino_acid_insertion_and_mutation
manulera commented 1 year ago

Then, this one: ctp1-delta60-100 is from the phaf files. I don't know why it was not fixed

I fixed this one manually as well, in svn revision 9086. I think the reason why it did not go through might be because in the file it says amino acid mutation instead of amino_acid_mutation in the type.

manulera commented 1 year ago

Hi @kimrutherford

I have fixed all of the ones mentioned in the other comment in the phaf files by hand in svn revision 9087.

Index: trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_1315954_phaf.tsv
===================================================================
--- trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_1315954_phaf.tsv   (revision 9086)
+++ trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_1315954_phaf.tsv   (working copy)
@@ -2,8 +2,8 @@
 #Submitter_ORCID: 0000-0003-4148-4606
 #Submitter_status: PomBase
 Gene systematic ID FYPO ID Allele description  Expression  Parental strain Strain background   Genotype    Gene name   Allele name Allele synonym  Allele type Evidence    Condition   Penetrance  Severity    Extension   Reference   taxon   Date    ploidy
-SPNCRNA.98 FYPO:0002060    U88G, nt84-88 deletion, 131 nucleotides inserted after nt83 Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,delta84-88,omega131nt     other   Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
-SPNCRNA.98 FYPO:0002061    U88G, nt84-88 deletion, 131 nucleotides inserted after nt83 Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,delta84-88,omega131nt     other   Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
+SPNCRNA.98 FYPO:0002060    U88G,84-88,131 nucleotides inserted after nt83  Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,delta84-88,omega131nt     other   Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
+SPNCRNA.98 FYPO:0002061    U88G,84-88,131 nucleotides inserted after nt83  Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,delta84-88,omega131nt     other   Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G72A,G78A,G100A,G107A,G112A,G141A   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G72A,G78A,G100A,G107A,G112A,G141A  srp7-G72A,G78A,G100A,G107A,Gl12A,G141A  nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002061    G72A,G78A,G100A,G107A,G112A,G141A   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G72A,G78A,G100A,G107A,G112A,G141A  srp7-G72A,G78A,G100A,G107A,Gl12A,G141A  nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002061    G153A,G155A Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G153A,G155A        nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
@@ -13,7 +13,7 @@
 SPNCRNA.98 FYPO:0002061    139-144 Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7delta139-144        partial nucleotide deletion Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002061    118-120 Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7delta118-120        partial nucleotide deletion Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002061    A146T,G159T,148-150 Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-A146U,G159U,delta148-150       nucleotide_deletion_and_mutation    Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
-SPNCRNA.98 FYPO:0002061    U88G, nt84 deletion, 8 nucleotides inserted after nt83  Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,delta84-88,omega8nt       nucleotide_insertion_and_mutation   Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
+SPNCRNA.98 FYPO:0002061    T84GCTGCAGC,T88G    Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,delta84-88,omega8nt       nucleotide_insertion_and_mutation   Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G4C Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G4C        nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G100A,C103A,G112A   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G100A,C103A,G112A      nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    C69T    Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-C69U       nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
@@ -60,7 +60,7 @@
 SPNCRNA.98 FYPO:0002060    T88G,T133C,A135C    Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,U133C,A135C       nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    T101C,A136C,G149C   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U101C,A136C,G149C      nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    T(-61)C,G(-75)C,T62C,T101C  Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-T(-61)C,G(-75)C,U62C,U101C     nucleotide mutation Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
-SPNCRNA.98 FYPO:0002060    U88G, UCGA inserted after nt84  Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,omegaUCGA     nucleotide_insertion_and_mutation   Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
+SPNCRNA.98 FYPO:0002060    T88G,T84TTCGA   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,omegaUCGA     nucleotide_insertion_and_mutation   Cell growth assay   FYECO:0000005,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G4C Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G4C        nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G100A,C103A,G112A   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G100A,C103A,G112A      nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    C69T    Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-C69U       nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
@@ -107,7 +107,7 @@
 SPNCRNA.98 FYPO:0002060    T88G,T133C,A135C    Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,U133C,A135C       nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    T101C,A136C,G149C   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U101C,A136C,G149C      nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    T(-61)C,G(-75)C,T62C,T101C  Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-T(-61)C,G(-75)C,U62C,U101C     nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
-SPNCRNA.98 FYPO:0002060    U88G, UCGA inserted after nt84  Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,omegaUCGA     nucleotide_insertion_and_mutation   Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
+SPNCRNA.98 FYPO:0002060    T88G,T84TTCGA   Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-U88G,omegaUCGA     nucleotide_insertion_and_mutation   Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G4A,G9A Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G4A,G9A        nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G4A Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G4A        nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
 SPNCRNA.98 FYPO:0002060    G9A Not specified   972 h-      ura4-D18 leu1-32 ade6-704       srp7-G9A        nucleotide mutation Cell growth assay   FYECO:0000004,FYECO:0000137             PMID:1315954    4896    2014-06-09  
Index: trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_1332977_phaf.tsv
===================================================================
--- trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_1332977_phaf.tsv   (revision 9086)
+++ trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_1332977_phaf.tsv   (working copy)
@@ -34,12 +34,12 @@
 SPBC1A4.03c    FYPO:0004056    43-75,1221-1485 not assayed 972 h-          top2    top2delta(42-74)-delta-Xba      partial_amino_acid_deletion microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
 SPBC1A4.03c    FYPO:0002061    1-54,1221-1485  not assayed 972 h-          top2    top2delta(1-53)-delta-Xba       partial_amino_acid_deletion cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
 SPBC1A4.03c    FYPO:0002779    1-54,1221-1485  not assayed 972 h-          top2    top2delta(1-53)-delta-Xba       partial_amino_acid_deletion microscopy  FYECO:0000005,FYECO:0000126         assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0002060    amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1221-1485 deleted  not assayed 972 h-          top2    top2-26-40/SV-delta-Xba     amino acid mutation cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0000838    amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1221-1485 deleted  not assayed 972 h-          top2    top2-26-40/SV-delta-Xba     amino acid mutation microscopy  FYECO:0000005,FYECO:0000126         assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0002060    amino acids 1-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1221-1485 deleted   not assayed 972 h-          top2    top2-1-40/SV-delta-Xba      amino acid mutation cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0004056    amino acids 1-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1221-1485 deleted   not assayed 972 h-          top2    top2-1-40/SV-delta-Xba      amino acid mutation microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000003    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0002061    amino acids 1-74 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1221-1485 deleted   not assayed 972 h-          top2    top2-1-74/SV-delta-Xba      amino acid mutation cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0004056    amino acids 1-74 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1221-1485 deleted   not assayed 972 h-          top2    top2-1-74/SV-delta-Xba      amino acid mutation microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0002060    27-41,T26TPKKKRKV,1221-1485 not assayed 972 h-          top2    top2-26-40/SV-delta-Xba     amino_acid_insertion_and_mutation   cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0000838    27-41,T26TPKKKRKV,1221-1485 not assayed 972 h-          top2    top2-26-40/SV-delta-Xba     amino_acid_insertion_and_mutation   microscopy  FYECO:0000005,FYECO:0000126         assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0002060    2-41,M1MPKKKRKV,1221-1485   not assayed 972 h-          top2    top2-1-40/SV-delta-Xba      amino_acid_insertion_and_mutation   cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0004056    2-41,M1MPKKKRKV,1221-1485   not assayed 972 h-          top2    top2-1-40/SV-delta-Xba      amino_acid_insertion_and_mutation   microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000003    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0002061    2-75,M1MPKKKRKV,1221-1485   not assayed 972 h-          top2    top2-1-74/SV-delta-Xba      amino_acid_insertion_and_mutation   cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0004056    2-75,M1MPKKKRKV,1221-1485   not assayed 972 h-          top2    top2-1-74/SV-delta-Xba      amino_acid_insertion_and_mutation   microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
 SPBC1A4.03c    FYPO:0002061    1-75,1200-1485  not assayed 972 h-          top2    top2delta(1-74)-delta-Sph       partial_amino_acid_deletion cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
 SPBC1A4.03c    FYPO:0002779    1-75,1200-1485  not assayed 972 h-          top2    top2delta(1-74)-delta-Sph       partial_amino_acid_deletion microscopy  FYECO:0000005,FYECO:0000126         assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
 SPBC1A4.03c    FYPO:0002060    1-18,1200-1485  not assayed 972 h-          top2    top2delta(1-17)-delta-Sph       partial_amino_acid_deletion cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
@@ -50,9 +50,9 @@
 SPBC1A4.03c    FYPO:0004056    43-75,1200-1485 not assayed 972 h-          top2    top2delta(42-74)-delta-Sph      partial_amino_acid_deletion microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
 SPBC1A4.03c    FYPO:0002061    1-54,1200-1485  not assayed 972 h-          top2    top2delta(1-53)-delta-Sph       partial_amino_acid_deletion cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
 SPBC1A4.03c    FYPO:0002779    1-54,1200-1485  not assayed 972 h-          top2    top2delta(1-53)-delta-Sph       partial_amino_acid_deletion microscopy  FYECO:0000005,FYECO:0000126         assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0002060    amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1200-1485 deleted  not assayed 972 h-          top2    top2-26-40/SV-delta-Sph     amino acid mutation cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0004056    amino acids 26-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1200-1485 deleted  not assayed 972 h-          top2    top2-26-40/SV-delta-Sph     amino acid mutation microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0002060    amino acids 1-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1200-1485 deleted   not assayed 972 h-          top2    top2-1-40/SV-delta-Sph      amino acid mutation cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0004056    amino acids 1-40 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1200-1485 deleted   not assayed 972 h-          top2    top2-1-40/SV-delta-Sph      amino acid mutation microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0002061    amino acids 1-74 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1200-1485 deleted   not assayed 972 h-          top2    top2-1-74/SV-delta-Sph      amino acid mutation cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
-SPBC1A4.03c    FYPO:0004056    amino acids 1-74 replaced by SV40 NLS sequence PKKKRKV, and amino acids 1200-1485 deleted   not assayed 972 h-          top2    top2-1-74/SV-delta-Sph      amino acid mutation microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000001    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0002060    27-41,T26TPKKKRKV,1200-1485 not assayed 972 h-          top2    top2-26-40/SV-delta-Sph     amino_acid_insertion_and_mutation   cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0004056    27-41,T26TPKKKRKV,1200-1485 not assayed 972 h-          top2    top2-26-40/SV-delta-Sph     amino_acid_insertion_and_mutation   microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0002060    2-41,M1MPKKKRKV,1200-1485   not assayed 972 h-          top2    top2-1-40/SV-delta-Sph      amino_acid_insertion_and_mutation   cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0004056    2-41,M1MPKKKRKV,1200-1485   not assayed 972 h-          top2    top2-1-40/SV-delta-Sph      amino_acid_insertion_and_mutation   microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000002    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0002061    2-75,M1MPKKKRKV,1200-1485   not assayed 972 h-          top2    top2-1-74/SV-delta-Sph      amino_acid_insertion_and_mutation   cell growth assay   FYECO:0000005               PMID:1332977    4896    2016-07-05  
+SPBC1A4.03c    FYPO:0004056    2-75,M1MPKKKRKV,1200-1485   not assayed 972 h-          top2    top2-1-74/SV-delta-Sph      amino_acid_insertion_and_mutation   microscopy  FYECO:0000005,FYECO:0000126     FYPO_EXT:0000001    assayed_using(PomBase:top2) PMID:1332977    4896    2016-07-05
manulera commented 1 year ago

I think we can close with this!