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#174 logs: equivalent allele descriptions aa vs nucleotide
Kim: these are nucleotide descriptions (which can be slightly more informative because of degenerate codons). Can awe allow each allele to have an AA and an NT description?
We need to devise the way for checking equivalence of these, and store both (for now, this is not urgent if we just store the first one, and this is only a warning if)
Curators: What if we display the AA one in PomBase by default, but make the nt one visible by mouse over if stored?
error in 58d8ad0dec113279: description for new allele "cdc10-K30(C1434T)" does not match the existing allele with the same name "cdc10-K30(T429I)"
error in 58d8ad0dec113279: description for new allele "cdc10-P2(A1209G)" does not match the existing allele with the same name "cdc10-P2(D354G)"
error in 58d8ad0dec113279: description for new allele "cdc10-M15(G1325A)" does not match the existing allele with the same name "cdc10-M15(A393T)"
error in 58d8ad0dec113279: description for new allele "cdc10-V50(C1232T)" does not match the existing allele with the same name "cdc10-V50(H362Y)"
error in 58d8ad0dec113279: description for new allele "cdc10-M71(G1325A)" does not match the existing allele with the same name "cdc10-M71(A393T)"
error in 58d8ad0dec113279: description for new allele "cdc10-I29(A1433G)" does not match the existing allele with the same name "cdc10-I29(T429A)"
error in 58d8ad0dec113279: description for new allele "cdc10-MBC4(C2268T)" does not match the existing allele with the same name "cdc10-MBC4(R707->STOP)"
error in 58d8ad0dec113279: description for new allele "cdc10-M47(G1607A)" does not match the existing allele with the same name "cdc10-M47(A487T)"
error in 58d8ad0dec113279: description for new allele "cdc10-M4(G1325A)" does not match the existing allele with the same name "cdc10-M4(A393T)"
error in 58d8ad0dec113279: description for new allele "cdc10-MBC41(C1434T)" does not match the existing allele with the same name "cdc10-MBC41(T429I)"
error in 58d8ad0dec113279: description for new allele "cdc10-K28(C1295T,C1705T,C1976T)" does not match the existing allele with the same name "cdc10-K28(P383S,R610C)"
error in 58d8ad0dec113279: description for new allele "cdc10-M17(G1325A)" does not match the existing allele with the same name "cdc10-M17(A393T)"
error in 16802f31036c5732: description for new allele "cut8-563(S201P)" does not match the existing allele with the same name "cut8-563(ntY1283C)"
error in 7bf893a86d94196c: description for new allele "cdc23-M36(D232G,V265I)" does not match the existing allele with the same name "cdc23-M36(A695C)"
error in 4d6014a904a1e84b: description for new allele "ned1-1(deletion)" does not match the existing allele with the same name "ned1-1(G402D)"
error in 4d6014a904a1e84b: description for new allele "ned1-1(deletion)" does not match the existing allele with the same name "ned1-1(G402D)"
error in 42b53662d27d7951: description for new allele "M6(C328A,C330A,C334A,C336A,C339A,H342A)" does not match the existing allele with the same name "M6( C328A,C330A,C334A,C336A,C339A,H342A)"
Transferred from duplicate ticket (example gene is cap1)
https://sourceforge.net/p/pombase/curation-tool/600/
Midori:
It's a canto thing, and still looks odd there. I curated the paper, and put these in as partial amino acid deletions. If I reactivate the session and go into the allele-editing interface, it shows that "partial deletion, amino acid" has been selected, but that info doesn't show up in the annotation summary table. I don't know where it goes behind the scenes.
The annotation table displays the names and numbers correctly, e.g. noname(303-367) but somehow "noname" is turning into "not recorded" by the time it reaches the gene page. I don't know whether that means there's something else going on in addition to canto ...
PMID:1550959 3bce65ea848fff57
We could do but it would mean a bit of mucking about with the code. Would you want to be able to store and display both descriptions in Canto?
If both the AA and the NT description come from the same group or paper isn't the AA one redundant? And if the two descriptions come from different groups couldn't they be different alleles (same AA sequence, different NT sequence)? I'm a bit confused.
If they are equivalent, do we need to store both?
Could I get a demo if this at some point?
I think it's turned into "not recorded" at the Ensembl end. If the allele has the name "noname" in Canto, it is stored in Chado with no name. I think the "not recorded" is just a display thing. Should it say "no name" instead? If so, I'll talk to Mark about it.
If we know the nucleotide, that is what we store.
Let nucleotide changes supercede amino acid changes.
If possible store the amino acid change 'somewhere' as we can use this later to check that the nucleotide change will specify the previusly captured amino acid change. if it does, do a replacement. if it doesmn't spawn a warning.
Display level changes: (requires a jira ticket)
convert nt changes to amino acid changes for display
From a chat with curators: we should store the most specific of AA and NT but warn about inconsistencies in the descriptions of alleles with the same name.
more examples
error in c2aaa605ef48b5f8: database inconsistency - there exists more than one allele feature with the name "sid4N–ppc89C"
error in 58d8ad0dec113279: description for new allele "cdc10-M71(G1179A)" does not match the existing allele with the same name "cdc10-M71(A393T)"
error in d2a1d493dc361259: description for new allele "caf3-89(C1565T)" does not match the existing allele with the same name "caf3-89(L522S)"