Closed pombase-admin closed 9 years ago
There's no problem in Chado with doing that - they just need to be unique.
Original comment by: kimrutherford
Original comment by: ValWood
Diff:
--- old
+++ new
@@ -1,5 +1,4 @@
-We want Mark to create "PomBase pages" for non-gene features centromeric repeats, LTRs
-so they will need "systemtic IDs" We also need to add systematic IDs to transposoms
+We want Mark to create PomBase pages for non-gene features such as centromeric repeats, LTRs, etc., so they will need systematic IDs. We also need to add systematic IDs to transposons.
We propose to name them
SPREPCEN.## (centromeric repeats)
Original comment by: mah11
better ID patterns (less redundancy; add chromosome code):
centromeric: SPRPTCEN[ABC].nn LTRs: SPLTR[ABC].nn others: SPRPT[ABC].nn
Original comment by: mah11
IDs are in! I'll close this if they load ok.
Original comment by: mah11
Original comment by: mah11
So what is next. Jira ticket for feature pages?
Original comment by: ValWood
I'm doing a load now to check that everything goes into the right slots in Chado.
Original comment by: kimrutherford
There were three new /systematic_id qualifiers add to genes that had one already - a feature can only have one /systematic_id. I've temporarily changed the second /systematic_id in these three features to a /note and checked it into SVN:
chr1: FT LTR complement(5190745..5191106) FT /systematic_id="SPLTRA.81" FT /systematic_id="Tf2-7" FT /SO="SO:0000286"
chr3: FT LTR complement(1196131..1196481) FT /systematic_id="SPLTRC.32" FT /systematic_id="Tf2-fragment5" FT /SO="SO:0000286"
chr3: FT repeat_region 1401219..1403077 FT /systematic_id="SPRPTC.5" FT /systematic_id="wtf12"
Original comment by: kimrutherford
I've fix a small problem with the load - the systematic ID for repeat_region, LTR and others was getting a ".1" added to it. Fixed now and I'm re-loading. (Apart from the IDs being wrong the load worked OK).
Original comment by: kimrutherford
Thanks - I caught a couple others but missed those 3. I've changed them to /synonym to match the ones I did catch.
Original comment by: mah11
ticket exists - https://www.ebi.ac.uk/panda/jira/browse/PB-400
Original comment by: mah11
Thanks for the fixes. I've just started a new load. I should finish in about 2 hours from now.
Original comment by: kimrutherford
Original comment by: kimrutherford
I'm closing this now. We can re-open if Mark reports problems.
Original comment by: kimrutherford
We want Mark to create PomBase pages for non-gene features such as centromeric repeats, LTRs, etc., so they will need systematic IDs. We also need to add systematic IDs to transposons.
We propose to name them SPREPCEN.## (centromeric repeats) SPRPTLTR.## (LTRs) SPRPTRPT.## (other types of repeat)
Shall we go ahead and do this? Do you foresee any problems?
Original comment by: ValWood