systematic IDs for non-gene features

[pombase-admin]

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

[pombase-admin]

There's no problem in Chado with doing that - they just need to be unique.

Original comment by: kimrutherford

[pombase-admin]

• Priority: 5 --> 6

Original comment by: ValWood

[pombase-admin]

• Description has changed:

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)

• assigned_to: Midori Harris

Original comment by: mah11

[pombase-admin]

better ID patterns (less redundancy; add chromosome code):

centromeric: SPRPTCEN[ABC].nn LTRs: SPLTR[ABC].nn others: SPRPT[ABC].nn

Original comment by: mah11

[pombase-admin]

IDs are in! I'll close this if they load ok.

Original comment by: mah11

[pombase-admin]

• summary: unique names for non-gene features --> systematic IDs for non-gene features
• status: open --> open-accepted

Original comment by: mah11

[pombase-admin]

So what is next. Jira ticket for feature pages?

Original comment by: ValWood

[pombase-admin]

I'm doing a load now to check that everything goes into the right slots in Chado.

Original comment by: kimrutherford

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

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

[pombase-admin]

ticket exists - https://www.ebi.ac.uk/panda/jira/browse/PB-400

Original comment by: mah11

[pombase-admin]

Thanks for the fixes. I've just started a new load. I should finish in about 2 hours from now.

Original comment by: kimrutherford

[pombase-admin]

• status: open-accepted --> closed-fixed

Original comment by: kimrutherford

[pombase-admin]

I'm closing this now. We can re-open if Mark reports problems.

Original comment by: kimrutherford