What's staying in postgres?
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Jump to navigationJump to searchFor now, we are keeping several types of annotations in postgres:
- ncRNA
- uncloned loci
- IEP evidence code - select ones; will need to add these back to Protein2GO and then delete from tazendra
- IEP evidence code annotations made to proteins will eventually be manually deleted from postgres and entered into protein2go other specific annotations that have unique issues
- fox-1 annotations that have yDp13 in with/from - will need to work out with uniprot how to handle these
- jnk-1 and sir-2.1 annotations that have a WBTransgene in the with/from column - will need to work out with uniprot how to handle these
- Cre-vbh-1 annotations - will be added to uniprot manually and then deleted from postgres
- gst-10 - annotations will be added to uniprot manually using a doi as reference id and then deleted from postgres
- MTCE.26 - annotations will be added to uniprot manually - need to update gp2protein file, but also need to check on status of uniprot identifiers in xrefs.txt file for elegans mitochondrial proteins
- Genes for which there isn't a 1:1 correspondence between gene and protein in UniProt (e.g., actins (fixed by Swiss-Prot; needs WB update), histones, eef-1A.1, .2, etc.)
- These genes will just have to be dealt with on a case-by-case basis.
Archiving, Deleting Old Annotations
- We created one new annotation, for mir-80, in the OA before we deleted all of the GO annotations housed in Protein2GO. We did this so that we'd have a new pgid (14232) from which to iterate new pgids going forward. We did this because the OA assigns pgid's by looking at the highest value and then iterating +1. Since the annotations remaining in the OA likely did not include the highest pgid, we wanted to create a new highest pgid so that if we ever had to restore the archived annotations, there would be no pgid collisions.
- As of 2013-11-22, there are a total of 170 WBGenes and their annotations left in the OA on tazendra.
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