Difference between revisions of "What's staying in postgres?"
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| − | For now, we | + | ==For now, we are keeping several types of annotations in postgres:== |
| − | + | *ncRNA | |
| − | + | *uncloned loci | |
| − | + | **sup-36 (note that sup-36(WBGene00006341) was killed right about the same time we were doing the new uploads, i.e. 2013-11-20. The sup-36 annotations to WBGene0006341 were included in the WS241 upload, but deleted from the OA on 2013-11-25 and added to sup-36(WBGene000018164) in Protein2GO on 2013-11-25. | |
| − | + | *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. | ||
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| + | ==Archiving, Deleting Old Annotations== | ||
| + | #We created one new annotation, for mir-80 (WBGene00003308), 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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| + | Back to [[Gene Ontology]] | ||
Latest revision as of 18:47, 25 November 2013
For now, we are keeping several types of annotations in postgres:
- ncRNA
- uncloned loci
- sup-36 (note that sup-36(WBGene00006341) was killed right about the same time we were doing the new uploads, i.e. 2013-11-20. The sup-36 annotations to WBGene0006341 were included in the WS241 upload, but deleted from the OA on 2013-11-25 and added to sup-36(WBGene000018164) in Protein2GO on 2013-11-25.
- 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 (WBGene00003308), 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.
Back to Gene Ontology
