Difference between revisions of "UniProt-GOA syntax checking"
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*szy-1 | *szy-1 | ||
*szy-2 | *szy-2 | ||
+ | *szy-3 | ||
+ | *szy-4 | ||
+ | *szy-5 | ||
+ | *szy-6 | ||
*unc-65 | *unc-65 | ||
Revision as of 15:24, 7 August 2012
Contents
Errors to Fix
With/From Column
- IC annotations need GO term in With/From - DONE
- ISS annotations need database identifiers in With/From
- 917 ISS annotations in postgres as of 2012-07-23
- Some annotations use transgenes in the WITH column - this syntax should be okay, see jnk-1 and sir-2.1 for examples
Phenotype2GO Pipeline
- Remove annotations mapping to ncRNA and pseudogenes
IEA Pipeline
- UniProtKB will perform InterPro2GO mappings in-house
- TMHMM-derived annotations need a resolvable accession in With/From column
- Is there an accession for TMHMM?
- If not, what could be used in place of this pipeline if we stand to lose annotations?
Annotations to ncRNAs
- Need a specific mapping file for those genes
- WBGene00003262 mir-34
Annotations to Uncloned Genes
- Need a specific mapping file for those genes
- Genes affected (partial list):
- cad-1
- exc-1
- exc-2
- exc-3
- exc-6
- exc-8
- ric-1
- seu-2
- seu-3
- sog-1
- sog-2
- sog-3
- sog-4
- sog-5
- sog-6
- sog-10
- szy-1
- szy-2
- szy-3
- szy-4
- szy-5
- szy-6
- unc-65
gp2protein File
- Need a version updated as often as possible - UniProtKB can upload nightly
Unsupported/Missing Reference
- Including doi's instead would be fine, if available
- WBPaper00004663 - added doi in paper editor, will need to dump doi in gaf
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