Difference between revisions of "UniProt-GOA syntax checking"
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#Genes affected (partial list): | #Genes affected (partial list): | ||
*cad-1 | *cad-1 | ||
+ | *exc-6 | ||
+ | *exc-8 | ||
*ric-1 | *ric-1 | ||
*seu-2 | *seu-2 |
Revision as of 15:13, 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-6
- exc-8
- ric-1
- seu-2
- seu-3
- 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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