Difference between revisions of "UniProt-GOA syntax checking"
From WormBaseWiki
Jump to navigationJump to searchLine 19: | Line 19: | ||
==Annotations to Uncloned Genes== | ==Annotations to Uncloned Genes== | ||
#Need a specific mapping file for those genes | #Need a specific mapping file for those genes | ||
− | #Genes affected: | + | #Genes affected (partial list): |
*WBGene00000278 cad-1 | *WBGene00000278 cad-1 | ||
+ | *unc-65 | ||
==gp2protein File== | ==gp2protein File== |
Revision as of 15:09, 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):
- WBGene00000278 cad-1
- 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
Back to Gene Ontology