UniProt-GOA syntax checking

Errors to Fix

With/From Column

• IC annotations need GO term in With/From - DONE
• ISS annotations need database identifiers in With/From

1. 917 ISS annotations in postgres as of 2012-07-23 - some are legacy annotations without With/From entry

• IMP annotations - some annotations use transgenes in the With/From column - this syntax should be okay, see jnk-1 and sir-2.1 for examples. Action - discuss with Rachael, Tony

Phenotype2GO Pipeline

1. Remove annotations mapping to ncRNAs (e.g. 21U RNAs) and check again for pseudogene exclusion

IEA Pipelines

1. UniProtKB will perform InterPro2GO mappings in-house
2. TMHMM-derived annotations need a resolvable accession in With/From column
   1. Is there an accession for TMHMM?
   2. 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

1. Action - contacted Rama to see if appropriate directories can be set up in GO CVS/SVN. Passed on to Mike C.

Annotations to Uncloned Genes

• Need a specific mapping file for those genes

1. Action - contacted Rama to see if appropriate directories can be set up in GO CVS/SVN. Passed on to Mike C.

• Genes affected (partial list):
• cad-1
• exc-1
• exc-2
• exc-3
• exc-6
• exc-8
• hid-2
• hid-4
• 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
• szy-7
• szy-8
• szy-9
• szy-10
• szy-11
• szy-12
• szy-13
• szy-14
• szy-15
• szy-16
• szy-17
• szy-18
• szy-19
• unc-65

gp2protein File

• Need a version updated as often as possible to keep IDs as closely in sync as possible.
• UniProtKB can upload file nightly.

1. Action - need to develop a pipeline for more frequent updates of WB gp2protein file, as well as gp2ncRNA and gp2unlocalized

Unsupported/Missing Reference

• Published papers without PMIDs - Including doi's instead would be fine, if available.

1. WBPaper00004663 - added doi in paper editor, will need to dump doi in WB GAF

• Some GO references still refer to meeting abstracts

1. WBPaper00011144 ced-11 meeting abstract. Action - deleted annotation. DONE.
2. WBPaper00022068 ced-11 meeting abstract. Action - deleted annotation. DONE. Added an IGI annotation with ced-3 from WBPaper00003815.
3. WBPaper00011088 ces-1 meeting abstract. Action - deleted annotation. DONE. Added an IC annotation with GO:0043565 in WITH/FROM.
4. WBPaper00018934 ceh-37 meeting abstract. R.

• Annotations from P2GO pipeline that reference a paper's erratum, not the original paper

1. WBPaper00006304 should be WBPaper00005637

• Annotations from P2GO pipeline that reference a duplicate paper object for which there is no bibliographic information in WormBase

1. WBPaper00005149 should be merged into WBPaper00005123

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