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 - ~400 are legacy annotations without With/From entry
2. Action - update as many as possible, but may need to move forward regardless; note that annotations would not be dumped/displayed.

• 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

1. Review annotations to make sure they're still consistent with GO annotation practice
2. Update transgene symbols to WB transgene identifiers

Phenotype2GO Pipeline

1. Remove annotations mapping to ncRNAs (e.g. 21U RNAs) and check again for pseudogene exclusion
2. Update syntax of WB Phenotypes in With/From column for Phenotype2GO-based IMP annotations

IEA Pipelines

• UniProtKB will perform InterPro2GO mappings in-house
• 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?
3. Remove this mapping pipeline from WB. Keep TMHMM results in another database tag? Motif?

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.
2. CVS update -d

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.
2. WBPaper00022068 ced-11 meeting abstract. Action - deleted annotation. Added an IGI annotation with ced-3 from WBPaper00003815.
3. WBPaper00011088 ces-1 meeting abstract. Action - deleted annotation. Added an IC annotation with GO:0043565 in WITH/FROM.
4. WBPaper00016619 dpr-1 meeting abstract. Action - deleted annotation. No published information to support meeting abstract.
5. WBPaper00018550 dpr-1 meeting abstract. Action - deleted annotation. No published information to support meeting abstract.
   1. Note - deleted all associated GO annotations for dpr-1, as evidence was based on unpublished results cited in Discussion of a paper.
6. WBPaper00011270 flp-3 meeting abstract. Action - deleted annotation and updated with annotation from published paper.
7. WBPaper00018934 ceh-37 meeting abstract. R.
8. WBPaper00011712 cpr-1 meeting abstract. R.
9. WBPaper00022817 cpr-1 meeting abstract. R.
10. WBPaper00011485 crh-1 meeting abstract. R.
11. WBPaper00017392 crh-1 meeting abstract. R.
12. WBPaper00018784 fat-7 meeting abstract. R.
13. WBPaper00019580 fkh-6 meeting abstract. R.
14. WBPaper00022748 flr-4 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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