GAF to .ace file

The new pipeline for uploading manual GO annotations will be different in that we will now get our manual annotations to protein-coding genes from UniProtKB.

Here's one possible scenario on how that could work:

Manual Annotations

1. Download a GAF from UniProtKB for all manual annotations to protein-coding genes
2. Add annotations to ncRNAs and uncloned genes to the GAF by dumping a GAF from tazendra, diffing the file, and then adding to the UniProt GAF, any annotations present on tazendra but not in the UniProt GAF (will need to check that this really only gives ncRNA and uncloned gene annotations)
3. With complete GAF, convert all UniProtKB identifiers to WBGene identifiers using most current gp2protein file

Phenotype2GO Annotations

1. Currently, the Phenotype2GO-based annotations are incorporated into WB as part of the database build.
2. The resulting annotations are converted to GAF format and then put on an ftp site corresponding to each build.
3. The Phenotype2GO GAF is combined with the manual and InterPro2GO GAF (see below) and the combined file is uploaded to the GO repository.

IEA Annotations

1. Currently, the InterPro2GO (IEA) annotations are incorporated into WB as part of the database build.
2. The resulting annotations are converted to GAF format and then put on an ftp site corresponding to each build.
3. The InterPro2GO GAF is combined with the manual and Phenotype2GO GAF (see above) and the combined file is uploaded to the GO repository.