Steven tasked me with updating our P.generosa genome annotation file (GitHub Issue) a while back and I finally managed to get it all figured out. Although I wanted to perform most of this using the GSEAbase package (PDF), as this package is geared towards storage/retrieval of gene set data, I eventually decided to abondon this approach due to the time it was taking and my lack of familiarity/understanding of how to manipulate objects in R. Despite that, GSEAbase was still utilized for its very simple use for identifying GOlims (IDs and Terms).
I also struggled with the UniProt API. They updated the API since I had previously created the initial annotation file on 20220419 and the update/change to the API rendered the previous API usage inoperable! I tried for a bit to get the new API figured out, but evenutally said “F it!” and used the data I had previously downloaded from UniProt (which, when I started, I didn’t actually realize I had kept).
Then, after all this, I decided to integrate the entire thing into an R Project. This kept things a bit more cohesive, as it didn’t need to bounc between a Jupyter Notebook and then into R.
Produced a tab-delimited file which added columns grouping GO IDs by Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). Also added a column grouping BP GOslims and corresponding BP GOslim terms for each gene.
See Results section below for file and layout.
RESULTS
Output folder:
20230328-pgen-gene_annotation-update (GiHub; R Project)
Annotation file
- 20230329-pgen-annotations-SwissProt-GO-BP_GOslim.tab (7.8MB; tab-delimited)
Table layout:
| gene | accessions | gene_id | gene_name | gene_description | alt_gene_description | all_GO_ids | BP_GO_ids | CC_GO_ids | MF_GO_ids | GOslim | Term |
|---|