In khughitt/EuPathDB: Provides access to pathogen annotation resources available on EuPathDB databases

BiocStyle::markdown()

Overview

I am thinking to use this document to play around with some (likely bad) ideas.

In this case, I am thinking about a request to the bioconductor mailing list on which Lori tagged me. At its root, it was asking how one may get ensembl IDs from eupathdb IDs, since the eupathdb keys off entrez, not ensembl.

I was thinking about this idly while sitting in a meeting and I realized I might already have a piece of code which handles this, among other things.

https://github.com/abelew/hpgltools/blob/master/R/annotation_uniprot.r

I should be able to give uniprot the species name from eupathdb, download and parse the uniprot annotations, and cross reference them against the existing eupathdb annotations; thus automagically getting the 40 or so other keys along with ensembl.

Of course, a more likely outcome is shenanigans. So let us see what happens.

library(hpgltools)
library(EuPathDB)

So, my workstation currently has the following installed:

org.Lmajor.Friedlin.v43.eg.db

library(org.Tcruzi.CL.Brener.Esmeraldo.like.v43.eg.db)
keytypes(org.Tcruzi.CL.Brener.Esmeraldo.like.v43.eg.db)
tc_annot <- load_orgdb_annotations("org.Tcruzi.CL.Brener.Esmeraldo.like.v43.eg.db", fields="all")
genes <- tc_annot[["genes"]]
## Hmm I wonder if I can modify my uniprot code to use the taxonomy ID?

##
test <- download_uniprot_proteome(taxonomy="353153")
uniprot_annot <- load_uniprot_annotations(file=test[["filename"]])
colnames(uniprot_annot)

merged <- merge(genes, uniprot_annot, by.x="annot_uniprot_id", by.y="primary_accession")
dim(merged)
## SWWWWEEEETTT!

khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.