khughitt / eupathdb

EuPathDB recipe for the Bioconductor AnnotationHub

EuPathDB AnnotationHub Recipes and access

This package contains code for generating Bioconductor objects (OrgDb, OrganismDbi, TxDb, GRanges, and BSGenome) for pathogens found on one of the EuPathDB databases:

• AmoebaDB
• CryptoDB
• FungiDB
• GiardiaDB
• MicrosporidiaDB
• PiroplasmaDB
• PlasmoDB
• SchistoDB
• ToxoDB
• TrichDB
• TriTrypDB

The primary purposes for this package are:

1. Generate organism-specific Bioconductor resources to be made available through AnnotationHub.
2. Generate installable packages for the various resources.
3. Provide shortcuts for accessing these resources.

To access EuPathDB resources via AnnotationHub, simply load the AnnotationHub package and use the query function like you would for any other AnnotationHub resource:

library(AnnotationHub)

# create an AnnotationHub connection
ah <- AnnotationHub()

# use AnnotationHub to get an OrgDb object for T. gondii ME49
res <- query(ah, c('Toxoplasma gondii ME49', 'OrgDb', 'EuPathDB'))
orgdb <- res[[1]]

To create a local package of a EuPathDB resource, and get information from it:

library(EuPathDB)
## I pretty much always use Leishmania major strain friedlin as my example.
lm_entry <- get_eupath_entry(species="Friedlin")
lm_name <- sc_entry[["Species"]]
lm_name
orgdb_pkgname <- make_eupath_orgdb(lm_entry)
txdb_pkgname <- make_eupath_txdb(lm_entry)
bsgenome_pkgname <- make_eupath_bsgenome(lm_entry)
organismdbi_pkgname <- make_eupath_organismdbi(lm_entry)

## Get a big monster data table of annotations
major_annotations <- load_orgdb_annotations(orgdb_pkgname)
## Or GO categories
major_go <- load_orgdb_go(orgdb_pkgname)

avail_columns <- AnnotationDbi::columns(orgdb_pkgname)

## Or interpro categories
chosen_columns_idx <- grepl(x=avail_columns, pattern="^INTERPRO")
chosen_columns <- avail_columns[chosen_columns_idx]
lm_interpro <- load_orgdb_go(lm_orgdb, columns=chosen_columns)

## Or Orthologs
chosen_columns_idx <- grepl(x=avail_columns, pattern="^ORTHOLOGS")
chosen_columns <- avail_columns[chosen_columns_idx]
lm_ortho <- load_orgdb_go(lm_orgdb, columns=chosen_columns)

## Or Pathway data
chosen_columns_idx <- grepl(x=avail_columns, pattern="^PATHWAY")
chosen_columns <- avail_columns[chosen_columns_idx]
lm_path <- load_orgdb_go(lm_orgdb, columns=chosen_columns)

## Or KEGG
chosen_columns_idx <- grepl(x=avail_columns, pattern="KEGG")
chosen_columns <- avail_columns[chosen_columns_idx]
lm_kegg <- load_orgdb_go(lm_orgdb, columns=chosen_columns)

Check the vignettes for more examples!

eupathdb's Issues

Cannot find OrgDB objects from EuPathDb in AnnotationHub

Hi,

The latest AnnotationnHub data only shows GRanges and TxDB objects from EuPathDB. I am specifically interested to get OrgDB objects from FungiDB. Is there any way to get that? I did that in the past with Bioc version 3.9. However, with the current version cannot see any OrgDB objects from FungiDB or EuPathDB.

How to download .sqlite file for all OrgDB in one go ?

Hi,

I got the list of species and OrgDB objects using code below. How can I download all .sqlite files in one go ?

library(magrittr)
#> Warning: package 'magrittr' was built under R version 4.1.2
metadata <- EuPathDB::download_eupath_metadata(webservice = "fungidb")
#> Unable to find species names for 1 species.
#> Pneumocystis sp. 'macacae' P2C
#> Warning in xref_species(valid = taxa_xref[["matched_metadata"]], invalid =
#> taxa_xref[["unmatched_metadata"]], : How in the flying hell are these still
#> here: Melampsora larici-populina 98AG31.

metadata_tbl <- tibble::enframe(metadata) %>% 
        dplyr::filter(name != "invalid") %>% tidyr::unnest()
#> Warning: `cols` is now required when using unnest().
#> Please use `cols = c(value)`

metadata_tbl_sub <- metadata_tbl %>% 
        dplyr::select(GenusSpecies, TaxonUnmodified, TaxonXref,DataProvider, Genome,OrgdbPkg, OrgdbFile)

metadata_tbl_sub$OrgdbFile %>% head()
#> [1] "EuPathDB/OrgDb/3.14/org.Aluchuensis.IFO.4308.v59.eg.sqlite"               
#> [2] "EuPathDB/OrgDb/3.14/org.Eglyceriae.E277.v59.eg.sqlite"                    
#> [3] "EuPathDB/OrgDb/3.14/org.Aversicolor.CBS.583.65.v59.eg.sqlite"             
#> [4] "EuPathDB/OrgDb/3.14/org.Asydowii.CBS.593.65.v59.eg.sqlite"                
#> [5] "EuPathDB/OrgDb/3.14/org.Pcinnamomi.var.cinnamomi.CBS.144.22.v59.eg.sqlite"
#> [6] "EuPathDB/OrgDb/3.14/org.Awentii.DTO.134E9.v59.eg.sqlite"

^{Created on 2022-10-18 with reprex v2.0.2}

Create README.md

• Point users to vignette / AnnotationHub
• Describe purpose of this package and how it might be used outside of it's use for AH package generation.

EOFs sneaking into results from posting to the new webservices

Hi Keith,
If you would like a puzzle, there appear to be EOFs finding their ways into the middle of results from various queries; but I haven't figured out where/why. Once upon a time I wrote a check for this in the old implementation.

Update GRanges vignette

How to get current release (41) data of fugiDB through annotationhub

Hi,

I am using annotation hub to use fungidb data. All the fungidb data (object class : OrgDB and GRages)
are of fungidb-release 39. However, current release of fungi db is 41. I wonder, how can I use fungidb release 41 data through annotation hub.

Thanks.

Update OrgDb vignette

OrgDb datasets missing from recent AH versions?

E.g.:

AnnotationHub with 895 records
# snapshotDate(): 2022-04-25
# $dataprovider: FungiDB, TriTrypDB, PlasmoDB, MicrosporidiaDB, ToxoDB, CryptoDB, AmoebaDB, PiroplasmaDB, GiardiaDB, TrichDB
# $species: Plasmodium falciparum, Trypanosoma cruzi, Toxoplasma gondii, Cryptosporidium hominis, Trypanosoma brucei, Plasmodium yoelii,...
# $rdataclass: GRanges, TxDb
...

Either the process needs to be updated to make those datasets available, or the README should be updated to not point to these files.

Revise Vignette

Hi Developers.

The current vignette of EuPathDB is quite old. Most of the commands in it does not work now. Kindly update them.