In ju-mu/PANTHER.db: A set of annotation maps describing the entire PANTHER Gene Ontology

Introduction to PANTHER.db {-}

The r Biocpkg("PANTHER.db") package provides a select interface to the compiled PANTHER ontology residing within a SQLite database.

PANTHER.db can be installed from Bioconductor using

if (!requireNamespace("BiocManager")) install.packages("BiocManager")
BiocManager::install("PANTHER.db")

The size of the underlying SQLite database is currently about 500MB and has to be pre downloaded using AnnotationHub as follows

if (!requireNamespace("AnnotationHub")) BiocManager::install("AnnotationHub")
library(AnnotationHub)
ah <- AnnotationHub()
query(ah, "PANTHER.db")[[1]]

Finally PANTHER.db can be loaded with

library(PANTHER.db)

If you already know about the select interface, you can immediately learn about the various methods for this object by just looking at the help page.

help("PANTHER.db")

When you load the PANTHER.db package, it creates a PANTHER.db object. If you look at the object you will see some helpful information about it.

PANTHER.db

By default, you can see that the PANTHER.db object is set to retrieve records from the various organisms supported by http://pantherdb.org. Methods are provided to restrict all queries to a specific organism. In order to change it, you first need to look up the appropriate organism identifier for the organism that you are interested in. The PANTHER gene ontology is based on the Uniprot reference proteome set. In order to display the choices, we have provided the helper function availablePthOrganisms which will list all the supported organisms along with their Uniprot organism name and taxonomy ids:

availablePthOrganisms(PANTHER.db)[1:5,]

Once you have learned the PANTHER organism name for the organism of interest, you can then change the organism for the PANTHER.db object:

pthOrganisms(PANTHER.db) <- "HUMAN"
PANTHER.db
resetPthOrganisms(PANTHER.db)
PANTHER.db

As you can see, organisms are now restricted to Homo sapiens. To display all data which can be returned from a select query, the columns method can be used:

columns(PANTHER.db)

Some of these fields can also be used as keytypes:

keytypes(PANTHER.db)

It is also possible to display all possible keys of a table for any keytype. If keytype is unspecified, the FAMILY_ID will be returned.

go_ids <- head(keys(PANTHER.db,keytype="GOSLIM_ID"))
go_ids

Finally, you can loop up whatever combinations of columns, keytypes and keys that you need when using select or mapIds.

cols <- "CLASS_ID"
res <- mapIds(PANTHER.db, keys=go_ids, column=cols, keytype="GOSLIM_ID", multiVals="list")
lengths(res)
res_inner <- select(PANTHER.db, keys=go_ids, columns=cols, keytype="GOSLIM_ID")
nrow(res_inner)
tail(res_inner)

By default, all tables will be joined using the central table with PANTHER family IDs by an inner join. Therefore all rows without an associated PANTHER family ID will be removed from the output. To include all results with an associated PANTHER family ID, the argument jointype of the select function must be set to left.

res_left <- select(PANTHER.db, keys=go_ids, columns=cols,keytype="GOSLIM_ID", jointype="left")
nrow(res_left)
tail(res_left)

To access the PANTHER Protein Class ontology tree structure, the method traverseClassTree can be used:

term <- "PC00209"
select(PANTHER.db,term, "CLASS_TERM","CLASS_ID")

ancestors <- traverseClassTree(PANTHER.db,term,scope="ANCESTOR")
select(PANTHER.db,ancestors, "CLASS_TERM","CLASS_ID")

parents <- traverseClassTree(PANTHER.db,term,scope="PARENT")
select(PANTHER.db,parents, "CLASS_TERM","CLASS_ID")

children <- traverseClassTree(PANTHER.db,term,scope="CHILD")
select(PANTHER.db,children, "CLASS_TERM","CLASS_ID")

offspring <- traverseClassTree(PANTHER.db,term,scope="OFFSPRING")
select(PANTHER.db,offspring, "CLASS_TERM","CLASS_ID")

SessionInfo {-}

sessionInfo()

ju-mu/PANTHER.db documentation built on March 20, 2021, 10:11 p.m.