Querying InterMine databases using R

2016-06-17

In the past, I had found some ways to do simple queries on InterMine web services using basic HTTP commands with R (see https://gist.github.com/cmdcolin/4758167bdd89e6c9c055)

However, the InterMineR (https://github.com/intermine/intermineR) package automates some of these features and makes it easier to load the data in R.

#Installation

One way to install InterMineR is to install from github with hadley/devtools

install.packages("devtools")
devtools::install_github("hadley/devtools")
devtools::install_github("intermine/intermineR")

#Usage

Basic usage includes loading the "intermine URL" using the initInterMine function. Then various functions can be called on this result.

library(InterMineR)
mine=initInterMine("http://bovinegenome.org/bovinemine/")
getVersion(mine) #18, intermine API version
getRelease(mine) #1.0, our data release version
getTemplates(mine) # lists all templates on interminer

#Run a template query

From the getTemplates function, if you see a template query that you want to run, you can use the getTemplateQuery function with it's name, and run it with the runQuery function

getTemplateQuery(mine,"TQ_protein_to_gene") # see what template looks like
template=getTemplateQuery(mine,"TQ_protein_to_gene") # save template
runQuery(mine,template) # run the template query with default params, receive data.frame

This method is good, but some improvement could be added to change default parameters in the template query, etc.

#Run query XML

Another option for running queries is to use the query XML that you can download from the InterMine query result pages.

# get all Ensembl genes on chr28 from bovinemine
query='<query model="genomic" view="Gene.primaryIdentifier
Gene.secondaryIdentifier Gene.symbol Gene.name Gene.source
Gene.organism.shortName Gene.chromosome.primaryIdentifier"
sortOrder="Gene.primaryIdentifier ASC" ><constraint
path="Gene.organism.shortName" op="=" value="B. taurus"
/><constraint path="Gene.chromosome.primaryIdentifier" op="="
value="GK000028.2" /></query>'
 
results=runQuery(mine, query)
 
head(results)

#Conclusion

The InterMineR package has a couple of nice features for getting InterMine data with a couple of functions for looking at templates. For many use cases, copying the Query XML from a InterMine webpage and pasting that into the runQuery function is sufficient and produces a data frame that can be analyzed.

PS it is not easy to post XML on tumblr after editing the post in markdown mode. You have to add the lt and gt shortcuts and even after that it gets filtered?!