Fetching Data With BioGroovy

With BioGroovy 1.1 we’ve added support for fetching data from a variety of RESTful webservices, including: EntrezGene, PubMed, UniProt and many others.

Fetching Data
In this example, we’ll fetch gene information from EntrezGene for 3 genes, and output the result to the console.

import org.biogroovy.io.eutils.EntrezGeneSlurper;
import org.biogroovy.models.Gene;
@Grab(group='org.biogroovy', module='biogroovy', version='1.1')

EntrezGeneSlurper slurper = new EntrezGeneSlurper();

println “Gene”
println “Symbol\tEntrezGeneID\tName”

List<Gene> geneList = slurper.fetchAll(‘675,1034,133’);
geneList.each{Gene gene ->
println “${gene.symbol}\t${gene.entrezGeneId}\t${gene.name}”

In the slurper.fetchAll() method call, we pass a string containing a comma-delimited list of EntrezGene IDs.  This return a list of Gene objects.  We iterate through the gene list and print the results out to the console.


About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.
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