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 Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
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