A Data Scraper for Amazonia (expression)

Today, we had a lecture about the "human induced pluripotent stem cells", presented by John De Vos. He introduced Amazonia, a free web atlas that allows an easy query of public human transcriptome data. Although there is no web service (REST/SOAP) to access this data, I was interested in getting some profiles of expression from this database as it is something I've failed to achieve with NCBI/GEO.

I wrote the following java scraper:

• Line 84: we search for a gene name
• 88: if there is a http redirection, the gene has been found
• 96: the HTML page is downloaded
• 100-112: fix the HTML to create a valid XML document
• 133: transform the HTML page to a DOM document
• 135-151: use XPATH to find the images and the labels
• 189-211; put the data into a java/SWING Dialog

Compilation

javac AmazoniaRobot.java

Execution

java AmazoniaRobot EIF4G1

Et voilà:

That's it !

Pierre