Challenge 12 - Obtaining a List of Human Genes via REST - Solution

0 ×

You have been working for a Life Sciences company for a month as a a data wrangler. Several coworkers from the Biology department would like to obtain a list of human genes related to specific hormones, but they do not know how to use REST services, GET requests, etc. Your task is to use the REST service provided by MyGene.info to obtain a list of human genes related to a list of hormones provided to you by your coworkers. Next, you should parse the JSON response into a table that is easy to read.

For example, if you use "http://mygene.info/v3/query?q=summary:" and append "insulin", then your request would return a JSON structure with 10 hits -- each one of them with the following fields: "_id", "_score", "entrezgene", "name", "symbol", and "taxid".

You should then parse this JSON into a table with columns "_id", "_score", "entrezgene", "name", "symbol", and "taxid". If the list provided by your coworkers contains more than one hormone, all the parsed information should be aggregated into a single table. Also, sometimes your request may return a response in XML instead of JSON. How could you include a way to also parse XML responses?

URL: MyGene.info https://mygene.info/

Nodes

• CASE Switch Start1 ×
• CSV Reader1 ×
• Component Input1 ×
• Component Output1 ×
• GET Request1 ×
• JSON Path1 ×
• JSON To XML1 ×
• String Manipulation1 ×
• String Widget1 ×
• Ungroup1 ×
• XPath1 ×

Extensions

• FeatureKNIME Base nodes
• FeatureKNIME Javasnippet
• FeatureKNIME JSON-Processing
• FeatureKNIME Quick Forms
• FeatureKNIME REST Client Extension
• Show all 6 modules

Links

• No links available