Icon

Challenge 12 - Obtaining a List of Human Genes via REST

Challenge 12 - Obtaining a List of Human Genes via REST
Challenge 12 - Obtaining a List of Human Genes via REST Description: You have been working for a Life Sciences company for a month as a a data wrangler. Several coworkers from the Biologydepartment would like to obtain a list of human genes related to specific hormones, but they do not know how to use REST services, GETrequests, 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 hormonesprovided 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 structurewith 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 byyour coworkers contains more than one hormone, all the parsed information should be aggregated into a single table. Also, sometimes yourrequest may return a response in XML instead of JSON. How could you include a way to also parse XML responses? DATA PREPROCESSING PARSE REST SERVICE RESULTS Read list of HormonesBuild RequestURLRequestlist of hormonesTop: JSON ParserBottom: XML to JSONParseXML (if available)Parsed JSON + Parsed XMLCSV Reader String Manipulation GET Request Rule-basedRow Splitter Parse JSON XPath Concatenate Challenge 12 - Obtaining a List of Human Genes via REST Description: You have been working for a Life Sciences company for a month as a a data wrangler. Several coworkers from the Biologydepartment would like to obtain a list of human genes related to specific hormones, but they do not know how to use REST services, GETrequests, 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 hormonesprovided 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 structurewith 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 byyour coworkers contains more than one hormone, all the parsed information should be aggregated into a single table. Also, sometimes yourrequest may return a response in XML instead of JSON. How could you include a way to also parse XML responses? DATA PREPROCESSING PARSE REST SERVICE RESULTS Read list of HormonesBuild RequestURLRequestlist of hormonesTop: JSON ParserBottom: XML to JSONParseXML (if available)Parsed JSON + Parsed XMLCSV Reader String Manipulation GET Request Rule-basedRow Splitter Parse JSON XPath Concatenate

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: USER
Created at: 2022-04-19
On NodePit since: 2022-04-20
Last update: 2024-05-02
Created with KNIME version: v4.5.0
Tags: #justknimeit#justknimeit-12

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!