MyGene.info documentation

Introduction

MyGene.info provides simple-to-use REST web services to query/retrieve gene annotation data. It’s designed with simplicity and performance emphasized. A typical use case is to use it to power a web application which requires querying genes and obtaining common gene annotations. For example, MyGene.info services are used to power BioGPS.

Tweets by mygeneinfo

What’s new in v3 API

• Refseq accession number now contains version

• “ensembl”, “refseq” and “accession” contains associations between RNA and protein

• Better mapping between Ensembl and Entrez gene IDs

• JSON structure slightly changed

• and more bugfixes

You can read more details about this version on our blog

Migration guide from v2 to v3 API

Still want to stick with v2 API for a while? It’s still there: v2 API, but annotation data there won’t be updated any more.

Quick start

MyGene.info provides two simple web services: one for gene queries and the other for gene annotation retrieval. Both return results in JSON format.

Gene query service

URL

http://mygene.info/v3/query

Examples

http://mygene.info/v3/query?q=cdk2
http://mygene.info/v3/query?q=cdk2&species=human
http://mygene.info/v3/query?q=cdk?
http://mygene.info/v3/query?q=IL*
http://mygene.info/v3/query?q=entrezgene:1017
http://mygene.info/v3/query?q=ensemblgene:ENSG00000123374
http://mygene.info/v3/query?q=cdk2&fields=symbol,refseq

Hint

View nicely formatted JSON result in your browser with this handy add-on: JSON formater for Chrome or JSONView for Firefox.

To learn more

• You can read the full description of our query syntax here.

• Try it live on interactive API page.

• Play with our demo applications.

• Batch queries? Yes, you can. do it with a POST request.

Gene annotation service

URL

http://mygene.info/v3/gene/<geneid>

Examples

http://mygene.info/v3/gene/1017
http://mygene.info/v3/gene/ENSG00000123374
http://mygene.info/v3/gene/1017?fields=name,symbol,summary

“<geneid>” can be any of valid Entrez or Ensembl Gene ids. A retired Entrez Gene id works too if it is replaced by a new one.

To learn more

• You can read the full description of our query syntax here.

• Try it live on interactive API page.

• Play with our demo applications.

• Yes, batch queries via POST request as well.

Documentation

• Try it live on interactive API page
• Migration from v2 API
  • URL change
    • Gene query service endpoint
    • Gene annotation service endpoint
  • Returned Objects
    • Accession number with version
    • “translation” field for RNA-protein mapping
    • “exons” data structure modification
    • “dotfield” notation default changed
    • Querying “reporter” data source
• Gene annotation data
  • Data sources
  • Gene object
  • _id field
  • _score field
  • Species
  • Genome assemblies
  • Available fields
• Data release notes
  • MyGene Releases
• Gene query service
  • Service endpoint
  • GET request
    • Query parameters
    • Query syntax
    • Returned object
    • Faceted queries
    • Scrolling queries
  • Batch queries via POST
    • Query parameters
    • Example code
    • Returned object
• Gene annotation service
  • Service endpoint
  • GET request
    • Query parameters
    • Returned object
  • Batch queries via POST
    • Query parameters
    • Example code
    • Returned object
• Server response
  • Status code 200
  • Status code 400
  • Status code 404
  • Status code 5xx
• Usage and Demo
  • Call from web applications
    • Calling services from server-side
    • Making AJAX calls from client-side
  • Demo Applications
    • Example 1: using CGI
    • Example 2: using tornado
    • Example 3: using JSONP
    • Example 4: using CORS
  • Autocomplete widget for gene query
    • Try it live first
    • About this widget
    • Use it in your website
• Third-party packages
  • MyGene python module
  • MyGene R package
  • MyGene autocomplete widget
  • Another MyGene Python wrapper
• Terms of Use

How to cite

See citation page here: http://mygene.info/citation/

FAQ

See FAQ page here: http://mygene.info/faq/

Related links

• mygene.info on Github

Contact us

• help@mygene.info

• @mygeneinfo