MyGeneset.info documentation¶
Introduction¶
MyGeneset.info provides simple-to-use REST web services to query, retrieve, and store annotation data for collections of genes. It’s designed with an emphasis on simplicity and performance.
Features¶
Access curated genesets from public databases, including: GO, KEGG, MSigDB, Disease Ontology/OMIM, Wikipathways, and Reactome.
Filter genesets to an organism of interest.
Retrieve gene collections with an identifier of choice.
Quick start¶
MyGeneset.info provides two simple web services: one for querying stored geneset objects and the other for geneset annotation retrieval. Both return results in JSON format.
Geneset query service¶
URL¶
http://mygeneset.info/v1/query
Examples¶
# Search genesets with 'glucose' in a default query field (geneset name or description)
http://mygeneset.info/v1/query?q=glucose
# Retreive NCBI gene ids for genes in genesets with 'glucose' in a default query field
http://mygeneset.info/v1/query?q=glucose&fields=genes.ncbigene
# Fetch all genesets containing the gene with symbol ABL1
http://mygeneset.info/v1/query?q=genes.symbol:ABL1
# Filter the previous query to human species
http://mygeneset.info/v1/query?q=genes.symbol:ABL1&species=human
# Fetch all genesets belonging to two mice or human organisms
http://mygeneset.info/v1/query?species=mouse,human
# Fetch all genesets from the source "wikipathways"
http://mygeneset.info/v1/query?q=source:wikipathways
# Wildcard queries
http://mygeneset.info/v1/query?q=genes.symbol=cdk?
http://mygeneset.info/v1/query?q=genes.symbol=IL*
# Search genesets containing all of the provided genes
http://localhost:8000/v1/query?q=genes.symbol:(ABL1 AND CEBPA AND FLT3)&fields=all
# Search genesets containing any of the provided genes
http://localhost:8000/v1/query?q=genes.symbol:(ABL1 OR CEBPA OR FLT3)&fields=all
Hint
View nicely formatted JSON results 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.
Batch queries? Yes, you can. do it with a POST request.
Geneset annotation service¶
URL¶
http://mygeneset.info/v1/geneset/<genesetid>
Examples¶
http://mygeneset.info/v1/geneset/WP100
http://mygeneset.info/v1/geneset/GO_0000002_9606
http://mygeneset.info/v1/geneset/R-HSA-112043?fields=genes.ensemblgene,reactome,taxid
To learn more¶
You can read the full description of our query syntax here.
Try it live on interactive API page.
Yes, batch queries via POST request as well.
Documentation¶
How to cite¶
See citation page here: http://mygeneset.info/about#cite
FAQ¶
See FAQ page here: http://mygeneset.info/about#faqs