Build a gene search service with elastic search

The main purpose of this code is to create indexes on an elastic search instance which in turn will enable searching of genes.

Why?

We wanted a simple service that we could host that would provide search functionality on human genes. This requirement was part of the Sydney Genomics Collaborative

Dependencies

• Go
• An Elasticsearch instance. Indexes for genes and chromosomes will be created on this server. See shusson/docker-bouncy for a containerised version of this.
• Ensembl SQL server. This is the server where we get the data from. By default we use one of ensembls public servers but you can also instantiate your own and populate it with data.

Installation

go get github.com/shusson/genesearch
go install github.com/shusson/genesearch

Usage

Run with default settings

$GOPATH/bin/genesearch

Customise with flags

$GOPATH/bin/genesearch -help
Usage of genesearch:
  -DSN string
    	Specify the Data Resource of the ensembl SQL server you want to connect to. More info: https://github.com/go-sql-driver/mysql#dsn-data-source-name (default "anonymous@tcp(asiadb.ensembl.org:3306)/homo_sapiens_core_87_38")
  -coord int
    	specify coordinate system id. defaults to 4 which is chromosome GRCh38. This value will depend on what release of ensembl is used (default 4)
  -elastic url string
    	Specify the Elastic search server you want to connect to. (default "http://127.0.0.1:32840")
  -replicas int
    	specify number of replicas. defaults to 0.
  -shards int
    	specify number of shards. defaults to 1. (default 1)
  -tests
    	run some functional tests against the elastic search instance

Tests

Once you have built the indexes you can run some simple sanity tests (currently only works for homo_sapiens_core_87_38)

$GOPATH/bin/genesearch -test

or use curl to manually test certain genes

curl -XGET 'localhost:32840/_search?pretty' -d'
{
    "query": {
        "match_phrase_prefix" : {
            "symbol" : {
                "query" : "REST"
            }
        }
    },
    "sort": "symbol.raw"
}'

Live Example

https://sgc.garvan.org.au/search

Notable alternatives

• ICGC - http://docs.icgc.org/portal/api-endpoints/#/keyword

• MyGene.Info - http://mygene.info/