ExAC

ExAC Resource Interface

Introduction

The Exome Aggregation Consortium (ExAC) Browser is a product created at the Broad Institue. It contains genomic information ono ver 60,000 individuals who were sequenced through a variety of projects. You can learn more about this project at the ExAC web site (exac.broadinstitute.org).

As part of the NIH BD2K PIC-SURE Center of Excellence http://www.pic-sure.org the HMS Department of Biomedical informatics https://dbmi.hms.harvard.edu extended the ExAC application by providing a REST service. These services enable a user to integrate ExAC services into their own tools, querying the variant information and returning the data in an easy to use JSON format.

You can learn more here: http://exac.hms.harvard.edu/

Installation

1. Run the latest version of the ExAC setup.sql script which can be found here.

2. Edit the following script parameters:

• {{exacresourcename.msg}} - The name of ExAC Service (e.g. HMS ExAC)
• {{exacresourceurl.msg}} - The URL of the ExAC service (e.g. http://exac.hms.harvard.edu)

3. Run the sql script against the IRCT DB.
4. Restart the IRCT

Where Clauses (Predicates)

- Query

• Display Name: Query
• Name: QUERY
• Description: Look up by a query string

Fields

Name	Path	Description	Required	Types	Supported Values
Query String	QUERY	Query String	True	String	NA

- Region

• Display Name: Region
• Name: REGION
• Description: Look up by region

Fields

Name	Path	Description	Required	Types	Supported Values
Chromosome	CHROMOSOME	Chromosome	True	String	NA
Start	START	Start Position	True	String	NA
Stop	STOP	Stop Position	True	String	NA

- Variant

• Display Name: Variant
• Name: VARIANT
• Description: Look up by variant

Fields

Name	Path	Description	Required	Types	Supported Values
Chromosome	CHROMOSOME	Chromosome	True	String	NA
Position	POSITION	Variant Position	True	String	NA
Reference	REFERENCE	Variant Reference	True	String	NA
Variant	VARIANT	Variant	True	String	NA

Processes

- Calculate Rarity

• Display Name: Calculate Rarity
• Name: RARITY
• Description: Calculate the rarity of a variant against the ExAC database

Fields

Name	Path	Description	Required	Types	Supported Values
Result	RESULTSET	Result Set	True	ResultSet	NA
Chromosome	CHROMOSOME	Chromosome Column	True	Column	NA
Position	POSITION	Position Column	True	Column	NA
Reference	REFERENCE	Reference Column	True	Column	NA
Variant	VARIANT	Variant Column	True	Column	NA