GeneNetwork (GN) data source plugin

User Manual

Introduction

The GN data source plugins allows the user to query the publicly available GeneNetwork database (http://www.genenetwork.org/) and retrieve a list of query results (Trait, include GeneExpression and Phenotype). Every Trait (include GeneExpression and Phenotype) contains about 100 strains.

Getting Started

To access the GN data source plugin

1. open the Search Workspace
2. switch to the keyword subworkspace by selecting Search > By keyword in the menu bar

Functional Specification

Search and Data types

The GN data source plugin supports the following search types:

1. Search by keyword

The GN data source plugin returns the following type of data:

1. Vector<mbQueryResult>, list of query results (Trait, include GeneExpression and Phenotype). Every Trait (include GeneExpression and Phenotype) contains about 100 strains. Put the strains into GeneExpression/Phenotype as Children (defined as Vector<mbAnnotatedObject> in class mbAnnotatedObject).

Annotations

For the GeneExpression, the following annotations are listed:

1. Name
2. Gene description
3. Dataset
4. Gene symbol
5. Chromosome
6. Tissue/Cell
7. Mb

For the Phenotype, the following annotations are listed:

1. Name
2. Source
3. Annotation
4. Author

Credentials

No credentials are required to query the GN database.

Database Connection Type

HTTP

Workspace Interoperability

Error Handling

LeiYan - 01 May 2009