Table of Contents
Allen Brain Atlas (ABA) data source plugin
User Manual
Introduction
The ABA data source plugins allows the user to query the publicly available Allen Brain Atlas database (
http://www.brain-map.org) and retrieve the images hosted on their website.
Getting Started
To access the ABA data source plugin
- open the Search Workspace
- switch to the query term subworkspace by selecting Search > By query terms in the menu bar
Functional Specification
Search and Data types
The ABA data source plugin supports the following search types:
- Search by query terms
The ABA data source plugin returns the following type of data:
- ABAImageSeries (derived from Image2DSeries)
Supported Query Terms
| Group | Parameter | Value | Supported | Notes |
|---|
| Experimental Info | Project | any | no | |
| Keyword (Project) | no | |
| |
| Gene/Molecule | Gene Attribute | Gene Symbol | yes | |
| Gene Name | yes | |
| Gene Name | yes | |
| Protein | no | |
| Keyword | yes | |
| |
| Subject/Organism | Species | Mouse | yes | |
| Strains | any | yes | |
| C57BL | yes | This is the default value |
| 129s6 | yes | |
| A/J | yes | |
| B6D2F1 | yes | |
| BALB/c | yes | |
| CBA | yes | |
| C3H | yes | |
| DBA | yes | |
| FVB | yes | |
| Developmental Stage | adult | yes | This is the default value |
| embryonic | yes | |
| fetal | yes | |
| neonate/infant | yes | |
| child/pup | yes | |
| juvenile | yes | |
| Sex | any | yes | |
| female | yes | |
| male | yes | |
| other | yes | |
| |
| Anatomical Area/Tissue | Anatomical Area/Tissue | any | yes | |
| CNS (tree) | yes | |
| Other Body Part | yes | |
Annotations
For the ABAImageSeries, the following annotations are listed:
- Area
- Gene
- Gene Name
- Group
- Num Images
- Plane
- Sex
- Stage
- Stain Type
- Strain
- nbci nucleotide
Credentials
No credentials are required to query the ABA database.
Database Connection Type
HTTP
Workspace Interoperability
- Comparison Viewer Workspace
- Open and visualize data using built-in 2D image plugin
Error Handling
| Method | Error | Exception thrown | Notes |
|---|
searchByKeyword() | error establishing connection | yes | |
| connection dropped after initial connection | yes | |
| internal server error | yes | |
searchByQueryTerms() | error establishing connection | yes | |
| connection dropped after initial connection | yes | |
| internal server error | yes | |
DarenLee? - 23 Apr 2009
