Table of Contents
GENSAT(Rockefeller) data source plugin
User Manual
Introduction
The GENSAT (Rockefeller) data source plugins allows the user to query the publicly available GENSAT database from
http://www.gensat.org) and retrieve the images hosted on at NCBI.
Getting Started
To access the GENSAT 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 GENSAT (Rockefeller) data source plugin supports the following search types:
- Search by query terms
The GENSAT (Rock data source plugin returns the following type of data:
- 2D Image Series
- Gene
- Gene Expression
Supported Query Terms
| Group | Parameter | Value | Supported | Notes |
|---|
| Experimental Info | Project | any | yes | |
| 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 | |
| 129s6 | yes | |
| A/J | yes | |
| B6D2F1 | yes | |
| BALB/c | yes | |
| CBA | yes | |
| C3H | yes | |
| DBA | yes | |
| FVB | yes | |
| Developmental Stage | adult | yes | |
| 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 Gene, the following annotations are listed:
- Name
- Gene Aliases
- Gene
- Gene ID
- PubMed ID
- Organism
- GenePaint URL
- Entrez URL
- GNF(Genomics Institute of the Novartis Research Foundation) URL
- NCBI UniGene URL
- KEGG URL
- MGI Gene Detail URL
- MGI Expression Data URL
For the GensatImageSeries, the following annotations are listed:
- Name
- Plane
- Number of Images
- Stage
- Sex
- Image Series ID
- Image Series Display Name
- Upload Date
- Technique
For the GensatExpression, the following annotations are listed:
- Name
- Gene
- Gene Density
- Gene Level
- Tissue
- Stage
Credentials
No credentials are required to query the GENSAT (Rockefeller) database.
Database Connection Type
SOAP
Workspace Interoperability
- Comparison Viewer Workspace
- Open and visualize data using built-in 2D image plugin
- GeneExpression Viewer
- It would be a new feature of future release.
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 | |
QueenieNg? - 27 Apr 2009
