Tutorial: Retrieving Genetic Data from GERMINATE using the GDPC browser

What is GDPC GDPC is the Genomic Diversity and Phenotype Connection. It was developed at University of Cornell by Terry Casstevens and Ed Buckler Advantages of GDPC include The ability to connect to multiple database in a single instance and retrieve datasets including data from multiple database sources Making data available as web services which facilitates the use of databases which are GDPC enabled can be used by analysis and visualization tools which are GDPC aware.

Adding database connection

Adding database connection Click OK to add connection Click to add GERMINATE SOAP connection

Adding database connection GERMINATE database connected. Other databases can be connected simultaneously

Using GDPC Once the database(s) is/are connected to the GDPC browser users can start retrieving datasets. The following slides give an introductory tutorial on how to select and retrieve genotype data using the GDPC Browser.

Selecting datasets Select Genotype Experiments

Selecting datasets Retrieve data Select fields to filter on Select filter criteria

Selecting datasets Filtered List - All data from criteria selected below retrieved here Working List - Can be decoupled from the filtered list to select a subset of entries from the data retrieved Button to unlink the filtered and working lists

Selecting datasets Clears the filtered list. If working and filtered lists are linked both will be cleared Clears selected elements from the working list Clears entire working list Unlinks filtered and working lists. Working lists will be used in other tabs

Selecting datasets Use this button to add selected entries from filtered list to working list Unlinked filtered and working lists. Working lists will be used in other tabs All entries in filtered list can be added to the working list with this button

Selecting Locations Select Localities Tab

Selecting Locations Retrieve data Data Returned from Database Properties for highlighted entry Select filter criteria Select fields to filter on

Selecting Taxa Locations selected to working list in Localities tab can be used here to select taxa

Selecting Taxa Retrieve data Select fields to filter on Select filter criteria

Retrieving genotype data Retrieve data Taxa working list from Taxa tab Genotype Experiments working list from Genotype Experiments tab Retrieves intersection of taxa and genotype experiments from lists below

Retrieving genotype data Deselects all from lists below Select one or more taxa with no experiments selected and all data from that set of taxa will be returned.

Retrieving genotype data Deselects all from lists below Select one or more experiments with no taxa selected and all data from that set of experiments will be returned.