Adding Data Sources
Before data can be retrieved, data sources must be added to identify where to get the data. The "Connections" tab is used to add these data sources and to view the properties of the data sources currently being managed.
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Add Conn
Connections Menu choice "Add SOAP Connection..."Add SOAP Connection...
Use this function from the Connections menu or the toolbar to add a data source which uses XML to request and retrieve data from a remote web service. There are three presets on this dialog...
- Pressing the Panzea button fills the fields to add the data source, Panzea, located at NCSU.
- Pressing the Gramene button fills the fields to add the data source, Gramene, located at CSHL.
- Pressing tcpmon is used for testing purposes allowing you to view the XML being passed between the client and server using the program tcpmon.
Connections Menu choice "Add Database Connection..." Add Database Connection...
NOTICE: If you are unsure whether to use this function, you probably want to use the Add SOAP Connection...
Use this function from the Connections menu or the toolbar to add a data source that creates the GDPC connection locally and communicates with a remote/local database using Java JDBC. This can be used for testing during the development of new GDPC Connections or to access non-public databases. You can also access public data with this method, although generally the "Add SOAP Connection" method would be used. There is one preset for the Panzea Connection. Pressing the Panzea button fills all the fields except user id and password.
Adding SOAP Connection...
Use this function to add a SOAP Connection
- End Point: This will normally be the URL identifying the web service.
- Service Name: This is the name of the web service.
Adding Database Connection...
Use this function to add a Database Connection
- Java Class: Java class implementing the DBConnection interface for a particular database.
- JDBC Driver: Java class identifying which JDBC driver to use.
- Database URL: Database URL that addresses the database.
- Data Source: Data source is used by GDPC to uniquely identify where the data originated. This will usually be the same as the Database URL.
- Description: Text description of this data source.
- User ID: User id to use when connecting to the database.
- Password: Password for the given user id.
Retrieving Data
There are tabs for each type of data that can be retrieved. Those tabs are Taxa, Loci, Genotype Experiments, Environment Experiments, Localities, Genotypes, and Phenotypes. By selecting filter criteria, these types of data can be retrieved from the currently managed data sources (see: Adding Data Sources).
Taxa, Loci, Genotype Experiments, Environment Experiments, and Localities
Retrieving taxa, loci, genotype experiments, environment experiments, and localities operate in the same way, and have the following components:
- Filtered List: This list shows the list of data elements matching the selected filter criteria. Selecting an item in this list displays that item's properties in top right window of the tab.
- Working List: The user builds this list by adding and removing data elements specific to their purpose. This will be identical to the filtered list if the two lists are linked together. Selecting an item in this list displays that item's properties in top right window of the tab.
- Property Values: In the upper right of the tab, the table displays the specific property/value pairs of the selected item from the filtered list or working list.
- Filter Criteria: Along the bottom of the tab is the filter criteria. The user can select which properties to include in the filter by clicking check boxes beside the property names. Included properties display a list of distinct values retrieved from the managed data sources. When nothing is selected from a property list, data with any value for that property is retrieved. When one or more values are selected, only data elements matching those values are retrieved.
For example... On the Loci tab, if values 3 and 4 are selected for the "Chromosome Number" property and values "Gene" and "SSR" are selected for the "Locus Type" property, the retrieved data will be items matching chromosome number 3 OR 4 AND locus type equal to "Gene" OR "SSR."
Controls
Pressing this button will unlink the Working List from the Filtered List. Unlinking the working list from the filtered list allows the user to build a custom working list of items. Pressing this button will link the Working List to the Filtered List. Linking the working list to the filtered list will keep all items in both lists the same. Some controls will be disabled since they are invalid when the lists are linked. Pressing this button adds the items selected in the Filtered List to the Working List. Pressing this button adds all the items in the Filtered List to the Working List. Pressing this button displays a dialog that allows the user to sort the filtered or working list based on the property values. Pressing this button removes the selected items from the working list. Pressing this button removes all the items from the working list or filtered list.
Genotypes and Phenotypes
Retrieving Genotypes and Phenotypes creates a table of values. In the case of genotypes, the table displays all values for the selected taxa and genotype experiments. The taxa and genotype experiments shown come from the working lists of their respective tabs. Retrieving phenotypes works basically the same way except that a phenotype ontology must also be chosen. In this case, the table displays the values for the chosen phenotype ontology, taxa, and environment experiments.
Tool Bar and Menu options
Open
File:Open...This button allows the user to select a XML file containing a group of any of the data elements (taxa, loci, genotype experiments, environment experiments, localities, genotypes, or phenotypes). The elements defined by the file are loaded into the working list of the appropriate tab.
Save As
File:Save As...This button allows the user to save the working list of the Taxa, Loci, Genotype Experiments, Environment Experiments, or Localities tabs as a XML file. In the case of Genotypes and Phenotypes, the resulting table is saved.
Export
File:Export...From the Taxa, Loci, Genotype Experiments, Environment Experiments, or Localities tabs, the user can export the respective groups as tab delimited text files. The column headings are the property names and the row headings are the name of the elements. From the genotypes tab, the user can export the first column of the current table as a PHYLIP or PHYLIP Interleaved formated file. Also, Genotypes can be exported as tab delimited text files. The row headings are the Taxon names and the columns can be either the Genotype Experiment names or the Loci names. From the Phenotypes tab, the user can export the table as a tab delimited text file. The row headings are the Taxon names and the columns are the Environment Experiment names. File:Exit This exits the program.
Get Data
View:Get DataPressing this button retrieves the data elements matching the selected filter criteria. If no filter criteria is selected, all data of the current type will be retrieved. WARNING: trying to retrieve very large results may not succeed. In that case, use the filters to reduce the size.
Deselect
View:Deselect AllPressing this button deselects all values in the filter criteria list(s).
Get Started
Help:Get StartedPressing this button pops up a dialog with documentation helping new users get started. Help:Help This pops up a help dialog.
GDPC Home Page: http://www.maizegenetics.net/gdpc/index.html