Welcome to Specify 6

1. What is the Specify 6 WorkBench?

In 2005 and 2006, the Specify Project development team spoke with many biological collection managers and curators to analyze requirements for our new, Java-based, Specify 6. While conducting interviews and reading evaluations it became clear that the collections community needed a separate tool for working with data before they were cataloged into Specify. Some collections require such a tool for entering legacy data; others want a small, standalone tool to take into the field, and still others need to manipulate their data before cataloging it in Specify without having to enter it into a spreadsheet first, and then re-enter it into Specify later.

2. Which collection data tasks is the WorkBench optimized for?

The WorkBench has been primarily designed as a tool for uploading batches of information into Specify 6. These could be files created in the field while collecting, legacy data existing in your collection but not digitized or any other file that may require manipulation before uploading. There may also be instances where you would like to make use of the special functions within the WorkBench to perform certain tasks.

3. Why should I use the Specify WorkBench rather than a spreadsheet application for specimen data entry?

The major advantage of the WorkBench over a spreadsheet is the Mapping function which allows you to map your column headers to existing fields in the Specify 6 data model for later uploading. It also obviates the need to enter data multiple times when using a spreadsheet. There are also functions and tools contained in the WorkBench that are not integrated into any existing spreadsheet package that are of great value to the collections community.

4. Where are data stored in the Specify WorkBench?

Data Sets are stored in a database that resides in the DerbyDatabase directory of the WorkBench. The WorkBench also makes MS Excel backup files of saved Data Sets to the Specify/Backups directory. Five copies of any of the Data Sets are saved, after which the first copy will be overwritten. In order to save information for data recovery, you should copy the DerbyDatabase directory to another location periodically.

5. How does the WorkBench relate to the full version of Specify 6?

The WorkBench is a component of the full Specify 6 release due out in early 2008. It is a feature of Specify that has been most often requested by users, and as such, is being released as a stand-alone component until the first shipment of Specify 6. It will also be an integral part of the full Specify release.

6. What technology components were used to develop the WorkBench?

Specify 6 and the WorkBench use the following technologies:

Apache Commons
Hibernate
JasperReports
Java
Java DB
JDBC
JFreeChart
Lucene
MySQL

7. Will the WorkBench be supported after the complete version of Specify 6 is released?

We will release an update to the WorkBench in early fall 2007. The present version of the WorkBench will be superseded by the version that ships with the full release of Specify 6 in early 2008.

8. What will happen to the data in the WorkBench when Specify 6 is released?

Data Sets saved in the WorkBench will be uploaded directly into Specify 6 once it is released. A validation step will ensure the integrity of data entering Specify 6 at which time all fields of information will be checked against existing data.

9. Why is there only one user “guest” and why can’t we add users?

The standalone version of the WorkBench was intended as a single user application and does not require user management, so there is a single login. The full version of Specify 6 will contain full functionality for user creation and security settings.

10. What is the distinction between a database and a Data Set in the WorkBench? And how will the full release of Specify 6 handle them?

A database holds multiple Data Sets. A Data Set represents the rows and columns of data from a spreadsheet.

11. Why are there a limited number of reports and charts in the WorkBench? How can I add more?

This version of the WorkBench provides a basic set of reports and charts as an overview of what the package is capable of producing. Specify 6 will enable you to create, add edit additional reports.

12. Why are the Google Earth and BioGeomancer icons not active and grayed out with some data sets?

Both Google Earth and BioGeomancer require certain fields to be pre-filled and certain fields to be present in order for them to work.
Google Earth requires latitude and longitude coordinates to be present in order to map points onto the landscape. BioGeomancer requires country, state, county and locality name fields to be pre-filled with data while also requiring a latitude and longitude field for transfer of the coordinate data generated.

13. What happens to all of the metadata (beyond latitude and longitude) returned by BioGeomancer?

The WorkBench will store all metadata created by BioGeomancer during record query. These fields cannot be viewed as columns in the Data Set itself, but will be available for upload into the full version of Specify 6. The following fields of information are stored together with the latitude and longitude fields:

Country Bounding Box
Bounding Box
Bounding Box Centroid
Bounding Box Centroid Error Radius
Bounding Box Centroid Error Radius Units l Multi Point Match l Weighted Centroid

14. How can I import and append a new batch of data to an existing data set in the WorkBench?

This feature will be available in Specify 6. At this time, it is best to create a new Data Set and reuse the column headers from an existing data Set.

15. What image formats are supported by the WorkBench Image Import feature?

Currently, the WorkBench supports JPG, GIF, and PNG file types. The full Specify 6 release will also support TIFF.