Specify Setup

Specify Setup

Specify's flexible design can accommodate a single user with a single collection, or multiple collections representing multiple disciplines within an institution - all sharing the same database. This is accomplished by creating relationships among collection data, as well as modeling how collections are organized within institutions themselves, and then configuring components within Specify specifically for each institutional level.

What this means for the user, is that Specify 6 can be configured to work congruently with existing collection management procedures, but it requires a thoughtful setup process. This process may vary depending on how Specify was installed. If you were a Specify 5 user and have worked with the Specify Consortium staff to convert your data, many of the setup steps will have been performed for you. However, we recommended that you read the help sections for each of the modules to better understand how each module can be utilized to meet your needs.

If you installed Specify 6 and ran the Specify Setup Wizard to create a new, blank database, we recommend that you now perform the following procedures to customize the Specify setup to your particular needs.

1. Add institutional levels (divisions, disciplines, collections)

Systems that were created by first running the Specify Setup Wizard will include one of each of the institutional levels (institution, division, discipline, collection and user). Most systems will require more than one of each of these institutional levels.

Add collections, disciplines and divisions in the System Configuration at System > System Setup > Configuration.


2. Add users and set user permissions

Once these institutional levels are configured, users can be added to each of the collections. Specify offers an extensive permission system that controls each user's access to both the data and tools within Specify.

Add users and set user permissions using the Security tools found at System > System Setup > Security Tools.

Once the institutional levels, users and permissions are complete, information specific to each discipline can be configured.


3. Check and/or set Tree Definitions

A Storage tree that can be accessed by the entire institution was created using the Setup Wizard. Taxon, Geography, Lithostratigraphy and Chronostratigraphy (if applicable) trees were also created, which are shared by each collection within the division.

The ranks in the trees as well as the Enforced ranks and Full Name configuration were also created for each tree in a division. These are considered part of the Tree Definition, and it is recommended that users check these Tree Definitions before entering data. Tree Definitions are found by clicking the Tree button on the Tab Bar, then clicking the appropriate Tree Definition button on the side bar.


4. Customize the Schema Configuration

A number of changes can be made to the fields and tables within Specify by using the Schema Configuration tool:

  • Hide Fields
  • Change Captions
  • Set Required Fields
  • Change Table Format
  • Change a Field Format
  • Configure Table Aggregation


Editing the schema configuration allows users to customize fields and tables within Specify for each of the disciplines. The Schema Configuration tool is found at System > Schema Configuration.

5. Customize System Pick Lists and Preparation Types

A variety of System Pick Lists exist within the Specify form system as drop-down lists. These can be edited in a System Configuration module, found at System > System Setup > Configuration. System Pick Lists refer to fields that are denoted as Pick Lists within Specify itself. Fields that are not denoted as Pick Lists by Specify are referred to as User-Defined Pick Lists. User-Defined Pick Lists require a change to any forms that include the field and should NOT be changed until the new form has been imported into Specify.

The Preparation Type pick list ships with specific data for each discipline, which can be edited in the Configuration tool as well.

6. Create Reports

Reports can be created for use in Specify. Reports may include labels for specimens or invoices for loans as well as reports for collection data. Each institution will have different needs. It is helpful to have reports created before users start entering data into the database that are based on your specific needs. Specify uses iReport 3.0, an open source report writing software package, by modifying the original iReport version to interact with Queries created in Specify 6 and data supplied from the Specify 6 database. SpecifyiReport is a separate application and must be launched separately from Specify. SpecifyiReport is located in the Specify application bin directory.

7. Change Attachment Storage Location

Attachments are copied, renamed using a unique name, and stored in an Attachment Storage location. Only the path to the attachment storage location is stored in the Specify database. The Specify Setup Wizard sets a default storage location on the local drive but this location can be changed in System Preferences:

  • For Mac: Specify > Preferences > System > Attachment Storage Location.
  • For PC and Linux: Choose Edit > Preferences > System > Attachment Storage Location.

8. Customize the Backup and Restore function

A Backup and Restore tool ships with Specify as a separate application. It allows IT personnel to backup and restore the database to the MySQL location on the server, or a local disk. BackupAndRestore is located in the Specify application directory, in the bin file, which stores the executable files for Specify.

9. Review the Specify Forms and contact the Specify team with any customization needs.

Forms in Specify can be customized to include new fields and/or exclude fields not being used by a collection. At this time, Specify 6 does not include a Form Editor, as was found in Specify 5. It is important to note that the forms have been created programmatically to be extremely flexible and can be exported as xml and either edited by on-site staff or emailed to the Specify staff. The original forms should not be edited from the hard drive, they must be exported and then re-imported! Forms are exported via the Importing/Exporting tool, which exports an entire form set. Form sets reside at the Discipline level in Specify, which means that all Collections within a Discipline access the same forms, but form sets can then be re-imported at any institutional level. For instance, the default form set for a discipline could be exported, edited, and re-imported at a collection level, allowing all users in that collection to use the new set of forms. Support with forms is available from the Specify team for members of the Specify Collections Consortium. For more information about membership visit www.specifysoftware.org.