Specify Setup & Configuration Checklist

Specify Configuration Checklist

Read the documentation and learn about Specify

See the above section – Introduction to Specify

Learn about the Specify Data Model:

Download and install Specify.

Specify 6 and 7 are interoperable, meaning that you can use both applications with the same database. They use the same database and schema, meaning that the two applications are just different front-end applications for the same database.

If you have any questions about this, you can create a topic in the Get Help category or send a message to support@specifysoftware.org.

Specify 7 Installation

Instructions on installing Specify 7 are available on the forum here:

Specify 6 Installation

Instructions on installing Specify 6 are available on the forum here:

Create a database to store the data.

This is done using the Specify Setup Wizard application packaged with Specify 6.

This needs to be used for both Specify 6 and 7 during the initial deployment.

Members can reach out to @Specify to request assistance during this configuration.

Setup a user account with administrative privileges.

You will need to remember the credentials of three user accounts. These are required and entered during the database creation in the previous step.

IT User: This is the MySQL or MariaDB administrator account, better known as the root user.

Master User: This is the next step down from the IT User. This MySQL/MariaDB user is granted elevated permissions for the database. The Master account has SELECT, INSERT, UPDATE, DELETE and TABLE LOCK privileges on data tables in your Specify database only and has no other MySQL privileges. Specify uses only one Master username and password for all users, but encrypts the Master information with the User information, creating an encrypted string. This allows the Master information to become unique for each user.

Specify User: This is the actual account created within Specify. Each database can have any number of these accounts, but initially an administrator account is created during the setup process. Additional Specify accounts can be created from within the application after the database is created.

Modify the schema configuration

“Schema” or “Interface Schema” in this context refers to the many data tables and fields that reflect the semantics and relationships of the data types processed by biological collections.

Set up your trees

For initial setup, it is import to configure the tree definition. The Tree Definition tool defines the levels, or ranks available in a tree as well as how these ranks are enforced during data entry, and used in aggregating the full name. Tree Definition tools are available for each of the trees. Nodes can not be added to a tree unless the rank is included in the tree definition. The Tree Definition is configured during both the Specify Setup Wizard and the Discipline Wizard that is run when a Discipline is added. The Tree Definition can be edited from within Specify later as well.

Set up the data entry forms.

The fundamentals of form editing are shared between Specify 6 and 7. First, read our documentation on What is a View Definition? This will give the necessary background information before proceeding to learn how to edit the XML files that tell Specify how to display the forms.

We have our comprehensive guide on Editing Forms available on the Speciforum. Our in-depth deconstruction of all field types and examples are available on the GitHub Wiki.

Second, make sure to watch out webinar introducing form editing. We have another webinar available for members of the Specify Collections Consortium that walks through advanced form editing.

Configure the security settings and add users to the system and assign roles.

Specify 7.7 and above have a role-based access system for granting privileges to user accounts to access Specify components, data tables and fields. The permissions system provides considerable flexibility for a collection institution to align data security policies with Specify functions to reflect institutional preferences for how curators, collection managers, researchers, students, guests and other kinds of users process collections data.

We have a webinar for members introducing and explaining how the Specify 7 permissions system works available here.

Configure the security settings.

You can run the Specify DB Security Wizard and follow the tutorial to perform a checkup on your database’s security. Members can contact support@specifysoftware.org with any questions or other action items that they need help with during this process.

Setup data exporting

Data exporting is important because it helps to make sure that data is accessible, sharable, and interoperable across multiple research platforms. Collections are able to make their data available to a wider audience and to facilitate collaboration between researchers and organizations.