This guide provides a step-by-step walkthrough on how to setup a new empty Specify database. If you are looking for instructions on how to add divisions, disciplines, or collections to an existing database, you can do this in System Config.
[!note]
Before you begin, you or an IT administrator must either install Specify 7 on a local server or you can reach out to our team to have a new deployment added on Specify Cloud.If you are looking to evaluate Specify, please reach out to membership@specifysoftware.org! Our team can deploy a new Specify instance for evaluation purposes.
After starting Specify for the first time with an empty database, you will be greeted automatically by the Guided Setup tool. This appears only during the initial run in a new Specify database.
This tool guides you through the foundational configuration of your institution’s hierarchy, including divisions, disciplines, collections, and your initial administrator account.
Guided Setup Interface
The Guided Setup consists of three main components:
1. Current Entry Form: where you will fill out the required fields to create a database.
2. Overview Panel: an “at-a-glance” view of all the fields and values entered throughout the Guided Setup process. A scroll bar appears upon hovering your cursor, allowing review of previous entries without using the Back button. This panel is shown to the left of the current entry form.
3. Progress Bar: reflects how far along you are in the Guided Setup process, offering an estimation of the remaining steps.
1. Institution
Guided Setup begins with entering your Institution information.
- The Name should be the formal name for your institution. It is a field within the Specify database, is displayed on the Institution form, and can be queried and used in reports.
- The Code is typically an acronym, codon, abbreviation, or short name for your institution.
- The Institution Address information, such as City, State, Country, Zip Code, and Phone Number, is also added to fields within the Specify database.
The Code and address information are vital for identifying your institution in the global research community. If your collections are published to GBIF, these values are used when registering or synchronizing with the Global Registry of Scientific Collections (GRSciColl).
Accurate codes and institutional metadata during setup ensures that your data is ready for integration with GBIF and other global aggregators, making your collection discoverable and properly attributed. If your collection is not already in GRSciColl, you can register here.
Once the required fields are filled, the Next button will be enabled.
Accessions are the formal process by which a specimen or object is legally accepted and recorded as a museum item. They can be recorded at the institutional level for all collections globally or at the division level. Managing accessions “globally” across the entire organization ensures that accession numbers and records are unique across all collections within the institution.
Accessioning is .
Some institutions have a formal accessioning process while some do not. If your institution does not use the concept of accessions (typically handled by a registrar or administrative curator), then leave this item unchecked and simply click the Next button to proceed.
2. Storage Tree
Specify visually presents some data types in hierarchical tree displays. These data types include the Taxon, Geography, (Specimen) Storage, Chronostratigraphy, Lithostratigraphy, and Tectonic Unit tables. You can learn more about how trees work in Specify here.
The Setup Wizard offers a table for each of the trees for creating tree definitions, or levels. Nodes for the Storage tree can be added within the Specify application. The storage tree operates at the Institution level and is available and visible to all Collections.
| Field | Definition |
|---|---|
| Name | The name of the rank used internally by Specify but not visible to the user. |
| Title | The name of the rank displayed to the user in the tree, queries, and reports. |
| Remarks | Allows remarks to be entered regarding the rank. |
| In Full Name | Will use the rank when displaying the full name for any associated Collection Objects (which appears in the Taxon Full Name field), with the Preferred Taxon field on the Determinations form, and is useful when running queries and reports when the full name is desired. The fullName field is automatically constructed based on this definition, so updating this will rebuild the full names that are already present in the tree. |
| Enforced | Ensures that the Rank can not be skipped when adding children. |
| Text Before | Adds text before the name at the given rank. |
| Text After | Adds text after the name at the given rank. |
| Full Name Separator | Dictates which separator is used between the given rank and the following rank. |
[!tip]
For more information on configuring tree definitions, please review our guide on Editing Tree Definitions & Ranks.
- Full Name Direction: dictates the order of ranks when displayed in the full name. Forward will display a full name from the highest rank to the lowest from left to right. Reverse displays the full name from lowest to highest from left to right. This can be edited from within Specify.
- Populate tree with default records: checking this will allow you to generate standard nodes to save time.
3. Division
This window is used to create a single Division within your institutional hierarchy. Additional divisions can be added later from within Specify.
[!info] Shared Records in a Division
Each division will share the same agents (person, group, or organization). If you are unsure how to organize your database, you can learn more about what an Agent is in Specify before proceeding!See all shared division records here.
- The Name will appear on the division form and can be queried and used in reports. A division is used to collectively name similar collections (e.g., the Division of Paleontology may include Vertebrate Paleontology, Invertebrate Paleontology, and Paleobotany collections).
- The Abbreviation can be a short name, acronym, codon, or abbreviation. If your Division does not have a Code, put in a placeholder; this can be edited at a later date.
4. Discipline
[!info] Shared Records in a Discipline
There are a number of default disciplines to choose from. This choice will dictate the default data entry forms, field captions and descriptions (Schema Config), pick lists (controlled vocabularies), and trees.All collections within a discipline will share trees (taxonomy and geography, and if applicable, chronostratigraphy, lithostratigraphy, tectonic unit). They will also share the same Collecting Events, Localities, Loans, Gifts, and Borrows.
See all shared discipline records here.
- Choose a taxonomic Type from the drop-down menu. Specify uses this information to load the correct default data entry forms, trees, and schema based on the predefined disciplines within Specify.
- The Name is pre-filled with the discipline type name but can be any user-specific variation. It can be edited, queried, and used in reports. Additional Disciplines can be added from within Specify.
5. Geography Tree
The Geography tree operates at the Discipline level and is used by all Collections within the Discipline. Nodes to the Geography tree can be added later from within Specify.
The columns and features available for defining the Geography tree function exactly as they do for the Storage Tree (see Section 2).
[!tip] Default Geography
Checking Populate tree with default records will automatically load data for the Geography tree, including Continents, Countries, and States throughout the world as well as Counties within the United States. Default data for the Geography tree is sourced from Geonames.org.
6. Taxon Tree
Most disciplines will have a default tree associated with it. To populate a tree with default records (See Taxon Files to see which ones are available), check the Populate tree with default records checkbox, then select a tree from the dialog.
Some disciplines will not have any default trees, in which case an empty tree will be created that can be populated after the institution is created.
7. Collection Information
[!info] Shared Records in a Collection
Within a collection, all users will share the same Collection Objects, Types, Groups, Preparations, Determinations, Pick Lists, and Prep Types.See all shared collection record here.
This step names your first collection and which primary numbering scheme its specimens will use.
- The Name is the full, formal name of the collection. This is what users will choose when selecting a collection to work in.
- The Code is a unique identifier (acronym or abbreviation) for the collection.
Just like the Institution Code, the Collection Code is an essential field for international data standards. It is a primary requirement for the Global Registry of Scientific Collections (GRSciColl). Providing a standard, recognized code here helps link your digital records in Specify to the physical collection’s global identity, facilitating better data tracking and citation metrics when your data is shared with aggregators like GBIF.
By default, the catalog number format will be set to CatalogNumberNumeric (a 9-digit auto-incrementing integer), but this can be changed to any of the other formats in the dropdown, or a new format can be created after the institution is created. If you choose None, this will not enforce any standard.
After the database is created, you can customize this right away to create any format you would like. This can be changed at any time, but all existing records must conform to the new format you set. You can learn more about Field Formatting and Auto-Numbering here.
8. Specify User
[!info] System Administrator
After the database is created, this user will have system administrator permissions. You can change the permissions of this user or change the password at any time in the future.More users can be created later!
Before pressing Create, review the Overview Panel to the left of the current entry form to verify all the information is correct.
After the user information is completed and the Create button is pressed, you’re done! The database is being constructed; this could take several minutes.
9. Log In
Once the login screen appears, the institution configuration has finished saving to the database! You can enter the admin user credentials you created in the previous step to access your new database.
Welcome to Specify!
Now that you have your initial structure created, you can begin creating additional divisions, disciplines, collections using System Config.