Adding Institutional Levels

Grant · March 17, 2022, 3:50pm

Adding Institutional Levels

The Specify data management levels mimic the common levels of hierarchy within institutions. Access to information and Specify tools are set at the various levels both within the application itself and through the User Permissions.

Institution
- Division
  - Discipline
    - Collection
      - Users

The Divisions, Disciplines and Collections for each institution are added and edited in the System Configuration module of Specify;Configuration at System > System Setup > Configuration. All tabs need to be closed before opening the Configuration. This tool is available to Administrators only.

Collection information in Specify 6 databases is also organized at these institution levels to meet requirements for data integrity and data sharing among collections. Some data elements are commonly shared among all collections within an institution, while others are shared only among collections in the same taxonomic discipline, i.e. “at the Discipline level” in Specify. Before creating the institution levels it is imperative that an administrator also understand the data that is held at each level to create the correct setup.

When using a database that was created using the Wizard any additional Division levels should be added first, then Discipline and then Collection. Each is added at the level above it. For instance, Divisions are added within the Institution form.

Edit Institution

Information for the Institution is edited in the Configuration tool; System > System Setup > Configuration. There may only be one Institution for each instance of Specify.

Open the Institution form by clicking Institution on the side bar.

Name is the official name of the institution.
Security can be turned on or off for the entire Specify application on the Institution form by checking the box Is Security On. The status of security is shown on the status bar with an icon; (security on), or (security off). It is recommended that most institutions leave security on unless the application is being used by a single user.
Alt. Name is typically used when more than one code is used by an institution.
The Code is typically an acronym, codon, abbreviation or short name for your institution (not your collection), if you don’t know of one, put in a placeholder, this can be edited at a later date. Institution codes is a Darwin Core field used for publishing data to aggregators.
Min. Password Length allows a minimum password length to be enforced within Specify. The Specify default is eight (8) characters.
GUID Authority refers to the location of institution information for the unique GUID number given by Specify. This is typically the URL for the institution.
IPR
Copyright, Terms of Use and Disclaimer may be used for legal information regarding the use of the name of the institution. This information can be queried and included on reports.
Remarks can be used for any additional information required regarding the institution.

Click on the Address button to edit the address of the institution.

Add/Edit Divisions

New divisions, disciplines and collections are added using the Configuration tool;Configuration at System > System Setup > Configuration.

Divisions are added within a sub form on the Institution form, and can be edited either from the institution sub form or the division form.

1. Click the Institution button on the side bar of the Configuration tool to edit the institution or add a division.

At least one division should appear in the division sub form.

Name is the only required field and is used in any lists of divisions within Specify as well as in the institution hierarchy.

Abbreviation refers to an existing abbreviation for the Division.

Alt Name provides another field for name. This is often useful when a particular Division has changed names or uses a longer name than is applicable to the Hierarchy list.

URI stands for Uniform Resource Identifier and refers to a resource on the internet (a Division web site).

Icon URI This is the path to an icon on the website that could be downloaded by another institution and displayed on their website to indicate a partnership.

Description can be used to store further information about the Division.

2. Click the (add) button to add a division. A Wizard will appear to help you setup your new division as well as one discipline and one collection within the division.

Create a Division

Division

This window is used to create a single division within your institutional hierarchy. Additional divisions can be added later from within Specify.

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 collection. The Name is a field within the Specify database and is displayed on the Institution form. It can be edited, queried and used in reports.

The Code can be a short name, acronym, codon or abbreviation. If your division does not have a code, put in a placeholder, (this is a required field), this can be edited at a later date. Division codes are sometimes required for web services.

Choose a Discipline Type

Discipline

Choose a taxonomic Discipline Type from the drop-down menu. Specify uses this information to load the correct default data entry forms, trees and schema (tables and fields) based on the predefined disciplines within Specify.

The Name will display within Specify and can be any user specific variation of the discipline type. It can be edited, queried and used in reports.

Configure the Taxon Tree

Taxon Tree

This table will create the tree definition for the taxon tree. The taxon tree operates at the discipline level and can be used by all collections within the discipline you created in the last window. Nodes to the taxon tree can be added later in the Wizard as well as from within Specify.

The Level column displays the available levels. This name can be edited from within Specify. Click the Include box to place the level in the tree.
Include places the level in the tree definition. Levels that are not included can not be Enforced or added to the full name.
Is Required is not editable, but an indication of the tree levels that are used by Specify as a system requirement. These are automatically added to the tree and can not be deleted on this screen or later.
Is Enforced ensures that the level can not be skipped when adding nodes lower down the tree.
Is in Full Name includes the level when building a full name expression for any associated Collection Objects (which appears in the Taxon Full Name field of the taxon table). The full name is also displayed in the Preferred Taxon field on the determinations form and is useful when running queries and reports when the full name is desired. The full name generally includes at least the binomial genus and species fields together with any levels below species (if used) . Create the full name by checking the desired boxes. At least one level for Full Name must be checked before the Next button will become enabled.
Separator refers to the character that separates the levels when displaying the full name. This can be any single character, such as a comma (,) or a space. To make the separator a space simply double click inside the column and delete the comma, then press your spacebar one time.
Full Name Order will reverse the full name as shown in the Full Name Example.

Preload Taxon Records/Nodes

Pre-Load Taxon Authority File

The Wizard not only defines the taxon tree but also allows loading of an authority file for the discipline you are creating. Authority files were created using data from the Catalog of Life Project for some of the disciplines within Specify. If this window does not appear, there are no existing authority files for your chosen discipline.

If you choose to load the data into your tree the Taxon tree will be populated with hundreds of taxon nodes and all associated data. Then, when adding Collection Objects into your database you can simply choose a taxa from the Taxon field rather than adding each individually as needed.

Please note that loading the Taxon tree will also affect the tree definition. If you load the provided Taxon authority file for your discipline the accompanying tree definition may include Levels that were not defined by you in the previous window, but are necessary to include all the predefined Taxon information.

Additional discipline-specific trees can be loaded from within Specify at the time new disciplines are created.

Click the Choose button for a list of taxon files for the discipline you are creating. Not all disciplines offer more than one taxon file. Once the taxon file is chosen, information will display in the Source, Coverage and Description fields for that file.

Note: Botany and Entomology authority files are partial due to the size of these files.

The Downloadable File section in this window allows you to choose taxon files from your hard drive. The Setup Wizard can only install files that were downloaded from the Specify website. The Specify team is currently in the process of creating more of these files.

Configure and Load Geography Tree

Geography

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 in the Wizard as well as from within Specify

The Level column displays the available levels. This name can be edited from within Specify. Click the Include box to place the level in the tree.
Include places the Level in the tree definition. Levels that are not included can not be Enforced or added to the Full Name.
Is Required is not editable, but an indication of the tree levels that are used by Specify as a system requirement. These are automatically added to the tree and can not be deleted on this screen or later.
Is Enforced ensures that the level can not be skipped when adding nodes lower down the tree.
Is in Full Name includes the level when building a full name expression, which can be queried and used in reports. Create the full name by checking the desired boxes. At least one level for Full Name must be checked before the Next button will become enabled.
Separator refers to the character that separates the levels when displaying the full name. This can be any single character, such as a comma (,) or a space. To make the separator a space simply double click inside the column and delete the comma, then press your spacebar one time.
Full Name Order will reverse the full name as shown in the Full Name Example.

The Wizard will automatically load data for the Geography tree, including Continents, Countries, and States throughout the world as well as Counties within the United States. Data for the Geography tree was converted from the website of the World Gazetteer. Unwanted or unnecessary nodes can be deleted later from within the Tree tool.

Create a Collection

Collection

Enter the Name and internationally recognized Collection Code to create a single Collection within the Discipline. This is the name that will appear within Specify on the Collection form and can be queried and used in reports.

The Code should be your standard collections community assigned code for your collection. This Code will be used in data exports and web interfaces in upcoming releases of Specify.

Create a Catalog Number Format

Catalog Number Format

Specify is able to accept data for collection objects or observations without assigning a Catalog Number, but when Catalog Numbers are used, they must be unique for each lot, specimen or observation. Many collections routinely assign catalog numbers to incoming specimens, perhaps as part of the accessioning process. These numbers may require a format with specific sections for data such as Institution Code and year or they may simply use an incrementing number.

Catalog Numbers can either be unique to each Collection, shared by several collections or be used throughout the Institution. The Catalog Number chosen at this time will not affect where it is used relative to other collections, this will be configured from within the Specify application. The Catalog Number format for this collection can not be edited once it is chosen.

Several formats are also available within this drop-down menu list:

Format offers several choices in the drop-down menu list:

None is the default setting, which is a 60 character string field.

Create allows you to create your own format. Choosing Create will open the Field Formatting Editor. Click HERE for the Field Formatting Editor help page.

CatalogNumber (2020-######) The year will appear automatically in the first section (2020) of the format, and can also be manually edited inside Specify. The ‘###’ section of the format is a number that is six digits in length. This section can be automatically incremented when Auto Numbering is turned on in Specify or manually entered when Auto Numbering is turned off. These two sections are separated by a dash.

CatalogNumberAlphaNumByYear (2020-######) The year will appear automatically in the first section (2020) of the format, and can also be manually edited from within Specify. The ‘###’ section of the format is a number that is six digits in length. This section can be automatically incremented when Auto Numbering is turned on in Specify or manually entered when Auto Numbering is turned off. These two sections are separated by a dash.

CatalogNumberNumeric (#########) This is a nine digit number that is automatically incremented when Auto Numbering is turned on in Specify or manually entered when Auto Numbering is turned off.

CatalogNumberString (XXXXXXXXXX) This is a ten digit string that can include numbers, alphabet or characters
Is Numeric will display a ‘yes’ if the format is numeric.
Pattern displays the pattern used to create each format (these are explained in further detail above).
Is Auto Incremented displays a ‘yes’ if the format is automatically incremented.

Collections that do not use one specific format for their Catalog Number may wish to choose CatalogNumberString from the list, this will allow any format to be entered as long as they are all of the chosen character length.

Note: Auto incrementing will not work with the Catalog Number format.

Create an Accession Number Format

Accession Numbers

Note: If you chose to manage your Accessions globally your accession number format will already be the same for each division and this screen will be inactive. If this is the case, simply click on the Next button to proceed in the Wizard.

Accession Numbers may require a format or may simply use a number. Choose None to leave the Accession Number as a text field on the Accession form. Accession Number formats are not editable once data has been entered in the database.

Format offers several choices in the drop-down menu list:

None is the default setting, which is a 60 character string field.

Create allows you to create your own format. Choosing Create will open the Field Formatting Editor. Click HERE for the Field Formatting Editor help page.

Accession Number (2020-AA-###) The year will appear automatically in the first section (2020) of the format, and can also be manually edited. The ‘AA’ section of the format is alphanumeric and accepts both characters a through z and numbers. The ### section of the format is a number that is automatically incremented when Auto Numbering is turned on in Specify and manually entered when Auto Numbering is turned off. This format offers two alphanumeric characters and three incremented numbers.

AccessionNumberByYear (2020-AA-AAA) The year will appear automatically in the first section (2020) of the format, and can also be manually edited. The ‘A’ sections of the format are alphanumeric and accept both characters a through z and numbers. This format offers two alphanumeric sections, the first is two characters in length and the second is three characters in length.

AccessionStringFormatter (AAAAAA) This is a single alphanumeric format that accepts characters a through z and numbers. The Accession number would be seven characters in length.
Pattern displays the pattern used to create each format (these are explained in further detail above).
Is Auto Incremented displays a ‘yes’ if the format is automatically incremented.

complete

Summary Window

Summary

Congratulations! You have finished the Specify Setup Wizard. This last screen displays all the data that has been created using the information provided in the preceding windows. If edits are required simply click the Back button until the desired window displays and re-enter the information.

Add/Edit Disciplines

New Divisions, Disciplines and Collections are added using the Configuration tool;Configuration at System > System Setup > Configuration.

Click the Division button on the side bar. The Division form includes a Discipline sub form for adding or editing a discipline.

Edit the discipline information on the division sub form:

Data Type
Specify uses the Type information to load the correct default data entry Forms, Trees and schema (tables and fields) within Specify.
The Name will display within Specify and can be anything you wish. It can be queried and used in reports.

The Division form includes information for each of the existing Divisions. The new Discipline will be added in the Division that is currently displayed in the work space. Use the navigation control at the very bottom of the window to step to the Division that will include the new Discipline.

Navigation Control

In the Discipline sub form click the (add) button to add a Discipline.

It is important to note that Specify will require users to shut down and reopen the application after adding a Discipline.

A Discipline Wizard will walk you through adding not only a Discipline, but a Collection within the Discipline as well as Taxon and Geography Tree Definitions and nodes (names of Taxa and Geographical locations) and Catalog and Accession number. Each of these windows is explained below.

Choose a Discipline Type

Discipline

Choose a taxonomic Discipline Type from the drop-down menu. Specify uses this information to load the correct default data entry forms, trees and schema (tables and fields) based on the predefined disciplines within Specify.

The Name will display within Specify and can be any user specific variation of the discipline type. It can be edited, queried and used in reports.

Configure the Taxon Tree