Collection Object Groups

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Introduction

When research specimens and samples are itemized in a Specify database, they are represented as Specify “Collection Objects” or “COs”. It is not uncommon in collections to have discrete Collection Objects that have, or have had, some type of physical relationship that needs to be recorded in data. For example, two different Collection Objects might have been part of the same physical object or biological organism in the field. Or perhaps specimens that were independent entities in the field are physically associated in a Collection by being permanently joined on a common storage medium.

Two or more Collection Objects that have common information about themselves based on some kind of physical integrity are treated in Specify as “Collection Object Groups” or “COGs”.

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Read Me First

Specify offers a flexible framework for cataloging specimens and samples at varying levels of abstraction. When setting up a collection database, it is crucial to decide how to represent items, specifically determining which artifacts should be cataloged as Collection Objects (COs) and which should be recorded as Preparations of Collection Objects.

Each Collection Object is assigned a globally unique identifier (GUID) and often a catalog number, linking them to essential information such as Collecting Events, Localities, Determinations, and Agents. As primary entities in the collection catalog, Collection Objects are the main data exported to research data aggregators, while Preparations serve as logical “children” that detail the individual physical components of a Collection Object.

The choice to use Collection Object Groups is optional and should reflect the level of abstraction a collection adopts for specimen characterization. This decision can be influenced by resource constraints, the nature of the specimens, or existing cataloging protocols. For instance, a collection may opt not to create individual records for closely associated specimens, documenting related items within a single Collection Object record instead.

However, in cases where logical associations among related Collection Objects are crucial—such as geological collections with embedded minerals or herbaria with multiple specimens per sheet—Collection Object Groups can effectively link these records. This enhances cataloging efficiency, facilitates querying and data exporting, and aids in maintaining accurate records for transactions like loans and exchanges.

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Usage

When entering data, you can create a COG to group together two or more Collection Objects, even if they are not physically attached to each other. For example, if you have several different plant species collected from the same location but stored separately, you can create a COG to represent all these Collection Objects together. This grouping helps in better managing related specimens and facilitates easier data retrieval during queries and reports.

COG Name

In most cases, you will need to assign a Name to the COG so that it can be easily queried on or searched from the form of a CO or COG. The name should be descriptive enough to convey the nature of the collection it represents or serve as a numerical identifier for the grouping.

COG Types

Each COG must have a COG Type assigned to indicate to Specify which application logic to use when managing the children within that COG. Each COG Type is captured in the “COG Type” table, which is very similar to the “Preparation Type” table.

Every COG Type has two primary components:

• Name (user-identifiable name, shown to the user)
• Type (referred to as the “super type”, must be one of three options: Consolidated, Discrete, or Drill Core)
  • Discrete: Two or more physical pieces from the same source in the field that are cataloged as distinct collection objects.
  • Consolidated: Samples or specimens comprising two or more Specify Collection Objects that in the Collection are physically joined either directly together or through a common substrate. Could be joined together naturally before collecting or could be done as a collecting or curatorial method.
  • Drill Core: A rock or ice drill core extracted from the earth in one or more segments, with pieces in linear order based on depth and age.

COG Type Creation

1. Create a new record in the ‘Collection Object Group Type’ table (via the data entry table list or direct URL (i.e. /specify/view/collectionobjectgrouptype/new/)
   
   
2. Enter the name of the COG Type (i.e. Rock Plate)
3. Select the appropriate super type. After the COG Type has been saved you will then be able to head to the COG form and add the COG Type to a COG.

COG Children

At the data model level, these children are captured in the Collection Object Group Join table (collectionobjectgroupjoin), or COJO for short. If you are adjusting schema field captions or visibility, you will need to make changes to this table.

Within a Collection Object Group (COG), children can be classified as either a Collection Object (CO) or another Collection Object Group (COG).

Each child has a Precedence field that determines the order in which they should be presented. If a CO is marked as primary, it will be displayed first, while the others will be ordered according to their precedence. If precedence is not manually filled out, the system will automatically assign it.

The ‘Children’ subview allows you to link collection objects or other COGs as children to the base COG. Clicking the button next to the Children subview opens this dialog:

This dialog enables you to add existing collection objects or create new ones. It functions like a query combo box, allowing you to select multiple COs or COGs using the Query Builder feature.

Designation of Primary and Substrate

When creating a COG, the designation of a primary Collection Object depends on the COG’s super type:

• Consolidated COG: If the COG super type is set to “Consolidated,” you must designate one of the Collection Objects as the Primary CO. The primary object is typically the most significant item in the group and is assigned a unique catalog number that identifies the entire COG.

• Discrete COG: If the COG super type is set to “Discrete,” there is no need to designate a primary object. In this case, all items within the COG are considered equally important.

Additionally, if your COG includes a shared substrate, such as a microscope slide containing multiple diatom species or a rock slab with several minerals, you can specify this by using the Substrate flag. This flag indicates which Collection Object serves as the physical base for the other items in the group.

Key Definitions

• Primary: The Collection Object designated as the most significant item in a Consolidated COG. A CO child must be set as “primary” when using a “Consolidated” COG.

• Substrate: The Collection Object that serves as the physical base for other items within the COG. This designation is useful for COGs with shared substrates. This is always optional.

Important Notes

• CO children can be designated as either the Primary child of a COG or the Substrate for the COG, or both.
• COG children may only be added as children to a COG and cannot be designated as ‘Primary’ or ‘Substrate’ themselves.
• A CO or COG can only have one parent, meaning they can only be a child of a single COG.

Add COG to CO form

Note: To learn more about form editing, form definitions, view definitions, and corresponding terminology, please review Editing Forms in Specify 7.

1. Navigate to the Form Meta Menu on the Collection Object (CO) form

2. Click on Form Definition

3. Click Edit Form Definition to navigate directly to the CO view definition

4. Add the following lines to an existing row, or create a new row and add the lines there:

   <row>
   	<cell type="subview" viewname="CollectionObjectGroupJoin_Sub" id="43" name="cojo" colspan="15"/>
   </row>
   

5. Click Save

6. Navigate to the CO form

7. See that there is now the “Collection Object Group” subview on the form

8. Navigate to Schema Config from the User Tools menu

9. Select the appropriate language and then select Collection Object

10. Select the field collectionObjectGroup under the “Relationships” subheading

11. Uncheck the “Hide Field” checkbox for collectionObjectGroup
    

    

12. Click Save and now it should appear in both the Query Builder and the WorkBench.

COG Type Special Behaviors

Discrete and Drill Core

If a COG has a super type of either Discrete or Drill Core, there are no special behaviors or business rules.

Consolidated

If a COG has a super type of Consolidated, it must include a CO child designated as the “Primary” object. This assists collections staff in reporting the number of individual specimens within a collection. A query can be created to return all COs that are either the primary CO in a COG or not included in a COG at all.

There are also special behaviors when managing and creating Interactions. When creating a new interaction record (e.g., Loan, Gift, Borrow, etc.), selecting a preparation from a CO that is a child of a COG signals to Specify that all preparations associated with any CO in that COG will be included. This is because Consolidated indicates that the objects cannot be transacted independently.

Example COG Types

COG Type Name	Description	Super Type	Primary Object Requirement	Example
Consolidated Specimen	Groups two or more Collection Objects that are physically joined together or associated via a substrate.	Consolidated	Must designate one CO as primary	A dinosaur skeleton where each bone is cataloged but linked together.
Discrete Specimen	Groups related Collection Objects that are treated as distinct entities with no physical attachment.	Discrete	No primary designation needed	Various plant species collected from the same habitat but stored separately.
Microscope Slide	Groups multiple specimens mounted on a single microscope slide.	Consolidated	Must designate one CO as primary	Several diatom species observed on the same glass slide.
Rock Plate	Groups multiple minerals or fossils embedded in a single rock slab.	Consolidated	Must designate one CO as primary	A rock slab containing various mineral specimens.
Herbarium Sheet	Groups multiple plant specimens pressed and mounted on a single herbarium sheet.	Consolidated	Must designate one CO as primary	Two different plant species pressed on the same sheet.
Bark Piece	Groups multiple lichen species growing on a single piece of bark.	Consolidated	Must designate one CO as primary	A bark sample with several distinct lichen species.
Fossil Matrix	Groups multiple fossil specimens found within the same geological matrix.	Consolidated	Must designate one CO as primary	Various fossils extracted from the same sediment layer.
Tissue Sample	Groups multiple tissue samples taken from the same organism for analysis.	Consolidated/Discrete	Must designate one CO as primary	Muscle, skin, and blood samples from a single animal specimen.
Cultural Artifact Set	Groups multiple artifacts from the same archaeological site or cultural context.	Consolidated	Must designate one CO as primary	Pottery fragments recovered from an excavation site.
Environmental Sample	Groups various environmental samples collected from the same location during a study.	Consolidated	Must designate one CO as primary	Soil, water, and air samples collected from a specific site.
Drill Core	A linear collection of rock or ice drill core segments extracted based on depth and age.	Drill Core	No primary designation needed	A segmented ice core drilled from a glacier, with each piece representing a different depth.