Specify Terminology

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:open_book: Specify Terminology Dictionary

This guide defines common terms you will encounter while managing your collections in Specify.

Major Terms

Collection Object

A general term for any item that can be part of a collection. This includes a physical specimen, a specimen lot, an observation, a sound recording, a slide, a tissue sample, or an extract. This is the central record that ties all other information together

Collection Object Type

Types allow users to define multiple collection object types, each with unique attributes and taxonomic trees. This capability overcomes previous limitations in managing various materials within a single collection. It also creates new opportunities for collections that include diverse materials cataloged together.

Collecting Event

A Collecting Event (CE) captures the “when” and “how” of a collection. It records the date, time, method, and the people (collectors) involved in capturing the specimen.

Some disciplines identify CEs by a field number, while others rely on the unique combination of the locality name and date.

Locality

Locality records define the “where.” They include the specific name of a locale, its geographic coordinates (point, line, or rectangle), the method used to determine latitude/longitude, the datum, and other georeferencing details.

  • Linkage: Localities can be shared with any number of Collecting Events, but they must belong to exactly one Geography.
  • Tools: GEOLocate is integrated into Specify to help find coordinates on the Locality form and within the WorkBench.

Determination

Sometimes referred to as an ‘Identification’, this record captures the taxonomic name assigned to a Collection Object. It includes data such as the determiner (the person who identified it), the date it was determined, confidence qualifiers (like “cf.” or “?”), type statuses, and remarks. A single Collection Object can have a history of many Determinations over time.

Preparation

Preparations represent the distinct physical components of a Collection Object (e.g., a skin, a tissue sample, a skeleton, a fluid-preserved jar, or a microscope slide). It supports a large number of extensible attributes and properties.

  • Interactions: Preparations are the foundation for most transactions in Specify. You loan a Preparation, not the abstract Collection Object.
  • Data: Includes information about the prep type, count, preparer, preparation date, and remarks.
  • Links: This is how you link specimens to the Storage Tree, DNA Sequences, Material Samples, and Conservation information.

Attributes

Attributes are custom fields that allow you to store data specific to your discipline that isn’t covered by the standard Specify fields. You can define attributes for Collection Objects, Collecting Events, and Preparations (e.g., “Tail Length” for mammals or “Flower Color” for botany).

Agent

An Agent record captures information about a “who”—this can be a person, a group, or an organization. Agents are linked to almost every table (Collectors, Determiners, Authors, Borrowers, Users).

Attachments

An attachment is any digital file linked to a specific data record to provide supplementary information or media. This could be a photograph of a specimen, a scanned permit document, a field notes PDF, or an audio recording. Instead of storing the file directly in the database, which would make it large and slow, Specify saves the file to a dedicated Web Asset Server and stores only a reference to that file in the database record.

Schema Config

“Schema” (or “Interface Schema”) refers to the data tables and fields that capture the semantics and relationships of your biological collections data. The Schema Config module in Specify 7 lets you tailor these tables and fields—changing captions, hiding unused items, adding descriptions, enforcing required fields, and defining field formats—so that Specify works precisely the way your discipline needs it.

:handshake: Interactions (Transactions)

These terms refer to the official documentation of items entering or leaving your collection.

Accession

The legal process of accepting items into the permanent collection, transferring ownership to your institution. Within the database there is a one-to-many relationship between Accessions and Collection Objects. Linked to Collection Objects.

Deaccession

The formal process by which a museum or collection institution removes an object or specimen from its permanent holdings. This usually happens when an item no longer fits the institution’s mission, is redundant, in poor condition, or needs to be repatriated or returned to its rightful owner. These can be linked to Disposals, Gifts, and Exchange Outs.

Disposal

A specific record documenting the physical removal or destruction of a preparation during a deaccession or process (e.g., a tissue sample being consumed for DNA analysis).

This may be a destructive sample, item lost in transport, the item was disposed, or simply no longer found in the collection. These are linked to Preparations.

Loan

An outgoing transaction where you lend preparations to another institution or researcher for a specific period. Loans are unique in that the items are expected to be returned; therefore extra fields can be added to the Loan form for tracking the status of the loaned items and Due Dates. These are linked to Preparations.

Borrow

Specimens that are on loan from another collection can be tracked in Specify by creating a Borrow. An incoming transaction where you receive material on loan from another institution for study or exhibition. These are linked to Preparations.

Gift

Specimens may be transferred outside of the collection and not expected to be returned. In these instances they may be considered a Gift. These are linked to Preparations.

Exchange Out

The Exchange Out table is connected to preparations for the exchanging of cataloged items. Functionality follows that of Gifts and Loans above. Forms can also be modified or augmented to incorporate the exchanging of non-cataloged items much like in unassociated Loans. These are linked to Preparations.

Exchange In

The Exchange In table is similar to the borrow table in recording incoming material.

:deciduous_tree: Trees & Hierarchy

Specify uses hierarchical “Trees” to organize standardized data.

Taxon

The classification tree used by Determinations to identify a specimen. It organizes names from Kingdom down to Species and Subspecies. It handles accepted names as well as synonymy (invalid names pointing to accepted ones). It is user-customizable and additional levels can be added to meet the collection’s needs.

Geography

The Geography Tree represents political boundaries. It organizes data from the broadest level down to the specific (e.g., Earth > Continent > Country > State > County). Localities link to nodes on this tree.

Storage

A hierarchy representing the physical location of your Preparations within the institution. A typical tree might look like: Building > Room > Cabinet > Drawer. Preparations link to locations on the Storage tree.

Paleo Context (Geologic Context)

A set of trees used primarily by paleontology collections to describe the geological setting of a Collecting Event.

  • Chronostratigraphy: The geological time scale (Eon > Era > Period > Epoch).
  • Lithostratigraphy: The physical rock units (Group > Formation > Member > Bed).
  • Tectonic Unit: Definitions for tectonic provinces or plates.

:busts_in_silhouette: People & Access

Specify User

This is the actual login account used to sign in to Specify. Every Specify User must be linked to an Agent record to track who created or modified data.

Permissions are specific to the collection for each Specify user.

:toolbox: Tools & Resources

WorkBench

The WorkBench is a “staging area” for uploading data. It allows you to import large datasets (from Excel or CSV files), validate the data against your database rules, and map it into the main collection in bulk.

App Resources

These are system configuration files stored in the database (SpAppResource) that define the user interface.

  • XML: The file format used for these definitions.
  • Form Definition: Determines the layout, captions, and available fields on data entry forms.
  • View Definition: Determines which columns appear in grid views (like query results) and their order.

Reports and Labels

Tools for generating printable documents from your data.

  • Jaspersoft Studio: The external software used to design report templates.
  • JRXML: The file format for report templates designed in Jaspersoft Studio. These files are uploaded into Specify resources.

Record Merging

A tool used to combine duplicate records (e.g., two Agent records for “J. Smith” and “John Smith”) into a single record. This is often processed as a background job.

Batch Edit

A function allowing users to modify a specific field across a large selection of records simultaneously (e.g., changing the “Storage Location” for 100 preparations at once).

Attachments

Digital assets associated with a record. You can attach images, PDFs, or other documents to almost any record type (Agents, Collection Objects, Localities, Loans, etc.).

:link: Record Relationships & Publishing

Collection Object Group

A group of two or more Collection Objects that have common information about themselves based on some kind of physical integrity. These can be discrete (managed separately) or consolidated (managed and transacted together).

Collection Object Relationships

Collection relationships in Specify allow specimens to be associated with either specimens in another collection or with a taxonomic name in another collection. Some examples of these types of relationships are tissue and voucher, plant and pollinator and host parasite, etc. Specify allows collection objects in two different collections to be related to one another for the purpose of documenting these types of relationships. The collections may be in different disciplines, but are required to use the same catalog number format.

Embedded Records vs. Shared Records

  • Embedded: A record that belongs exclusively to one parent record (e.g., in some collections, a Collecting Event is “embedded” and only exists for that one specimen).
  • Shared: A record linked to multiple items. For example, one Locality is shared by many Collecting Events, preventing you from having to re-type the coordinates for every new specimen found at that spot.

Host Taxonomy

A field used to link a Collecting Event to a specific Taxon record, denoting the host organism from which a specimen was collected.

Data Publishing

The process of making collection data publicly available.

  • GBIF: The Global Biodiversity Information Facility, a common destination for published data.
  • Darwin Core Archive (DwCA): A standard file format used to share biodiversity data. See the quick reference guide here.
  • Darwin Core Mapping: The configuration that maps your internal Specify fields (like CatalogNumber) to standard Darwin Core terms (like dwc:catalogNumber) for export.
  • RSS Feed: A web feed used to notify aggregators (like GBIF) that your dataset has been updated.

:floppy_disk: Database Concepts

Scoping

Relational Database

Specify uses a relational database (MariaDB, largely similar to MySQL). This means data is stored in separate tables (like CollectionObject or Locality) connected by unique IDs.

Database Schema

The structure or “blueprint” of the database. It defines exactly what tables exist, what fields they contain, and how they connect to each other. This is fixed and cannot be changed by users, unlike the Schema Config which can be used to change field captions, descriptions, and visibility within the software.

SQL

Structured Query Language. The programming language used by the system to communicate with the database. Specify handles this automatically, but advanced users can use SQL for complex queries.

Normalized Data

In Specify, data is organized to minimize redundancy. Instead of typing “United States” in every specimen record, it is stored once in a Geography table and linked. This makes updates safer and faster.

Denormalized Data

Data that has been flattened or combined into a single table, often used for exporting reports or analysis where reading speed is prioritized over data structure efficiency.

One-to-Many Relationship

A relationship where a single record relates to multiple others (e.g., One Collection Object has Many Preparations).

Many-to-One Relationship

A relationship where multiple records point to a single record (e.g., Many Collection Objects point to One Collecting Event).

One-to-One Relationship

A relationship where a record is linked to exactly one other record (e.g., a Collection Object linked to a single Collection Object Attribute record).

:computer: Technical

Docker

A platform used to deploy Specify 7. It packages the application and its dependencies (web server, database, backend) into isolated “containers,” simplifying installation and maintenance.

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