Specimen Barcode and Labeling Guide

From iDigBio
Jump to navigation Jump to search

Specimen Barcode and Labeling Guide

(February 6, 2015)
This guide aims to provide information about what a barcode is and isn't, how it should be used, what equipment to use to read and manage barcodes, and what best practices exist for different collection types (e.g., wet, pinned, on a sheet or packet). Additional information about specimen labels, and labeling is also included. This guide will not discuss at any length RFID tags. These encoded labels are used for electronically tagging assets in a collection, e.g., aisles, cabinets, shelves, drawers and carts, but are not likely to be cost-effective for individual specimens. A survey to collect information from collections staff was sent out in early November, 2014 to the idigbiodigi-l listserv, with a 15% response rate, the verbatim results are here.

Definition & Scope

From the perspective of biodiversity specimen collections and this guide, a barcode is an optical machine-readable encoding of a unique identifier that is attached to a specimen record. A barcode is used to efficiently manage specimens and to quickly locate them in the specimen database. A barcode reader scans the encoding and because the barcode is part of the specimen database record, the record can be called up and used in collection management tasks, for example, when re-locating specimens or processing loans. Additionally, using a barcode reader to enter the code into a new database record, or to query for an existing record means that mistakes in barcode entry are essentially eliminated.

Character encoding

See How to Identify a Barcode Type (Symbology) for complete guide to encodings.

1D barcodes

  • Code 39 (also known as Alpha39, Code 3 of 9, Code 3/9, Type 39, USS Code 39, or USD-3) is a widely used, variable length, discrete barcode symbology and smaller in footprint than Code 128. Of the two 1D encodings described here, this is the one used more often by the survey respondents.
262px-Code 3 of 9.svg.png

  • Code 128 is a very high-density barcode symbology. It is used for alphanumeric or numeric-only barcodes. It can encode all 128 characters of ASCII and, by use of an extension character (FNC4), the Latin-1 characters defined in ISO/IEC 8859-1
    262px-Code 128B-2009-06-02.svg.png

2D barcodes

  • Data Matrix code is a two-dimensional matrix barcode consisting of black and white cells arranged in either a square or rectangular pattern. The information to be encoded can be text or numeric data. Usual data size is from a few bytes up to 1556 bytes. The length of the encoded data depends on the number of cells in the matrix. Error correction codes are often used to increase reliability: even if one or more cells are damaged so it is unreadable, the message can still be read. A Data Matrix symbol can store up to 2,335 alphanumeric characters. They look similar to a QR code but have different encoding.


  • QR code (abbreviated from Quick Response Code) is the trademark for a type of matrix barcode (or two-dimensional barcode) first designed for the automotive industry in Japan. A barcode is a machine-readable optical label that contains information about the item to which it is attached. A QR code uses four standardized encoding modes (numeric, alphanumeric, byte / binary, and kanji) to efficiently store data; extensions may also be used.

    220px-Wikipedia mobile en.svg.png

Barcode labels

Barcodes can be used to track curation/digitization/accession work in progress and as a way to ensure that a group of specimens are handled in their entirety. The usual way we think about them is to permanently identify specimens and link them to the institutional database.

The label material

A key aspect of the barcode label material is for it to be able to be permanently affixed in some way to the specimen according to correct specimen handling practices (i.e., if attached directly, then the glue should not degrade or damage) and at the same time last as long as the object to which it is attached (i.e., not peel away or fade).

Sheets and packets

If a label is for an herbarium sheet it must be acid-free in content and fixative, and it should be placed in a uniform location (as much as possible given the exigencies of a pressed plant arranged and glued to a sheet) to aid in rapid processing.

Wet collections

The best material for wet collections is a spun bound polyester label medium used with wax/resin SDR ribbon and a thermal transfer printer (Datamax, Zebra etc.). Print quality is excellent and barcodes can be generated from collections management systems for printing and reading on labels. Sold from Alpha Systems (http://www.alphasystemsva.com) as a museum solution.

Pinned specimens

Best practices here would include consideration of size so as not to have to re-tray or, to consider barcoding when specimen re-traying is planned as part of curation and / or digitization efforts. Also note that several entomology collections (e.g., Harvard, Digitarium in Finland) have found it very useful to print their QR Codes on the front and back side of their barcode labels for pinned specimens. In this manner, a barcode can be read from above or below. It's also important to think about printing and handling. Cutting out tiny barcode labels is time-consuming and tedious.


In the case of unit trays, drawers, skins, and egg boxes the barcode label needs to fit into the unit tray or drawer and be readily visible.

What's printed on the barcode label

The text printed on the barcode label is not always just the encoded characters. Sometimes the barcode label includes other identifying information about the specimen, such as institution and collection name. The barcode designer should pay special attention to distinguishing between the code itself and the information printed on the label. A good barcode label contains the least amount of high quality information possible. This insures that you do not have to replace the specimen’s barcode every time information (like taxon) changes. A unique identifier, possibly with the specimen collection code and institution code, is a good start. It might be helpful to reproduce the code itself in visible human-readable characters, but care should be taken not to add extraneous text that might be confused with the encoded information. This duplication of information can be useful when a barcode reader is not handy for checking a specimen against its database record.


Barcode readers

A barcode reader or scanner is sometimes called a 'wedge'. The Symbol scanner (https://www.zebra.com/us/en/products/scanners/general-purpose-scanners/handheld/ls2208.html) is a good all-around reader according to some sources.

Barcode printers

In order for a barcode reader to read the encoding on the label, it must be legible for the lifetime of the specimen. That means it must be produced on a quality printer whose ink will not smudge or deteriorate over time, and printed on label stock that will not degrade in its environment (e.g., in a wet collection), or have longevity less than that of the specimen to which it is attached (e.g., herbarium sheets).

Why some institutions have chosen not to use barcodes

Below are some anecdotes directly from institutions who have chosen not to use barcodes on their specimens:

  • Currently SBMNH invertebrate zoology does not use barcodes on specimen labels. "We see loan processing as the primary use of barcodes. While we do have dozens of loans per year, the added effort to integrate a barcode system into our cataloguing scheme is not worth the time/cost to implement at this time.”
  • KU Ichthyology has chosen not to use barcodes due to the cost per unit effort being too high. "Due to the fact that we only use barcodes for processing loans and inventories and process relatively small loans of material, the cost of adding barcodes to every jar (43,000 of them) far outweighs the gain achieved." from Andy Bentley (abentley@ku.edu)

Barcodes and GUIDs

Barcode labels typically contain identifiers that are locally unique, that is, unique within a collection or museum, but not globally unique, that is, unique outside of the collection.

Global uniqueness cannot be achieved without adopting some international standard for identifier structure.

Groups have achieved global uniqueness by using an identifier strategy coupled with unique barcode symbology. For instance, UPC barcode labels (those that we find on products that we buy), are created with a combination of identifiers that are unique within the UPC domain and a format for the barcode symbols that is used only in that domain. An international agreement divides up the possible identifiers and assigns a range of numbers to an issuer. The barcode symbol has a specific format that is recognized by scanners as UPC.

The UUID (universally unique identifier) scheme is a strategy for generating and using large numbers (128 bit value) as identifiers. The UUID generation strategy assures uniqueness. A UUID is represented by 32 lowercase hexadecimal digits, displayed in five groups separated by hyphens, in the form 8-4-4-4-12 for a total of 36 characters (32 alphanumeric characters and four hyphens) For example: f47ac10b-58cc-4372-a567-0e02b2c3d479.

In general

  • A digital specimen GUID is what identifies the specimen (part of an individual, an individual, a set of individuals) in the digital world, while a barcode label identifies the specimen in the physical world.
  • A digital specimen GUID does not need to be physically attached to the specimen as long as some other type of identification (e.g., a barcode label) can be used to locate/link the digital record to the physical specimen.
  • A barcode label may be useful for reading and writing by people, a GUID (especially a UUID) is typically too long to be read or written and is intended to be scanned and processed only by machine and input devices.
  • GUIDs such as UUIDs are typically too long for 1D barcode labels but can be represented using QR code labels. It is not typical to include the text of the GUID as part of the label.

Labels and Labeling

A lot of the same concerns related to barcode labels (e.g., what's printed, the label paper and ink, overall robustness, and conservation issues) apply to specimen labeling. Your institution may have some provenance or archive guidelines for what specimen labels should include. Common sense says a label should include at a minimum taxon identification, who collected it, their field or collection number, when it was collected, locality description, institution name and code, accession/catalog number. Other very useful additions might be habitat description, latitude and longitude, and phenology. Below you will find some specimen label examples kindly offered by the survey respondents. Modern practices suggest that this information is generated in the field and conveyed electronically to the institutional database when the specimens are digitized (imaged and accessioned into the collection), ensuring that no errors are introduced by re-entering. Barcoding can also occur in the field.

Examples Provided By Survey Respondents


Specimen labels


References and Resources