Catalog

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Catalogs are administrative lists with inconsistent relationships to physical items. Therefore, a Cataloged Item is an abstraction, i.e., it is an item that has been cataloged, and hence defined, by the administrator of a catalog.

In a catalog of mammals or birds, a cataloged item usually coincides with a biological individual. A large mammal will be given one catalog number even though it may be composed of many specimen parts, e.g., a skin, a skull, frozen tissue samples, fluid-preserved soft parts. In a catalog of fish or parasites, a cataloged item often is numerous individuals of one species from the same collecting event. There are also situations where parts of the same biological individual may occur in more than one catalog. For example, some museums maintain one catalog for skins and another for skeletal material, or separate parts of the same individual may have been cataloged at more than one institution.

Catalog Number is the string (usually integer) assigned to a Cataloged Item. It must be unique within the particular catalog.

Catalogs are most usefully defined by way of Collection.Guid_Prefix, which in conjunction with catalog number forms a unique identifier within Arctos, and in conjunction with Arctos’ URI forms a Globally Unique Identifier (GUID) for the specimen record. GUIDs, once formed, must never be allowed to change or expire. See deleting specimens for guidelines. All specimen citations should occur by way of GUID.

Collection:  A short name for a particular collection.  A Collection signifies a specific catalog.  For example:

• UAM Mammals
• MSB Parasites
• Alaska Lepidoptera

Collection Code: This is an abbreviation for a collection type, such as “Mamm” or “Bird.” (code table) This field is most importantly used in code tables, which determine the values provided to drop-downs in specimen-editing applications. Thus, if you are editing the record for a mammal specimen, you have the option of using an attribute such as ear length, and you do not have to see irrelevant attributes such as beak length.

Description:
An extended name/description of the collection. For example:

• University of Alaska Museum, Mammal Collection
• Parasite Collection at the Museum of Southwestern Biology, Albuquerque, NM
• Kenelm W. Philip lepidoptera collection

Institution Acronym: Abbreviation of the institution that hosts the catalog. For example, “MVZ” for Museum of Vertebrate Zoology, “UAM” for University of Alaska Museum (of the North), “MSB” for Museum of Southwestern Biology.  Generally, these values are the same as those traditionally used for specimen citations within discipline-specific publications.  There is now a demand for globally unique specimen identifiers on the Internet, and at least one registry for such abbreviations has been established.

Locating Specimens by Identifier
Each specimen in Arctos receives a single catalog number, along with any number of identifying numbers, often referred to as “Other IDs.” There are several ways, each with their own limitations, to search these numbers. The data available for searching vary wildly based on what collectors have recorded and what collections have entered. Some exploration is often involved in finding a particular set of specimens.

Other IDs

Along with catalog numbers, Arctos provides the capacity to attach any number of identifiers of various types to specimens.

Other Identifiers, like catalog numbers, have three components: A prefix, an integer, and a suffix. Individual collections define how these components should be used, acceptable values, and how data are to be entered, and these decisions affect what sorts of queries are possible. It is often not possible to deduce these rules and practices – contact us if you need help.

To get Other ID search, click More Options on the Identifiers pane of SpecimenSearch.

This will provide options to select Other ID Type and to provide an Other ID Number. (We generally use “number” in the sense of a license plate rather than an integer.) Additionally, you can choose whether the number is an exact match or a “contains” match. Exact match searches are case-sensitive.

It’s often unclear what type of ID might have been assigned to a number, and the descriptions currently do little to clarify that problem. It is therefore possible (and often most practical) to search by the number component, entirely ignoring ID Type.

The above example finds all specimens with any type of identifier (except catalog number)
containing the string “123.” As of this writing, that search returns 9330 specimens. Additional criteria, coupled with Arctos’ sorting capability, is hopefully enough to find the specimen data of interest.

To get all search options, click Customize (near “Show More Options”), select a “My Other Identifier” (which will also then appear in results and on various forms), and choose “Show 3-part ID Search.”

Click Close and the form will reload with total of eight search options. For this example, we’ll use Collector Number. The simplest use case is to search for a string, here “1234″:

This sends the query upper(customIdentifier.Display_Value) LIKE ‘%1234%’ (display_value is a concatenation of prefix, number, and suffix). This returns specimens with Collector Numbers of:

• ABC-1234-X
• 1234
• 1234567

regardless of how the data were entered and are stored. (“ABC-1234-X” could be entered as prefix=”ABC-1234-X” or as prefix=”ABC-”, number=”1234″, suffix=”-X”; “1234″ could have been entered as a number or as a prefix.)

Changing the dropdown from “contains” to “is” will, of the above examples, return only “1234.”

The “in list” option accepts a comma-separated list of values.

The above example sends SQL upper(customIdentifier.DISPLAY_VALUE) IN (‘A’,'B’,'C’), and as of this writing returns three specimens:

The in range option works only for enforced-integer types of identifiers (currently only AF and NK). Attempting to use it for collector number will result in a datatype mismatch and return an error.

Three-part search to the rescue! (At least in the cases where data are entered correctly.) All of the above deal with the concatenation of prefix, number, and suffix. It is also possible to search these independently. Search for integer component=1234:

to send SQL customIdentifier.other_id_number = 1234.

This is a numeric match of the numeric part of other IDs. It will not find specimens which have the numeric information entered into prefix. This information is not available to public users, but is evident from the edit form. This specimen will NOT be found with the previous search!

Prefix and suffix work similarly. This search:

Deleting records from Arctos

1. Encumber the record(s) to be deleted. Create an appropriate encumbrance first, if necessary. Records may be flagged from individual specimens, or en masse by using the Manage widget from SpecimenResults. Once records are flagged, they may be deleted by users with the appropriate privileges.
2. Find the encumbrance (under Tools). Click See Specimens and carefully review what you’re about to delete.
3. From Manage Encumbrances, click Delete Encumbered Specimens. You’ll again be asked to review your decision, and must click the proceed button at the bottom of the page to delete the records from the database.

Note that there may be reasons to keep masked records in the database instead of deleting them.

Recataloging Specimens

It is sometimes necessary to move cataloged items from one collection or catalog number to another. When doing so, it is important to maintain a way of finding the specimen by it’s original identifiers. In this, be as specific as possible. Use specific identifier types and GUIDs if possible. (See more at Other IDs)

Arctos provides HTTP redirect capability, under which one URL (http://arctos.database.museum/guid/KNWR:Ento:7193, for example) can be automatically redirected to another (http://arctos.database.museum/guid/UAM:Ento:228334). This helps in maintaining a record of the specimen rather than the specimen’s identifying numbers, and allows users to continue using bookmarks and links.

To do this,

1. Ensure that the “old” URL returns a 404 HTTP status code. You may do this in two ways:
   1. Delete the specimen. All users will then get the redirect.
   2. Encumber the specimen with a “mask record” encumbrance. Users who do not have rights to bypass the encumbrance (e.g., all public users) will then be redirected, while operators will be able to continue to access the record.
2.  Insert into table REDIRECT (Manage Data/Tools/Redirects) old and new paths. For example, if DGR:Mamm:123 is recataloged as MSB:Mamm:456, enter: old_path=/guid/DGR:Mamm:123; new_path=/guid/MSB:Mamm:456.

Other ID documentation has moved to it’s own page.