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. The term “specimen” is used synonymously with “cataloged item” throughout Arctos.

Cataloged_Item . Cat_Num
NUMBER not null

Catalog Number is the string (sometimes integer) assigned to a Cataloged Item. It must be unique (case-insensitive) within a particular catalog. Arctos currently supports three formats of catalog number.

  1. Integer: Catalog number must be positive integers. Arctos provides tools to predict the next number (e.g., data entry can leave catalog number blank), find gaps in sequences, search by ranges, and provide GUIDs of the “expected” format. Only this format comes with these tools and abilities, and it is often worthwhile to convert existing mixed-string catalog “series” to Integer catalog numbers and store the old numbers as other IDs.
  2. Prefix-Integer-Suffix: An integer is required, and may be accompanied by a prefix and/or suffix. The concatenation of prefix-integer-suffix must be unique. No predictive tools are available. Search is by the concatenation or substrings thereof.
  3. String: Any unique non-NULL string is accepted. No predictive tools are available. Search is by the concatenation or substrings thereof.

Searching

From SpecimenSearch, Catalog Number accepts arguments of several forms. The following table is illustrative.

Input Matches Why
12 12 No-operator inputs are string matched.
12-14 12, 13, or 14 Dash-separated smaller–>larger integers specify a range. Note that there is a 1000-item limit on ranges and lists.
=12-14 12-14 “=” (equals) prefix overrides all other operators and assumptions.
12-11 12-11 “Second” item is smaller than “first” item; not considered as range.
12-0110 12-11 “Second” item is zero-padded so not considered an integer; not considered as range.
12,13,14 12, 13, or 14 Commas are treated as list delimiters unless the value is prefixed with an equals sign. Note that there is a 1000-item limit on ranges and lists.
12,13a,14 12, 13a, or 14 Commas are treated as list delimiters unless the value is prefixed with an equals sign. Neither catalog numbers nor list elements must be numeric. Note that there is a 1000-item limit on ranges and lists.
%12% 12, 121, 12a, 999483612345, …. “%” is “match anything.” This matches anything CONTAINING 12.
%12 12, 112, AABC-5-a12, …. “%” is “match anything.” This matches anything ENDING WITH 12.
_12 012, a12, 912, …. “_” is “match any single character.”
1_2 102, 112, 1A2, …. “_” is “match any single character.”


Guid Prefix

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 . Collection
VARCHAR2(15) not null

Collection:  A short name for a particular collection type. For example:

  • Mammal Specimens

Collection . Collection_Cde
VARCHAR2(4) not null

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.

Collection . Desc
VARCHAR2(255) not null

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

Collection . Institution_Acronym
VARCHAR2(20) not null

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:

sends SQL AND upper(customIdentifier.other_id_prefix) LIKE ‘%A%’ AND customIdentifier.other_id_number = 123 (note prefix is a CONTAINS match and is not case-sensitive) and returns these specimens:

Understanding Cataloged Items

We address assigning catalog numbers to material with a few brief examples.

In short, we strongly recommend cataloging the item of scientific interest: the material that Researcher #2 will ask to borrow for confirmation when they find your citations in GenBank or publications. Any other approach complicates tracking citations and data management.

We present as example a brief list of things that may be cataloged in Arctos.

  • A biological individual
    • Standard practice in vertebrate collections, and the method we strongly encourage when possible. Biological individuals are generally the item of scientific interest, and the thing a future researcher will wish to examine if attempting to replicate results.
  • A biological individual and their parasites
    • Common practice in vertebrate collections, but makes locating or citing a parasite more complicated and less reliable than it needs to be. Rather, we recommend cataloging the host, cataloging the individual parasites (or donating them to someone who can), and establishing proper relationships.
  • A lot (e.g., all intestinal parasites from an individual; all members of a taxon from a time and place, or all insects from a trap)
    • While lots are a convenient and sometimes necessary  “working group,” (e.g., due to the number of individuals involved or the available expertise in identification) we strongly discourage making lots available for citation. Insect collections often loan lots, and the borrowing researcher will sort the lot to individuals for which they are provided catalog numbers, a situation we find acceptable. Attaching cryptic and fragile “individual tags” to members of a lot when someone uses a specimen for molecular analysis makes little sense to us.
  • An Occurrence (e.g., each instance of the capture of an individual)
    • This situation inevitably leads to confusing citations and bad science when an individual sampled multiple times at multiple locations is assumed by users to be multiple distinct individuals. Arctos supports cataloging encounters as events under one cataloged item.
  • Your “share” of an individual (e.g., tissues; the bones being cataloged elsewhere)
    • Similar to Occurrences in that this leads to multiple identifiers being assigned to an individual (and potentially the two being compared in a study), this should be avoided when possible. When unavoidable, both systems should support resolvable identifiers and link to each other, and specimen downloads should include the relationship. Arctos also adds a distinctive style to “same individual as” specimens.
  • Various parts of an individual (e.g., tissues cataloged separately from vouchers)
    • This denormalization of data inevitable leads to divergence and confusion (not to mention increased Curatorial workload), in addition to the aforementioned implications of assigning the item of scientific interest multiple primary identifiers. Having reconciled the data in similar systems, we cannot possibly be vigorous enough in discouraging the continuation of such methodology.
  • An entire collection
    • We include this to stress the fact that cataloged items are wholly arbitrary concepts assigned to whatever someone wanted to catalog. That is, the scientific value of a cataloged number is entirely up to the person deciding upon the material to catalog.
  • Several of the above
    • An individual or physical item (or anything else) may have any number of catalog numbers within or across collections. While this is occasionally necessary for various political or administrative reasons, we strongly encourage avoidance, and the proper use of resolvable OtherIDs (in a system which supports them) to clearly link all of the components of the item of scientific interest together when multiple numbers are for some reason necessary.

Re: http://mailman.yale.edu/pipermail/nhcoll-l/2016-March/009178.html

Collections with “less citable” catalog number schemes are extremely unlikely to support actionable citations, and so little is lost if the “traditional catalog numbers” are subsumed under a “citable catalog number.” This approach has been used to unify and disambiguate several Arctos collections; we find tradition little excuse to go forward under systems which discourage good science

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.