Catalog

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

The term “record” may be used synonymously with “cataloged item” throughout Arctos, and is favored over “specimen”, which is generally understood as referring to biological objects.

Catalog Number

Cataloged_Item . Cat_Num VARCHAR2(40) not null

Catalog Number is the identifier assigned to a Cataloged Item. It must be unique (case-insensitive) within a particular collection (duplicate catalog numbers within a collection are not allowed). Various formats are supported and bring various functional limitations with them. See code table for more information.

Cataloged Item Type

Cataloged_Item . Cataloged_Item_Type VARCHAR2(20) not null

The code table is available to explicitly label various types of cataloged material, also referred to as the DarwinCore term Basis of Record.

Remarks

Coll_Object_Remark . Coll_Object_Remarks VARCHAR2(4000) null

Use remarks to document non-standard information pertaining to the record. Do not use remarks for any information which could be recorded with more structure elsewhere, including remarks better stored with a part, event, or any other “piece of the specimen.”

Entered By

Coll_Object . Entered_Person_ID NUMBER(22) not null

Agent creating the catalog record in Arctos.

Entered Date

Coll_Object . Coll_Object_Entered_Date NUMBER(7) not null

Date on which the record was created.

Edited By

Coll_Object . Last_Edited_Person_ID NUMBER(22) null

Agent last editing the catalog record.

Edited Date

Coll_Object . Last_Edit_Date NUMBER(7) null

Date on which the record was last edited.

Flags

Coll_Object . Flags VARCHAR2(20) null

Flags mark a specimen as missing information during the entry process. It is sometimes more convenient to bulkload data after the catalog record exists than to enter data with the record; flags serves as a marker to facilitate locating those records still needing attention.

Associated Species

Coll_Object_Remark . Associated_Species VARCHAR2(4000) null

Free-text description of species associated with the specimen.

GUID Prefix

Public	Required	Editable	Max Length	Value Code Table	What it does
Yes	Yes	No	20	None	In conjunction with catalog number it forms a unique identifier within Arctos, and in conjunction with Arctos’ URI forms a Globally Unique Identifier (GUID) for the specimen record.

Although not controlled by a code table, GUID_PREFIX is required to be 20 or fewer characters, and contain exactly one colon : not at the beginning or end of the string.

GUIDs, once formed, must never be allowed to change or expire, so selection of GUID Prefix is an important task in new collection set-up. See Creating a Meaningful GUID. All catalog record citations should occur by way of GUID. Note that while GUID Prefix generally appears to be a concatenation of institution and collection code, it is in fact an independent concept; several collections from an institution may use the ‘Herb’ collection_cde (e.g. for vascular plants, cryptogams, and marine algae collections, for example).

Collection

Collection . Collection VARCHAR2(50) not null

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

Mammal Specimens

Collection Type

Public	Required	Editable	Max Length	Value Code Table	What it does
No	Yes	No	5	ctcollection_cde	Links collection catalogs to collection-type-specific code tables.

Code applied to a collection that provides context for types of parts and attributes that the collection will use. Exploring the “filter” option of Attribute Type or Part Name will provide an idea of how a collection type has been used.

Description

Collection . Descr VARCHAR2(4000) null

An extended name or description of the collection, free text. 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

Public	Required	Editable	Max Length	Value Code Table	What it does
No	Yes	No	20	None	Linked to barcode series and provides a method for sorting collections by institution.

Acronym of the institution that hosts the catalog and collection. For example, “MVZ” for Museum of Vertebrate Zoology, “UAM” for University of Alaska Museum (of the North) and “MSB” for Museum of Southwestern Biology.

Arctos generally follows global collection registries that include institution acronyms including:

Institution

Expanded Institution Acronym

Taxonomy Source

Collections may choose and order any number of Taxonomy Source, code table. Classifications are applied to records from the first source which includes data for all taxa used in an identification.

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; only a matching string is returned.
12-11	`12-11`	“Second” item is smaller than “first” item; not considered as range.
12-0110	`12-0110`	“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`, `12`1, `12`a, 9994836`12`345, ….	”%” is “match anything.” This matches anything CONTAINING 12.
%12	`12`, 1`12`, AABC-5-a`12`, ….	”%” is “match anything.” This matches anything ENDING WITH 12.
_12	0`12`, a`12`, 9`12`, ….	“_” is “match any single character.”
1_2	`1`0`2`, 1`12`, `1`A`2`, ….	“_” is “match any single character.”

Understanding Cataloged Items

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

In short, we strongly recommend cataloging the item of interest: the material that Researcher #2 will ask to borrow, the item that a collection needs to track conservation or preservation or internal locations, the object that will be audited by administrators, etc. Any other approach complicates tracking citations and data management.

We present as example a brief list of things that have been cataloged and some considerations

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 or fish from a trap)
- Lots are a convenient and sometimes necessary ”working group,” (e.g., due to the number of individuals involved or the available expertise in identification) but lots may also complicate items available for citation. Creating parts of a record may be needed to track loans and usage of a single individual from a lot. Insect collections often loan lots, and the borrowing researcher will sort the lot to individuals for which they are provided catalog numbers.
An occurrence (e.g., each instance of the capture of an individual)
- Arctos supports cataloging encounters as specimen events under one catalog record. However there are situations where the blood sample of wild caught banded birds is cataloged as independent records, and instead use of relationships such as same individual as or Arctos Entity collection may be used instead to indicate the shared origin of the samples.
Your “share” of an individual (e.g., tissues wiht the bones being cataloged and housed 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), which can be avoided when both systems support resolvable identifiers and link to each other as in Arctos. Specimen downloads should include the relationship, and Arctos also adds reciprocal links with records tied as “same individual as” .
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. Instead a single record can have several parts. Each part has its own unique attributes.
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.

Understanding Catalog Records

As a highly normalized system, there is no real meaning to the term “catalog record” in Arctos. Most views of the data provide information somewhat equivalent to Simple DarwinCore. No view contains everything that might be considered the entire record. The available information varies wildly across records and collections.

Understanding DarwinCore mapping

The primary entity in DarwinCore (DWC) is the Occurrence (https://dwc.tdwg.org/terms/#occurrence). Mapping Arctos records to Occurrences is not straightforward (it’s like going from a color palette of 255 to only the 5 primary colors); new OccurrenceIDs must be minted for DWC transfer by appending “seid” (Specimen Event ID, although identifiers should be viewed only as identifiers). A GUID + SEID URI will highlight the relevant Event determination in Arctos records (example below). A few examples follow; these are not the only complex situations possible in Arctos, but are the most common. (Data in Arctos change frequently; please let us know if an example does not make sense or function as described.)

https://arctos.database.museum/guid/MSB:Mamm:55245 is a “simple” record with one Event determination in Arctos, and is sent to DWC as a single Occurrence.
https://arctos.database.museum/guid/DMNS:Mamm:12344 and https://arctos.database.museum/guid/MSB:Mamm:233616 together represent one Occurrence, with parts in different collections. These are provided to DWC as two Occurrences; we make no attempt to merge them.
https://arctos.database.museum/guid/MVZ:Egg:10460 represents at least two Occurrences (the thrush and the cuckoo, although individual eggs could be considered Occurrences as well). We provide this to DWC as a single Occurrence.
https://arctos.database.museum/guid/MSB:Mamm:193703 represents two Occurrences, and is provided via DWC as two Occurrences. In this case a single individual was sampled multiple times, and the samples were cataloged as one record. (The improbable use of event type “collection” for both events makes this record difficult to interpret.)
https://arctos.database.museum/guid/UAMb:Herb:26709 represents two Occurrences, and is provided via DWC as two Occurrences. In this case there is uncertainty as to which “interpretation” of the original data is most appropriate; the data as provided have no spatial information, the spatial information (from automation) are occasionally wildly wrong, and the collection simply does not have the resources to review each record and choose the best at this time, so both are made available.

DWC Mapping

Current DarwinCore Mapping for IPT

Minimum Data

The minimum possible catalog record is a catalog number, although “core” data such as Identifications and Accessions are difficult or impossible to avoid in the interfaces. There are “we don’t know” values for all “required” fields and concepts; “unidentifiable” is a valid taxon which may be used in identifications, for example.

All Data

The “full record” consists of the core data and all data linked to those data at any depth. The full record should not be viewed as something that resides entirely within Arctos. There are currently no views which could be considered “the full record.” A record may contain any number of Attributes, Collectors, Citations, record or specimen-Events, Identifications, Media, Identifiers, Parts, Transactions, etc. Many of these objects are linked to other objects, which are in turn linked to more. Some incomplete examples:

Identifications may be linked to any number of taxa. Taxa may have any number of classifications, including those in external systems (such as WoRMS).
Citations are linked to Publications. Publications may be linked to CrossRef, which may link to other publications (references and referenced by), author data in the ORCID system, funding data in FundRef, etc. Additionally, the context of other specimens - and therefore everything they are linked to, including more specimens - cited from publications may be critical to understanding the current specimen.
Other Identifiers may form links to various sources of data including GenBank, UCMP’s Locality Database, specimens in other collections in and out of Arctos, etc.
In addition to the direct link through Collectors, most “nodes” employ to Agents in various capacities - as publication authors, identifiers, attribute determiners, verifiers of specimen-events, etc. Agents in turn may contain:
- Any number of names
- Any number of status reports
- Any number of addresses, including any data which resides at dereferencable addresses (such as publications from ORCID, funding information through Projects, linked data from WikiData, etc.)
- Any number of Media, which may contain anything - images, text, videos, static or linked data, etc.
- The context of activity within Arctos, which often includes thousands of other specimens which may include everything mentioned here
- Any number of related Agents, including all similar information from them and the agents to whom they are related

Any of these data - and those not mentioned here - may be critical to answering some questions involving a collection object or item, and should therefore be considered “the record.” It is unlikely that any question requires all of these data, and assembling them into one view would be, at best, difficult. Arctos links to related data when possible, and we are always receptive to adding more or different data to “default views,” adding pathways to records through any of these data, or otherwise providing tools to access various data in the context of other data.

Defining Collections

Collections in Arctos are wholly administrative. Collections may be comprised of a taxa (e.g. mammals), of various taxa organized for some purpose (such at the Hildebrandt Collection at MVZ), by legacy usage, or anything else. The sole functional or technical consideration is code tables, which are tied to collection type (collection_cde). For example, see the diversity of Attributes available to collections, which can select which ones to use and view.

Legacy collections often exist for various reasons, and these may have duplicate catalog numbers, unpredictable formats which may confuse users, or contain arbitrary divisions which no longer are relevant. Combining these into a unified collection in Arctos is generally trivial, and Arctos provides various mechanisms (such as actionable identifiers and redirects) to ensure that no functionality is lost. Collections with “less citable” catalog number schemes are 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.

Recataloging Records

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 its 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 (see Redirect), 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.

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last edited 24 February 2025