Other Identifying Numbers (Other IDs) and Relationships

Other IDs (identifiers) are any identifiers applied to specimens. These identifiers may allow tracking specimens (as in the case of collector numbers), reference other resources (e.g., GenBank numbers), or form relationships among specimens (such as hosts of parasites).

Other Identifier Type

Coll_Obj_Other_ID_Num . Other_ID_Type VARCHAR2(75) not null

This field describes the kind of identifier using a controlled vocabulary. Users who are logged in can choose one Other ID Type to be their “preferred identifier.” Your preferred identifier will then be the default displayed in several forms.

This same vocabulary can be used to systematically form URLs from pre-set strings plus Other ID values. For example, the complete code-table entry for GenBank is

The columns above are “other ID type,” “definition,” and “base_URL.”

The full base_url is

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=GenBank&term=

and the code from, for example, http://arctos.database.museum/guid/UAM:Mamm:86892

is

returning the link to the GenBank record for that specimen

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&doptcmdl=GenBank&term=EU139271

Other Identifier

Coll_Obj_Other_ID_Num . Other_ID_Prefix VARCHAR2(255) null

Coll_Obj_Other_ID_Num . Other_ID_Number NUMBER(22) null

Coll_Obj_Other_ID_Num . Other_ID_Suffix VARCHAR2(60) null

This is the value of an Other ID. Data are stored in three fields:

• Prefix (text)
• Number (integer)
• Suffix (text)

which are automatically concatenated into display_value. Display value can, for most purposes, be considered “the number”; the tripartite structure exists primarily to facilitate numerical sorting.

The main purpose of Other IDs is a link between specimen data and other related information, such as collector notes or related specimen records. Therefore, format can be critical: “ABC 123,” “ABC123,” ABC-123,” and “ABC0123,” are not equivalent values.

Many other IDs are alphanumeric, and there is often a need to sort, order, and increment them as if they were numeric, it is sometimes desirable to treat them as true numbers, but with the option of prefixes, suffixes, or both. Any (but not all) of these three components may be null.

There is no built-in concatenation operator, and the integer component does not maintain leading zeroes. How data should be entered is primarily a function of how the data might be used. GenBank number “ABC123” should probably be entered into Prefix; it will never be sorted by the integer component, and adding artificial splits just increases the chance of errors. Collector number “ABC-123-2014” (where ABC is perhaps the collector’s initials, 2014 is a “series designator,” and 123 is the 123d specimen in the series) should probably be split out into prefix, number, and suffix to facilitate sorting.

Examples:

ID Issued By

ID Issued By is the Agent issuing the identifier.

ID Assigned By

ID Assigned By is the Agent issuing the identifier. Note that some identifiers my be assigned by bot agents, and these should receive extra scrutiny.

ID References

ID References is a controlled vocabulary defining the item to which the other ID was originally applied. “Self” is the value used when an ID was applied to the current item; all other values create a (sometimes-resolvable) relationship to another item. Note that the “other half” of an ID-created relationship does not necessarily resolve to a cataloged item (though it should), and is not limited to other records in Arctos (relationships can be formed to any online resource).

Relationships should be reciprocal, and all possible relationships should be made explicitly; there is nothing automatic or reciprocal about the system. (Arctos will email suggested reciprocal relationships; accepting them is 2 clicks.) See below for more information in specificity of identifiers, but relationships should be made to resolvable identifiers; ones with a URL in the code table.

Relationships (non-self references) express a subject-relationship-object directionality in which the “subject” is the current record and the object is the indicated record. Example, given three cataloged items:

• ABC:123 (a parent of ABC:124 and ABC:125)
• ABC:124 (a child of ABC:123)
• ABC:125 (a child of ABC:123)

the following Other IDs would be appropriate for the listed items:

General Guidelines

Be as specific and complete as possible in choosing both an Other ID Type and assigning an Other ID Number. Everything that follows is an elaboration of this simple concept.

Other ID numbers are in a zero-or-one-or-many:1 relationship with Cataloged Items. There is no limit to the number of Other IDs that may be assigned to a catalog item, and there is no implication that IDs must be unique, particularly identifying, or even useful. Capture every identifier associated with a specimen – someone at some time considered the identifier useful, and may wish to locate the specimen using it.

Loaned specimens occasionally return with de-facto other IDs (in the form of attached barcodes, GenBank numbers, “personal numbers,” etc.). Record all these as Other IDs.

There are very roughly three types of OtherIDs in Arctos:

1. Those with a base_uri. When the identifier value is appended, these become resolvable and therefore actionable - these form links between specimens and GenBank, between specimens (which supports queries such as “what parasites of Canis are in Arctos?”), and to external resources (such as specimen data in other collections or non-collection databases).

2. “Internal” IDs, such as AF and NK (former “tissue catalogs” which are still curatorially useful) or collector number. These are not resolvable, and are not expected to become resolvable. These vary from fairly specific and well-defined to very generic (“original identifier”).

3. The Rest, which are somewhat in limbo. For example, if there’s some realistic chance that “Albuquerque Biopark” will bring online some mechanism for resolving identifiers (at which point these become Category One IDs), then “Albuquerque Biopark” should be maintained as an ID type in anticipation. If however “Albuquerque Biopark” is unlikely to become resolvable, moving these to Category Two should be considered. For example, current ID

Albuquerque Biopark: 1234

might be recorded as

original identifier: Albuquerque Biopark 1234

which will reduce clutter, increase usability, and serve the same purposes as the original data.

Actionable Other IDs (those that can or could be used to form URIs) should always be recorded as specific types. Everything else is subject to curatorial discretion.

Bulk-loading Rules

The bulk-loader accepts a single string which is parsed out into three fields at runtime. Strangely formatted strings may be manually entered into the correct fields under Specimen Detail.

The specimen bulk-loader has only one field for (each of several) Other IDs. At load, the values provided in this field are parsed into individual fields according to the following rules:

• Integers are loaded as Number.
• Square brackets ( [ and ] ) may be used to explicitly define the numeric portion of an identifier.
• Curly brackets ( { and } ) may be used around the entire Identifier only to force the Identifier into Prefix. This is most useful when leading zeros would otherwise be lost in the numeric portion of the Identifier.
• Strings consisting of a single alpha character followed by a number (V12345) are split into Prefix and Number (V and 12345, respectively).
• Strings consisting of a number and a single alpha character (12345a) are split, as above, into Number and Suffix.
• Strings containing one or two “separator characters” ( | – . ; ) are split at those characters.
• The results of the above are checked to ensure that Number is an integer.
• Any errors or ambiguities result in the entire input being recorded as Prefix.

Examples:

Searching by Other ID

Most searches by Other ID match text strings (or substrings) to the concatenated value of Other ID (Prefix + Other ID Number + Suffix). To search by the integer component (Other ID Number) of an Other ID:

1. Click Customize on the Identifiers pane.
2. Change “Show 3-part ID Search” to “yes” and click “Close.”
3. In the Number box, enter a range of values, e.g., “50000-50110.”
4. The submitted SQL is ...AND customIdentifier.other_id_type = 'ALAAC' AND customIdentifier.other_id_number between 50000 and 50110

Note that this relies on having other IDs entered as a 3-part number. Many Other IDs have been entered entirely in Prefix. Note also that you may specify Prefix and/or Suffix in the 3-part search boxes to produce SQL like:

...AND customIdentifier.other_id_type = 'ALAAC' AND upper(customIdentifier.other_id_prefix) LIKE '%I TYPED THIS IN THE PREFIX BOX%' AND customIdentifier.other_id_number between 50000 and 50110

The “contains/is/in list” option works as follows:

• contains matches substrings of the concatenation (display value), so that search term “1” finds “1” and “12” and “21”
• is matches the entire concatenation. Search term “1” finds only “1”, not “11” or “{space}1”
• in list matches entire terms, with delimiters and spaces removed from the search term. Search terms “1, 2”, “1,2”, “1 2”, “1;2” all find exactly and only “1” and “2”. There is no way by which an “in list” search can find other ID “1 2” or “1;2”; use one of the other options to find such values.

How To

Instructions for doing specifc tasks related to identifiers in Arctos

• How to Record Prior Inclusion in Another Collection
• Searching Arctos
• How to Identify National Park Specimens

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